Contacts of the helix formed by residues 2324 - 2347 (chain B) in PDB entry 1CVU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY2324 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2322B GLU 4.1 0.4 + - - -
2323B TRP* 1.3 74.8 - - - +
2325B ASP* 1.3 65.0 + - - -
2326B GLU 3.4 2.4 + - - -
2327B GLN* 3.6 7.3 + - - +
2328B LEU* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2245B ARG* 2.8 26.2 + - - -
2247B PHE* 3.2 35.4 - - - +
2248B LYS* 2.8 14.3 + - - +
2249B ASP 4.3 4.2 - - - +
2250B GLY* 2.6 43.5 + - - +
2324B GLY* 1.3 71.1 - - - -
2326B GLU* 1.3 58.3 + - - +
2328B LEU* 3.2 3.0 + - - +
2329B PHE* 2.8 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR* 2.7 34.3 + - + +
136A TYR* 3.7 9.6 - - - +
2242B HIS* 4.8 3.8 - - - -
2245B ARG* 2.6 42.5 + - - +
2247B PHE* 4.8 1.2 - - - -
2324B GLY 3.4 0.8 - - - -
2325B ASP* 1.3 79.2 + - - +
2327B GLN* 1.3 59.2 + - - +
2329B PHE* 3.2 1.2 + - - +
2330B GLN* 2.8 49.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A MET* 5.9 0.8 - - - +
136A TYR* 3.4 57.4 + - + +
2323B TRP* 3.3 55.3 + - + +
2324B GLY 3.6 9.6 + - - +
2325B ASP 3.4 0.4 - - - -
2326B GLU* 1.3 75.7 - - - +
2328B LEU* 1.3 60.9 + - - +
2331B THR* 2.4 46.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2249B ASP* 3.4 40.8 - - + +
2250B GLY* 4.1 1.3 - - - -
2313B CYS* 4.3 4.7 - - - +
2316B LEU* 4.0 9.1 - - + +
2317B LYS* 3.8 43.5 - - + +
2320B HIS 5.6 0.2 - - - +
2323B TRP* 3.9 36.6 - - + +
2324B GLY 3.0 31.4 + - - +
2325B ASP 3.5 3.8 - - - +
2327B GLN* 1.3 76.3 - - - +
2329B PHE* 1.3 60.6 + - - +
2331B THR* 4.0 1.3 - - - -
2332B SER* 2.7 33.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2234B TYR* 3.6 40.2 - + - -
2241B GLN* 3.7 34.5 - - + -
2245B ARG* 3.8 40.4 - - + +
2250B GLY* 3.3 26.4 - - - +
2252B LEU* 3.9 3.4 - - + -
2309B HIS* 3.6 10.7 - + - -
2325B ASP 2.8 17.1 + - - +
2326B GLU 3.5 2.7 - - - +
2328B LEU* 1.3 75.6 - - - +
2330B GLN* 1.3 89.9 + - + +
2332B SER* 3.1 4.7 + - - -
2333B LYS* 2.9 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR* 3.5 13.3 + - + -
136A TYR* 4.0 10.1 - - + +
137A LYS 5.6 0.4 - - - -
138A SER* 3.6 32.3 - - - -
139A TRP* 3.7 7.8 + - - +
140A GLU* 3.7 20.9 + - - +
2241B GLN* 4.6 5.3 + - - +
2245B ARG* 4.5 2.0 - - - +
2326B GLU* 2.8 51.4 + - - +
2329B PHE* 1.3 98.6 - - - +
2331B THR* 1.3 62.1 + - - +
2333B LYS* 3.3 6.4 + - - +
2334B LEU* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR2331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TYR* 5.0 4.0 - - - -
137A LYS 5.5 1.2 + - - -
2316B LEU* 3.8 18.2 - - + -
2323B TRP* 3.5 16.1 - - + -
2327B GLN* 2.4 35.4 + - - +
2330B GLN* 1.3 71.6 - - - +
2332B SER* 1.3 66.3 + - - +
2334B LEU* 3.3 8.3 + - - +
2335B ILE* 3.1 22.2 + - - +
2549B THR 4.0 5.1 + - - +
2550B PHE* 3.5 37.2 - - - +
2551B GLY 3.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER2332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2234B TYR* 4.3 2.2 - - - -
2309B HIS* 3.6 20.0 - - - -
2312B VAL* 3.6 22.7 - - - +
