Contacts of the helix formed by residues 2463 - 2472 (chain H) 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 PRO2463 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2459H ARG 3.8 3.4 - - - +
2460H SER* 4.3 9.2 - - - +
2461H LEU 3.3 11.9 - - - +
2462H VAL* 1.3 91.4 - - + +
2464H LEU* 1.3 65.8 + - - +
2465H ASP* 3.1 13.3 + - + +
2466H ASP* 3.4 16.7 + - + +
2467H LEU* 3.6 8.5 + - - +
2506H PHE* 5.2 0.5 - - - -
2511H TYR* 3.8 14.8 - - - +
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Residues in contact with LEU2464 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2463H PRO* 1.3 72.6 - - - +
2465H ASP* 1.3 58.5 + - - +
2466H ASP 3.4 0.2 - - - -
2467H LEU* 3.3 14.9 + - + +
2468H VAL* 2.9 32.4 + - - +
2507H LEU* 4.6 14.8 - - + -
2511H TYR* 3.6 55.8 + - + -
2519H LEU* 5.4 14.1 - - + -
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Residues in contact with ASP2465 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2378H LEU* 4.9 2.9 - - - +
2463H PRO* 3.1 10.6 - - + +
2464H LEU* 1.3 77.3 - - - +
2466H ASP* 1.3 58.7 + - - +
2468H VAL* 3.1 11.1 - - - +
2469H GLY* 2.9 26.7 + - - -
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Residues in contact with ASP2466 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2377H LEU* 3.7 27.5 - - + +
2378H LEU* 4.8 11.5 - - + +
2462H VAL* 3.6 28.0 - - + -
2463H PRO* 3.4 9.8 + - + +
2464H LEU 3.4 0.2 - - - -
2465H ASP* 1.3 78.0 - - - +
2467H LEU* 1.3 57.8 + - - +
2469H GLY* 3.4 1.6 + - - -
2470H ILE* 2.9 30.8 + - - +
2503H MET* 6.0 1.1 - - - -
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Residues in contact with LEU2467 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2462H VAL* 4.9 1.6 - - - +
2463H PRO 3.6 7.1 + - - +
2464H LEU* 3.3 19.2 + - + +
2465H ASP 3.2 0.4 - - - -
2466H ASP* 1.3 77.9 - - - +
2468H VAL* 1.3 58.7 + - - +
2470H ILE* 3.3 5.8 + - - +
2471H ILE* 2.9 34.4 + - + +
2503H MET* 5.2 9.1 - - + +
2506H PHE* 4.8 20.9 - - + -
2507H LEU* 4.4 22.0 - - + -
2511H TYR* 6.0 0.2 - - + -
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Residues in contact with VAL2468 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2464H LEU* 2.9 17.4 + - + +
2465H ASP* 3.1 21.3 - - + +
2467H LEU* 1.3 77.4 - - - +
2469H GLY* 1.3 57.4 + - - +
2471H ILE* 3.7 10.3 - - + +
2472H SER* 2.9 31.6 + - - -
2507H LEU* 5.5 3.1 - - + +
2519H LEU* 6.0 6.7 - - + -
2522H VAL* 3.7 30.1 - - + -
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Residues in contact with GLY2469 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2378H LEU* 3.5 30.2 - - - +
2465H ASP 2.9 13.6 + - - -
2466H ASP 3.8 0.7 - - - -
2468H VAL* 1.3 80.6 - - - +
2470H ILE* 1.3 60.1 + - - +
2472H SER* 3.4 12.2 + - - -
2473H LEU* 3.4 21.3 + - - +
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Residues in contact with ILE2470 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2377H LEU* 6.0 3.6 - - + -
2378H LEU* 3.8 4.6 - - + +
2381H ILE* 5.7 5.2 - - + -
2466H ASP 2.9 18.0 + - - +
2467H LEU 3.8 2.9 - - - +
2469H GLY* 1.3 73.3 - - - +
2471H ILE* 1.3 66.6 + - - +
2473H LEU* 3.4 32.3 + - + +
2495H PHE* 5.9 1.9 - - - -
2500H LYS* 4.6 5.5 - - - +
2503H MET* 3.8 36.7 - - + +
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Residues in contact with ILE2471 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2467H LEU* 2.9 22.4 + - + +
2468H VAL* 3.7 10.5 - - + +
2470H ILE* 1.3 77.3 - - - +
2472H SER* 1.3 57.4 + - - +
2473H LEU 3.1 4.7 + - - +
2500H LYS* 3.3 34.2 + - + +
2503H MET* 3.8 22.0 - - + +
2504H VAL* 3.7 31.4 - - + +
2507H LEU* 4.9 13.9 - - + -
2522H VAL 5.8 0.4 - - - +
2523H LEU* 6.2 0.9 - - - -
2526H GLY* 4.0 29.0 - - - +
2527H PHE* 4.4 17.9 - - + -
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Residues in contact with SER2472 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2468H VAL* 2.9 21.5 + - - -
2469H GLY* 3.8 8.3 - - - -
2470H ILE 3.3 0.4 - - - -
2471H ILE* 1.3 75.8 - - - +
2473H LEU* 1.3 63.6 + - - +
2474H PRO* 3.6 4.9 - - - +
2526H GLY* 5.0 11.4 - - - -
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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