Contacts of the helix formed by residues 2463 - 2472 (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 PRO2463 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2459B ARG 3.8 3.6 - - - +
2460B SER* 4.3 9.9 - - - +
2461B LEU 3.3 11.2 - - - +
2462B VAL* 1.3 92.3 - - + +
2464B LEU* 1.3 65.9 + - - +
2465B ASP* 3.1 13.0 + - + +
2466B ASP* 3.4 17.0 + - + +
2467B LEU* 3.6 8.8 + - - +
2506B PHE* 5.2 0.3 - - - -
2511B TYR* 3.8 14.1 - - - +
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Residues in contact with LEU2464 (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 PRO* 1.3 73.3 - - - +
2465B ASP* 1.3 58.0 + - - +
2467B LEU* 3.3 14.7 + - + +
2468B VAL* 2.9 32.6 + - - +
2507B LEU* 4.6 15.9 - - + -
2511B TYR* 3.6 55.2 + - + -
2519B LEU* 5.4 14.1 - - + -
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Residues in contact with ASP2465 (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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2378B LEU* 4.9 3.6 - - - +
2463B PRO* 3.1 10.7 - - + +
2464B LEU* 1.3 77.7 - - - +
2466B ASP* 1.3 57.8 + - - +
2468B VAL* 3.1 11.8 - - - +
2469B GLY* 2.9 26.3 + - - -
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Residues in contact with ASP2466 (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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2377B LEU* 3.7 28.2 - - + +
2378B LEU* 4.8 11.1 - - + +
2462B VAL* 3.6 27.4 - - + -
2463B PRO* 3.4 10.8 + - + +
2464B LEU 3.4 0.2 - - - -
2465B ASP* 1.3 78.0 - - - +
2467B LEU* 1.3 58.8 + - - +
2469B GLY* 3.4 1.8 + - - -
2470B ILE* 2.9 30.5 + - - +
2503B MET* 6.0 0.7 - - - -
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Residues in contact with LEU2467 (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 VAL* 4.9 1.9 - - - +
2463B PRO 3.6 7.3 + - - +
2464B LEU* 3.3 19.2 + - + +
2465B ASP 3.2 0.4 - - - -
2466B ASP* 1.3 78.6 - - - +
2468B VAL* 1.3 58.2 + - - +
2470B ILE* 3.3 6.4 + - - +
2471B ILE* 2.9 34.5 + - + +
2503B MET* 5.2 9.7 - - + +
2506B PHE* 4.8 20.2 - - + -
2507B LEU* 4.4 22.9 - - + -
2511B TYR* 6.0 0.2 - - + -
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Residues in contact with VAL2468 (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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2464B LEU 2.9 18.4 + - - +
2465B ASP* 3.1 21.1 - - - +
2467B LEU* 1.3 75.9 - - - +
2469B GLY* 1.3 57.9 + - - +
2471B ILE* 3.7 10.0 - - + +
2472B SER* 2.9 30.5 + - - -
2507B LEU* 5.5 3.1 - - + +
2519B LEU* 6.0 6.7 - - + -
2522B VAL* 3.7 30.5 - - + -
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Residues in contact with GLY2469 (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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2378B LEU* 3.5 31.6 - - - +
2465B ASP 2.9 13.4 + - - -
2466B ASP 3.8 0.2 - - - -
2468B VAL* 1.3 80.4 - - - +
2470B ILE* 1.3 59.7 + - - +
2472B SER* 3.4 12.5 + - - -
2473B LEU* 3.4 21.0 + - - +
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Residues in contact with ILE2470 (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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2377B LEU* 6.0 3.6 - - + -
2378B LEU* 3.8 4.6 - - + +
2381B ILE* 5.7 4.5 - - + -
2466B ASP 2.9 17.8 + - - +
2467B LEU 3.8 2.7 - - - +
2469B GLY* 1.3 73.7 - - - +
2471B ILE* 1.3 68.2 + - - +
2473B LEU* 3.4 32.1 + - + +
2495B PHE* 5.9 1.7 - - - -
2500B LYS* 4.6 5.5 - - - +
2503B MET* 3.8 37.1 - - + +
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Residues in contact with ILE2471 (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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2467B LEU* 2.9 24.4 + - + +
2468B VAL* 3.7 10.8 - - + +
2470B ILE* 1.3 77.7 - - - +
2472B SER* 1.3 56.7 + - - +
2473B LEU 3.1 4.5 + - - -
2500B LYS* 3.3 34.5 + - + +
2503B MET* 3.8 20.0 - - + +
2504B VAL* 3.7 31.4 - - + +
2507B LEU* 4.9 13.9 - - + -
2522B VAL 5.8 0.4 - - - +
2523B LEU* 6.2 0.9 - - - -
2526B GLY* 4.0 27.7 - - - +
2527B PHE* 4.4 19.5 - - + -
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Residues in contact with SER2472 (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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2468B VAL* 2.9 19.5 + - - -
2469B GLY* 3.4 8.9 + - - -
2470B ILE 3.3 0.4 - - - -
2471B ILE* 1.3 74.8 - - - +
2473B LEU* 1.3 64.0 + - - +
2474B PRO* 3.6 5.0 - - - +
2526B GLY* 5.0 10.5 - - - -
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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