2313B CYS* 3.3 19.2 - - - -
2316B LEU* 3.6 12.4 - - - +
2328B LEU 2.7 22.0 + - - -
2329B PHE 3.5 4.7 - - - -
2331B THR* 1.3 78.9 - - - +
2333B LYS* 1.3 56.8 + - - +
2335B ILE* 3.1 2.1 + - - +
2336B LEU* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A TRP* 3.7 39.2 - - + +
2229B ASP* 3.1 27.1 + - - +
2230B LEU 4.9 0.8 + - - -
2231B ASN* 5.3 1.2 - - - +
2234B TYR* 3.4 57.9 + - + +
2235B GLY 5.0 5.3 + - - -
2241B GLN* 4.7 10.3 - - - +
2329B PHE* 2.9 24.3 + - + +
2330B GLN* 3.6 12.6 - - - +
2331B THR 3.3 0.2 - - - -
2332B SER* 1.3 76.4 - - - +
2334B LEU* 1.3 62.5 + - - +
2336B LEU* 3.4 2.1 + - - +
2337B ILE* 3.1 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LYS* 3.8 24.2 - - + +
138A SER* 4.3 1.1 - - - +
139A TRP* 4.0 36.6 - - + +
2330B GLN 3.1 16.3 + - - +
2331B THR* 3.5 10.5 - - - +
2332B SER 3.2 0.2 - - - -
2333B LYS* 1.3 77.1 - - - +
2335B ILE* 1.3 62.4 + - - +
2337B ILE* 3.4 8.5 + - + +
2338B GLY 3.2 15.4 + - - -
2539B ILE* 4.2 22.6 - - + +
2544B TYR* 5.1 5.4 - - + -
2549B THR* 3.6 37.7 - - + +
2550B PHE* 4.0 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2312B VAL* 3.9 24.0 - - + -
2316B LEU* 4.1 9.4 - - + -
2331B THR 3.1 14.0 + - - +
2332B SER 3.1 7.6 + - - +
2334B LEU* 1.3 74.9 - - - +
2336B LEU* 1.3 59.8 + - - +
2338B GLY* 3.1 3.1 + - - -
2339B GLU* 2.8 30.4 + - - +
2550B PHE* 3.6 37.9 - - + +
2555B GLY* 3.6 19.3 - - - +
2558B ILE* 3.5 35.7 - - + -
2559B ILE* 3.6 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2230B LEU* 3.8 12.1 - - + -
2233B ILE* 4.6 7.4 - - + -
2234B TYR* 3.3 22.4 - - + +
2305B TRP* 3.8 45.2 - - + +
2308B GLU* 4.0 8.3 - - + +
2309B HIS* 3.9 12.6 - - + +
2312B VAL* 3.8 20.0 - - + -
2332B SER 2.9 21.7 + - - +
2333B LYS 4.0 1.1 - - - +
2335B ILE* 1.3 73.4 - - - +
2337B ILE* 1.3 60.7 + - - +
2339B GLU* 3.5 21.3 - - - +
2340B THR* 2.7 35.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A TRP* 3.5 36.6 - - + -
2228B VAL* 3.5 21.5 - - + +
2229B ASP 4.1 9.9 - - - +
2230B LEU* 3.8 22.4 - - + -
2333B LYS* 3.1 33.7 + - + +
2334B LEU* 3.5 15.3 - - + +
2336B LEU* 1.3 76.4 - - - +
2338B GLY* 1.3 63.8 + - - +
2340B THR* 3.3 4.9 + - - -
2341B ILE* 3.0 29.4 + - + +
2537B ASN* 3.8 20.0 - - - +
2539B ILE* 4.4 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY2338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2334B LEU 3.2 4.8 + - - -
2335B ILE 3.1 7.2 + - - -
2337B ILE* 1.3 78.7 - - - +
2339B GLU* 1.3 58.5 + - - +
2341B ILE* 3.3 4.3 + - - +
2342B LYS* 2.9 30.0 + - - +
2361B PHE* 4.0 2.3 - - - -
2539B ILE* 3.7 21.3 - - - +
2559B ILE* 3.7 22.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2305B TRP* 4.2 8.5 - - + -
2308B GLU* 2.6 37.5 - - - +
2311B ARG* 4.6 0.3 + - - -
2312B VAL* 3.8 0.2 - - - +
2335B ILE* 2.8 18.4 + - + +
2336B LEU* 3.5 26.0 - - - +
2338B GLY* 1.3 71.4 - - - +
2340B THR* 1.3 56.8 + - - +
2342B LYS* 3.2 1.8 + - - +
2343B ILE* 2.9 39.7 + - + +
2558B ILE* 3.3 31.1 - - + +
2559B ILE* 4.2 3.3 - - - +
2562B ALA* 3.9 25.8 - - + +
