Contacts of the helix formed by residues 2349 - 2367 (chain B) in PDB entry 2OVP
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 SER2349 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2264B GLN* 4.4 1.8 - - - +
2316B GLU* 2.8 36.5 + - - -
2318B ASN* 2.5 35.0 + - - +
2321B TRP* 4.0 2.3 - - - -
2347B ILE 3.7 0.2 + - - -
2348B HIS* 1.3 72.4 - - - +
2350B PRO* 1.3 64.1 - - - +
2351B TRP 2.9 1.3 + - - -
2352B LYS* 3.2 23.3 + - - +
2353B SER* 2.8 26.8 + - - -
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Residues in contact with PRO2350 (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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2264B GLN* 4.7 2.2 - - - +
2318B ASN* 2.9 29.8 - - - +
2333B PRO* 3.6 10.5 - - + -
2334B LEU 3.0 23.2 + - - +
2335B HIS* 3.4 39.5 - - + +
2348B HIS 3.3 9.6 - - - +
2349B SER* 1.3 80.1 - - - +
2351B TRP* 1.3 56.3 + - + +
2353B SER* 3.3 2.5 - - - +
2354B ALA* 3.0 22.7 + - - +
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Residues in contact with TRP2351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2318B ASN* 3.1 30.7 + - - -
2319B LEU* 5.8 0.8 - - + +
2321B TRP* 3.2 22.0 - - + -
2322B ARG* 3.0 64.0 - - + +
2325B CYS* 3.1 41.6 - - + -
2330B ILE* 4.1 0.4 - - + -
2331B ASP* 3.0 40.8 - - - -
2332B GLU 3.6 3.1 - - - -
2333B PRO* 3.2 43.6 - - + +
2349B SER* 2.9 3.7 + - - +
2350B PRO* 1.3 77.1 - - + +
2352B LYS* 1.3 57.1 + - - +
2353B SER 3.1 1.3 - - - -
2354B ALA* 3.9 0.4 - - - -
2355B TYR* 2.6 31.7 + - - +
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Residues in contact with LYS2352 (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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1156A GLU* 4.4 14.8 + - - -
1157A ASN* 3.7 20.2 - - - +
2302B LEU* 4.3 0.4 - - + -
2305B ALA* 5.8 1.3 - - + -
2315B ALA 4.4 2.5 - - - +
2316B GLU* 2.9 33.5 + - + +
2321B TRP* 3.3 48.4 - - + +
2348B HIS* 4.4 6.1 + - - -
2349B SER* 3.0 22.8 + - - +
2351B TRP* 1.3 77.3 - - - +
2353B SER* 1.3 76.7 + - - +
2355B TYR* 3.2 3.1 + - - +
2356B ILE* 2.7 58.9 + - + +
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Residues in contact with SER2353 (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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2334B LEU* 3.3 26.5 + - - +
2336B ILE* 4.6 14.8 - - - +
2348B HIS* 5.4 2.4 - - - +
2349B SER 2.8 17.8 + - - -
2350B PRO* 3.0 15.4 + - - +
2352B LYS* 1.3 84.2 - - - +
2354B ALA* 1.3 54.4 + - - -
2356B ILE* 3.0 7.7 + - - +
2357B ARG* 2.6 36.4 + - - +
2706B MET* 4.0 12.0 - - - +
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Residues in contact with ALA2354 (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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2325B CYS* 4.4 1.3 - - - -
2330B ILE* 4.0 12.9 - - + +
2332B GLU 3.6 8.7 - - - +
2333B PRO* 3.4 11.2 - - + -
2334B LEU* 3.0 29.8 - - + +
2350B PRO 3.0 22.5 + - - +
2351B TRP* 3.4 5.6 - - - +
2353B SER* 1.3 76.2 + - - +
2355B TYR* 1.3 62.8 + - - +
2357B ARG* 3.3 5.4 + - - +
2358B GLN* 3.1 20.4 + - - +
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Residues in contact with TYR2355 (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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1159A TRP* 3.9 27.6 - + - -
2298B PRO* 3.1 40.7 - - + +
