Contacts of the helix formed by residues 2325 - 2341 (chain B) in PDB entry 6X34
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 ASN2325 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2306B CYS* 3.8 30.3 + - - +
2307B GLY* 4.4 1.3 - - - -
2309B GLN 4.8 0.2 + - - -
2311B CYS* 4.2 12.8 - - + +
2314B LEU* 3.7 30.1 - - + -
2322B ILE* 5.3 0.4 - - - -
2323B GLY 3.7 3.0 + - - -
2324B TRP* 1.3 77.5 - - - +
2326B PRO* 1.3 67.9 - - - +
2327B CYS 3.5 0.2 - - - -
2328B GLY* 4.5 6.1 - - - +
2329B GLY* 3.4 15.4 + - - -
2426B PHE* 4.8 0.7 - - - -
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Residues in contact with PRO2326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2314B LEU* 3.6 21.8 - - + -
2322B ILE* 4.4 11.4 - - + -
2324B TRP* 3.4 28.5 - - + +
2325B ASN* 1.3 82.9 - - - +
2327B CYS* 1.3 67.5 + - + +
2329B GLY 3.7 0.2 + - - -
2330B GLU* 3.4 20.4 + - - +
2422B ALA* 3.6 39.6 - - + +
2423B ILE* 4.3 4.3 - - + +
2426B PHE* 4.0 9.2 - - + +
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Residues in contact with CYS2327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2314B LEU* 3.6 39.7 - - - -
2326B PRO* 1.3 80.0 - - + +
2328B GLY* 1.3 71.6 + - - +
2330B GLU* 3.3 6.9 + - - +
2331B ARG* 3.2 21.4 + - - +
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Residues in contact with GLY2328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2306B CYS* 4.1 15.6 - - - -
2314B LEU* 6.1 0.4 - - - -
2325B ASN* 4.2 4.9 + - - +
2326B PRO 3.5 0.2 - - - -
2327B CYS* 1.3 85.2 - - - +
2329B GLY* 1.3 56.2 + - - +
2331B ARG* 3.8 7.6 - - - +
2332B TYR* 2.9 30.8 + - - +
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Residues in contact with GLY2329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2303B LEU* 5.8 3.3 - - - +
2306B CYS* 4.0 8.1 - - - -
2325B ASN 3.4 13.7 + - - -
2327B CYS 3.2 1.0 - - - -
2328B GLY* 1.3 76.1 - - - +
2330B GLU* 1.3 56.5 + - - +
2332B TYR* 3.3 5.0 + - - +
2333B LEU* 2.9 34.4 + - - +
2426B PHE* 3.6 26.9 - - - -
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Residues in contact with GLU2330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2326B PRO 3.4 11.8 + - - +
2327B CYS* 3.3 9.7 + - - +
2329B GLY* 1.3 75.1 - - - +
2331B ARG* 1.3 57.6 + - - +
2333B LEU* 3.8 5.6 - - - +
2334B ASP* 2.9 43.0 + - - +
2425B SER* 5.5 3.1 - - - +
2426B PHE* 3.9 11.7 - - + +
2429B ALA* 5.0 12.8 - - + -
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Residues in contact with ARG2331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2274B LEU* 3.5 39.9 - - + +
2327B CYS 3.2 13.9 + - - +
2328B GLY* 3.8 9.2 - - - +
2329B GLY 3.3 0.2 - - - -
2330B GLU* 1.3 77.9 - - - +
2332B TYR* 1.3 60.9 + - - +
2334B ASP* 3.9 14.0 + - - +
2335B PHE* 4.1 4.2 + - - +
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Residues in contact with TYR2332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2274B LEU* 5.7 2.5 - - - -
2299B VAL* 4.2 15.8 - - + +
2302B TYR* 5.4 2.9 - - + -
2303B LEU* 4.1 31.2 - - + +
2306B CYS* 5.8 2.9 - - + -
2328B GLY 2.9 17.3 + - - +
2329B GLY* 3.8 5.4 - - - +
2330B GLU 3.2 0.2 - - - -
2331B ARG* 1.3 78.8 - - - +
2333B LEU* 1.3 60.6 + - - +
2335B PHE* 3.6 18.3 + - - +
2336B LEU* 4.2 5.2 + - - +
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Residues in contact with LEU2333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2303B LEU* 5.1 11.2 - - + -
2329B GLY 2.9 20.2 + - - +
2330B GLU* 4.0 4.3 - - - +
2332B TYR* 1.3 73.5 - - + +
2334B ASP* 1.3 61.6 + - - +
2335B PHE 3.1 2.5 - - - -
2336B LEU* 3.3 13.2 + - + +
2337B ARG* 2.9 25.8 + - - +
2358B LEU* 5.6 5.8 - - + -
2364B CYS 6.0 1.1 - - - +
2426B PHE* 3.6 27.8 - - + +
2429B ALA* 4.7 9.9 - - + +
2430B LEU* 4.1 40.8 - - + +
2433B LEU* 3.3 30.8 - - + +
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Residues in contact with ASP2334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2274B LEU* 6.0 1.6 - - + -
2278B ALA* 5.2 0.9 - - + -
2330B GLU* 2.9 28.3 + - - +