2567B LEU* 4.7 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR2340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2201B PHE* 5.2 2.7 - - + -
2205B PHE* 3.6 35.0 - - + -
2208B GLN* 4.7 0.2 - - - +
2228B VAL* 3.8 10.1 - - + -
2230B LEU* 3.7 21.6 - - + +
2232B HIS* 5.9 0.9 - - + +
2305B TRP* 3.4 25.9 - - + -
2336B LEU 2.7 23.2 + - - -
2337B ILE 3.4 5.2 - - - -
2338B GLY 3.2 0.2 - - - -
2339B GLU* 1.3 77.8 - - - +
2341B ILE* 1.3 57.6 + - - +
2343B ILE* 3.8 2.6 - - - +
2344B VAL* 2.9 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2228B VAL* 4.3 10.3 - - + -
2337B ILE* 3.0 29.9 + - + +
2338B GLY 3.8 3.4 - - - +
2340B THR* 1.3 76.4 - - - +
2342B LYS* 1.3 62.9 + - - +
2344B VAL* 3.9 0.9 - - - +
2345B ILE* 3.1 32.4 + - + +
2361B PHE* 3.3 33.2 - - + -
2534B LEU* 3.7 46.4 - - + +
2537B ASN* 3.9 20.0 - - + +
2539B ILE* 4.4 11.7 - - + -
2540B CYS* 4.5 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2338B GLY 2.9 19.0 + - - +
2339B GLU 3.4 4.3 - - - +
2341B ILE* 1.3 78.5 - - - +
2343B ILE* 1.3 57.1 + - - +
2345B ILE* 3.9 0.2 - - - -
2346B GLU* 3.0 72.3 + - + +
2361B PHE* 3.8 24.2 + - + -
2559B ILE 3.4 18.6 - - - +
2560B ASN* 2.9 33.2 + - - +
2561B THR* 4.5 1.3 - - - +
2562B ALA* 3.2 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2201B PHE* 4.0 23.8 - - + -
2305B TRP* 4.1 22.2 - - + -
2339B GLU* 2.9 23.0 + - + +
2340B THR* 3.9 3.8 - - - +
2342B LYS* 1.3 73.6 - - - +
2344B VAL* 1.3 62.3 + - - +
2346B GLU* 5.3 0.2 - - - -
2347B ASP* 2.9 44.6 + - + +
2348B TYR 3.0 8.1 + - - -
2562B ALA* 4.1 4.9 - - + -
2563B SER* 3.6 40.4 - - - +
2564B ILE* 4.1 10.3 - - + +
2567B LEU* 4.4 15.7 - - + -
2580B PHE* 4.4 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2201B PHE* 3.8 24.7 - - + -
2205B PHE* 3.7 34.8 - - + -
2340B THR* 2.9 22.9 + - + +
2341B ILE* 3.9 4.0 - - - +
2343B ILE* 1.3 75.9 - - - +
2345B ILE* 1.3 53.9 + - - +
2348B TYR* 3.6 16.4 - - + -
2349B VAL* 2.7 40.9 + - + +
2534B LEU* 3.8 30.5 - - + -
2701B ACD 4.3 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2113B MET* 4.6 5.6 - - + -
2341B ILE* 3.1 22.4 + - + +
2342B LYS 4.0 1.3 - - - +
2344B VAL* 1.3 78.8 - - - +
2346B GLU* 1.3 62.4 + - + +
2349B VAL* 3.7 6.9 - - + +
2350B GLN* 3.2 24.6 + - - +
2359B LEU* 3.8 18.9 - - + +
2360B LYS 3.9 25.8 - - - +
2361B PHE* 3.6 33.9 - - + -
2534B LEU* 4.2 11.9 - - + -
2535B MET* 4.0 6.3 - - - -
2701B ACD 3.6 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2109B ARG* 4.1 8.6 + - - -
2342B LYS* 3.0 53.6 + - + +
2345B ILE* 1.3 77.6 - - + +
2347B ASP* 1.3 67.3 + - - +
2350B GLN* 3.0 20.6 - - - +
2359B LEU 3.7 20.8 - - - +
2360B LYS* 3.6 8.1 - - - +
2361B PHE* 2.8 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2343B ILE* 2.9 21.1 + - + +
2346B GLU* 1.3 85.6 - - - +
2348B TYR* 1.3 59.3 + - - +
2349B VAL 3.6 0.2 - - - -
2350B GLN* 3.6 1.2 - - - +
2351B HIS* 3.0 31.4 + - - +
2562B ALA 4.5 0.5 - - - +
2563B SER* 3.1 17.5 - - - -
2564B ILE* 2.8 37.6 + - + +
2580B PHE* 3.7 19.8 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il