2302B LEU* 5.3 1.8 - - + -
2321B TRP* 3.7 21.8 - + + -
2324B LYS 3.5 21.8 - - - -
2325B CYS* 3.6 12.1 - - - -
2328B GLU* 3.5 36.6 + - + +
2330B ILE* 4.7 2.2 - - + -
2351B TRP 2.6 20.5 + - - +
2352B LYS 3.3 4.7 - - - +
2354B ALA* 1.3 70.7 - - - +
2356B ILE* 1.3 67.6 + - + +
2358B GLN* 3.1 8.0 + - + +
2359B HIS* 2.8 32.9 + - + +
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Residues in contact with ILE2356 (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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1156A GLU* 2.9 30.3 - - + +
1158A GLN 5.4 3.6 - - - +
2302B LEU* 4.5 16.8 - - + -
2352B LYS* 2.7 54.4 + - + +
2353B SER* 3.5 6.1 - - - +
2355B TYR* 1.3 75.3 - - + +
2357B ARG* 1.3 59.2 + - - +
2359B HIS* 2.9 9.8 + - + -
2360B ARG* 2.6 77.9 + - + +
2706B MET* 4.0 5.6 - - + -
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Residues in contact with ARG2357 (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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2334B LEU* 3.1 31.6 - - + -
2353B SER 2.6 15.8 + - - +
2354B ALA* 3.3 11.8 + - - +
2356B ILE* 1.3 73.4 - - - +
2358B GLN* 1.3 52.6 + - - +
2360B ARG* 3.2 3.1 + - - +
2361B ILE* 2.5 53.3 + - + +
2679B ASN* 3.2 27.7 - - - +
2680B THR* 4.2 6.3 + - - -
2703B ASP* 2.4 37.5 + - - +
2704B VAL* 4.2 5.3 + - + +
2706B MET* 3.5 18.1 - - + -
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Residues in contact with GLN2358 (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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2328B GLU* 5.1 5.8 - - + +
2330B ILE* 3.5 32.8 - - + +
2354B ALA 3.1 3.6 + - - +
2355B TYR* 3.1 9.3 + - + +
2356B ILE 3.1 0.4 - - - -
2357B ARG* 1.3 82.1 + - - +
2359B HIS* 1.3 54.5 + - - +
2361B ILE* 2.8 9.8 + - - +
2362B ASP* 2.5 74.0 + - - +
2634B LYS* 4.7 12.7 - - - +
2635B ASN* 4.9 1.6 - - - +
2679B ASN* 2.8 40.0 + - - +
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Residues in contact with HIS2359 (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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1158A GLN 4.2 6.1 - - - -
1159A TRP* 3.1 84.5 + + - -
2302B LEU* 5.3 0.9 - - + -
2328B GLU* 6.1 0.2 - - - -
2355B TYR* 2.8 31.4 + - + +
2356B ILE* 3.4 11.2 - - + +
2358B GLN* 1.3 71.7 - - - +
2360B ARG* 1.3 63.7 + - + +
2362B ASP* 3.4 10.8 - - - +
2363B THR* 2.6 54.0 + - - -
2367B ARG* 5.0 2.9 - - - -
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Residues in contact with ARG2360 (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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1155A LYS* 2.9 28.7 + - - +
1156A GLU* 3.5 20.2 + - - +
1158A GLN* 4.4 12.8 + - + +
2356B ILE* 2.6 37.2 + - + +
2357B ARG 3.5 1.3 - - - +
2359B HIS* 1.3 78.4 - - + +
2361B ILE* 1.3 54.9 + - - +
2363B THR* 2.9 8.4 + - - -
2364B ASN* 2.4 38.6 + - - +
2704B VAL* 3.4 31.3 - - + +
2705B ASP 4.4 4.4 + - - -
2706B MET* 3.1 36.3 - - - +
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Residues in contact with ILE2361 (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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2357B ARG* 2.5 73.6 + - + +
2358B GLN* 3.3 10.5 - - - +
2360B ARG* 1.3 70.6 - - - +
2362B ASP* 1.3 66.2 + - - +
2364B ASN* 2.9 3.1 + - - +
2365B TRP* 2.7 36.4 + - + -
2679B ASN* 3.1 39.7 - - - +