2331B ARG* 4.1 10.1 - - - +
2332B TYR 3.3 0.4 - - - -
2333B LEU* 1.3 77.6 - - - +
2335B PHE* 1.3 57.8 + - - +
2337B ARG* 3.5 11.0 - - - +
2338B PHE* 2.9 53.6 + - + -
2429B ALA* 4.9 9.9 - - - +
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Residues in contact with PHE2335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2255B LEU* 4.6 10.5 - - + -
2259B LEU* 5.8 4.9 - - + -
2274B LEU* 4.4 11.0 - - + +
2277B ALA* 3.7 31.4 - - + -
2278B ALA* 4.0 24.2 - - + -
2281B VAL* 4.1 19.7 - - + +
2291B LEU* 5.8 2.5 - - + -
2295B ASP* 4.9 11.2 - - + -
2296B LEU* 5.0 12.1 - - + -
2299B VAL* 3.7 38.6 - - + -
2331B ARG 4.1 5.5 + - - +
2332B TYR* 3.6 14.3 + - - +
2333B LEU 3.1 0.8 - - - -
2334B ASP* 1.3 77.5 - - - +
2336B LEU* 1.3 65.7 + - + +
2338B PHE* 3.3 2.4 + - - +
2339B ALA* 2.9 33.5 + - + +
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Residues in contact with LEU2336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2296B LEU* 3.5 32.5 - - + -
2299B VAL* 3.8 21.5 - - + -
2300B VAL* 3.9 24.9 - - + -
2303B LEU* 6.0 3.1 - - + -
2332B TYR 4.7 5.6 - - - +
2333B LEU* 3.3 12.9 + - + +
2335B PHE* 1.3 82.3 - - + +
2337B ARG* 1.3 58.6 + - - +
2339B ALA* 3.7 4.2 - - + -
2340B VAL* 2.9 38.0 + - + +
2354B VAL* 4.8 11.4 - - + -
2358B LEU* 4.7 9.6 - - + -
2433B LEU* 3.5 32.1 - - + -
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Residues in contact with ARG2337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2333B LEU 2.9 16.4 + - - +
2334B ASP* 3.5 14.4 - - - +
2335B PHE 3.2 0.2 - - - -
2336B LEU* 1.3 77.0 - - - +
2338B PHE* 1.3 87.6 + - + +
2340B VAL* 3.3 17.6 - - - +
2341B PHE* 3.2 45.1 + - - +
2429B ALA 6.0 0.9 - - - +
2432B ASP* 5.3 13.5 - - - +
2433B LEU* 3.9 15.6 - - + +
2436B ARG* 5.1 6.1 - - - -
2505B LEU* 6.3 0.8 - - - +
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Residues in contact with PHE2338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2278B ALA* 3.6 35.4 - - + +
2281B VAL* 4.8 2.7 - - - +
2282B ILE* 3.2 43.3 + - + +
2334B ASP* 2.9 35.6 + - + +
2335B PHE 3.9 2.9 - - - +
2337B ARG* 1.3 103.5 - - + +
2339B ALA* 1.3 59.2 + - - +
2341B PHE* 3.3 10.7 - - - +
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Residues in contact with ALA2339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2281B VAL* 4.0 25.8 - - + +
2288B ALA* 5.3 7.4 - - - +
2291B LEU* 4.9 12.0 - - + +
2296B LEU* 5.2 4.9 - - + -
2335B PHE* 2.9 26.8 + - + +
2336B LEU* 3.1 12.3 + - + +
2338B PHE* 1.3 77.9 - - - +
2340B VAL* 1.3 65.4 + - + +
2341B PHE 3.5 3.3 + - - +
2342B VAL* 5.6 2.1 - - - +
2347B VAL* 6.1 0.5 - - - +
2350B ASN* 5.6 4.5 - - - +
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Residues in contact with VAL2340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2336B LEU* 2.9 24.3 + - + +
2337B ARG* 3.3 15.9 - - - +
2339B ALA* 1.3 79.2 - - + +
2341B PHE* 1.3 61.3 + - + +
2342B VAL* 3.9 2.4 + - - +
2346B SER* 3.9 26.4 + - - -
2347B VAL* 4.3 5.0 + - - +
2350B ASN* 5.8 5.8 - - + +
2351B ALA* 5.3 5.8 - - + +
2354B VAL* 4.1 34.8 - - + -
2433B LEU* 5.4 7.0 - - + +
2436B ARG* 3.9 28.9 - - + +
2437B CYS* 4.6 13.0 - - + +
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Residues in contact with PHE2341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2281B VAL 5.6 0.5 - - - +
2282B ILE* 3.7 15.1 - - + +
2337B ARG* 3.2 51.9 + - - +
2338B PHE 3.3 16.2 - - - +
2339B ALA 3.3 2.8 - - - +
2340B VAL* 1.3 83.3 - - + +
2342B VAL* 1.3 59.9 + - - +
2343B ASN 4.3 0.7 - - - -
2344B GLY* 3.3 34.5 - - - +
2345B GLU 4.5 0.2 - - - -
2346B SER* 4.4 9.4 - - - -
2436B ARG* 3.5 31.4 - - + -
2509B ARG* 4.3 22.0 - - - -
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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
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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) + - + + + + + -
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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