Contacts of the helix formed by residues 2462 - 2470 (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 SER2462 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2163B MET* 3.3 28.6 + - - +
2461B GLN* 1.3 80.2 - - - +
2463B LEU* 1.3 66.0 + - - +
2464B ASN* 3.3 5.6 + - - +
2465B GLU* 3.2 33.5 + - - +
2466B TYR* 3.2 13.3 + - - -
2499B ASP 3.3 27.4 + - - -
2500B VAL* 4.5 0.2 - - - -
2501B MET 3.6 7.6 - - - -
2502B GLU* 5.1 0.4 - - - +
2503B LEU 4.7 0.7 - - - -
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Residues in contact with LEU2463 (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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2462B SER* 1.3 71.6 - - - +
2464B ASN* 1.3 63.9 + - - +
2466B TYR* 3.2 5.3 + - - +
2467B ARG* 2.9 44.4 + - + +
2475B TYR* 4.0 24.5 - - + -
2481B LEU* 4.3 5.4 - - + -
2498B ILE* 4.9 4.0 - - + -
2501B MET* 2.8 34.8 + - + +
2502B GLU 3.9 11.0 - - - -
2503B LEU* 4.0 19.9 - - + +
2506B ALA* 3.7 28.9 - - + -
2510B GLU* 6.3 0.2 - - - -
2521B THR* 4.2 20.4 - - + +
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Residues in contact with ASN2464 (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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2462B SER* 3.2 7.7 + - - +
2463B LEU* 1.3 81.9 - - - +
2465B GLU* 1.3 64.2 - - + +
2467B ARG* 3.4 13.0 + - - +
2468B LYS* 3.0 32.7 + - + +
2474B PRO* 3.3 18.6 - - + +
2475B TYR* 2.9 42.0 - - - +
2498B ILE* 3.9 9.5 + - - +
2499B ASP* 2.7 35.5 - - - +
2501B MET 4.7 0.4 + - - -
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Residues in contact with GLU2465 (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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2038B SER 4.6 2.1 - - - +
2039B ASN* 3.6 34.4 - - - +
2152B LEU* 3.7 8.3 - - + +
2163B MET 6.0 0.4 - - - +
2461B GLN* 3.5 29.3 - - + +
2462B SER* 3.2 24.3 + - - +
2464B ASN* 1.3 77.7 - - - +
2466B TYR* 1.3 59.6 + - - +
2468B LYS* 3.4 33.1 + - - +
2469B ARG* 2.9 27.2 + - - +
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Residues in contact with TYR2466 (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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2150B ARG* 3.8 6.4 + - - -
2151B ALA* 4.3 2.7 - - + -
2152B LEU* 3.5 33.5 + - + +
2153B PRO 5.2 0.2 + - - -
2380B GLU* 2.4 52.3 + - + +
2460B TYR* 4.1 15.3 - + - -
2461B GLN* 3.4 31.5 + - + -
2462B SER 3.2 19.8 + - - -
2463B LEU 3.2 8.3 + - - +
2465B GLU* 1.3 78.4 - - - +
2467B ARG* 1.3 64.0 + - - +
2469B ARG* 3.2 5.2 + - - +
2470B PHE* 3.0 35.3 + + - +
2503B LEU* 4.0 19.7 - - + -
2525B LEU* 4.1 24.9 - - + +
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Residues in contact with ARG2467 (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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2463B LEU* 2.9 23.9 + - + +
2464B ASN* 3.6 18.6 - - - +
2466B TYR* 1.3 77.4 - - - +
2468B LYS* 1.3 60.8 + - - +
2470B PHE 3.0 7.4 + - - -
2472B LEU* 2.8 53.3 + - + +
2473B LYS* 2.6 39.5 + - - +
2474B PRO* 4.0 1.3 - - + +
2475B TYR* 3.7 45.1 + - - -
2510B GLU* 3.9 0.2 + - - -
2520B GLU* 2.7 32.3 + - - -
2521B THR* 2.7 40.4 + - + +
2525B LEU* 5.1 0.4 - - - -
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Residues in contact with LYS2468 (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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2042B GLN* 3.0 33.5 + - - +
2044B ARG* 6.0 1.0 - - - +
2464B ASN* 3.0 24.8 + - + +
2465B GLU* 3.4 33.6 + - - +
2467B ARG* 1.3 76.2 - - - +
2469B ARG* 1.3 64.5 + - - +
2471B SER* 2.8 16.4 + - - +
2472B LEU 3.7 7.0 - - - +
2474B PRO* 4.2 29.2 - - + -
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Residues in contact with ARG2469 (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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2044B ARG* 3.0 49.8 - - - +
2123B LEU* 2.8 36.8 + - - +
2124B ILE* 4.3 2.6 - - - +
2125B ASP* 3.7 13.3 + - - +
2151B ALA* 3.6 23.9 + - - +
2152B LEU* 3.6 30.7 - - + +
2465B GLU 2.9 16.0 + - - +
2466B TYR* 3.2 15.3 - - + +
2467B ARG 3.2 0.2 - - - -
2468B LYS* 1.3 75.3 - - - +
2470B PHE* 1.3 91.5 + - + +
2471B SER* 3.5 1.1 + - - -
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Residues in contact with PHE2470 (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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2123B LEU* 4.0 24.6 - - + +
2124B ILE* 4.2 11.4 - - + -
2151B ALA* 4.2 12.1 - - + -
2380B GLU* 6.4 0.2 - - + -
2466B TYR* 3.0 23.8 + + - +
2467B ARG 3.0 4.8 + - - +
2468B LYS 2.9 1.2 - - - -
2469B ARG* 1.3 111.4 - - + +
2471B SER* 1.3 69.3 + - - +
2472B LEU* 3.2 16.7 + - + +
2524B GLU* 3.6 20.5 - - - +
2525B LEU* 3.4 43.3 - - + -
2528B PRO* 4.0 16.4 - - + -
2529B PHE* 3.8 24.7 - + - -
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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