2680B THR* 3.5 8.1 - - - +
2702B PHE 3.6 20.9 - - - +
2703B ASP* 4.1 3.1 - - - +
2704B VAL* 3.6 10.5 - - + +
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Residues in contact with ASP2362 (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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2328B GLU* 4.1 9.5 - - - +
2358B GLN* 2.5 54.2 + - - +
2359B HIS* 3.4 9.1 - - - +
2361B ILE* 1.3 72.9 - - - +
2363B THR* 1.3 51.9 + - - +
2365B TRP* 3.0 6.0 + - - +
2366B ARG* 2.7 38.7 + - - +
2633B ASN* 5.9 0.3 + - - -
2635B ASN* 3.2 31.3 + - - +
2636B PHE* 3.1 23.8 - - + -
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Residues in contact with THR2363 (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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1159A TRP 4.5 5.4 - - - +
2359B HIS* 2.6 43.4 + - - -
2360B ARG* 2.9 8.5 + - - -
2362B ASP* 1.3 71.9 - - - +
2364B ASN* 1.3 55.1 + - - +
2365B TRP 3.1 0.3 + - - -
2366B ARG* 3.2 7.4 + - - +
2367B ARG* 2.8 58.3 + - + +
2368B GLY* 2.7 28.1 + - - +
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Residues in contact with ASN2364 (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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2360B ARG 2.4 24.8 + - - +
2361B ILE* 3.3 5.4 - - - +
2363B THR* 1.3 73.4 - - - +
2365B TRP* 1.3 59.2 + - - +
2368B GLY* 2.7 46.5 + - - +
2369B GLU 4.2 2.9 + - - +
2371B LYS* 3.2 21.2 + - - +
2701B ASP 3.8 0.4 + - - -
2702B PHE* 2.9 49.5 - - - +
2703B ASP 3.1 12.6 + - - -
2704B VAL* 4.5 4.7 - - + -
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Residues in contact with TRP2365 (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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2361B ILE* 2.7 35.0 + - + -
2362B ASP* 3.1 10.5 - - - +
2364B ASN* 1.3 74.2 - - - +
2366B ARG* 1.3 60.6 + - - +
2633B ASN* 6.0 3.3 - - - +
2636B PHE* 3.5 18.6 - + + -
2638B ILE* 3.3 31.4 - - + -
2648B LEU* 4.0 19.3 - - + -
2658B ARG* 2.4 32.2 + - - -
2660B LEU* 3.8 20.9 - - + +
2677B ALA* 4.0 1.1 - - + -
2678B SER 3.7 11.0 - - - -
2679B ASN 2.9 19.3 + - - -
2681B LYS 3.6 17.9 - - - -
2682B LEU* 3.4 24.0 - - + -
2702B PHE* 3.3 52.1 - + + +
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Residues in contact with ARG2366 (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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2362B ASP* 2.7 26.1 + - - +
2363B THR* 3.6 4.2 - - - +
2365B TRP* 1.3 69.3 - - - +
2367B ARG* 1.3 81.1 + - + +
2635B ASN* 4.3 9.7 + - - +
2636B PHE* 3.2 40.4 - - + -
2648B LEU* 3.6 13.2 - - - -
2650B ASP* 2.8 37.4 + - - -
2657B ILE* 3.6 22.6 - - + +
2658B ARG* 2.4 36.9 - - - -
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Residues in contact with ARG2367 (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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1159A TRP* 3.7 16.4 + - - -
2359B HIS* 5.0 3.2 - - - -
2363B THR* 2.8 43.5 + - + +
2366B ARG* 1.3 112.3 - - + +
2368B GLY* 1.3 65.8 + - - +
2369B GLU* 3.1 3.6 + - - -
2657B ILE* 5.5 0.4 - - - -
2658B ARG* 3.4 7.2 + - - +
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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
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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