Contacts of the helix formed by residues 2496 - 2511 (chain F) 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 VAL2496 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2491F MET 5.4 3.8 - - - +
2492F SER* 5.6 5.6 - - - +
2494F SER 3.6 4.9 + - - +
2495F PHE* 1.3 87.1 - - - +
2497F PRO* 1.3 72.9 - - + +
2498F ASP* 2.9 33.0 + - + +
2499F HIS* 3.2 37.1 + - + +
2550F ALA* 4.6 11.0 - - + -
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Residues in contact with PRO2497 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2475F LEU* 6.3 2.9 - - + -
2495F PHE* 4.4 8.3 - - + +
2496F VAL* 1.3 89.8 - - + +
2498F ASP* 1.3 58.7 + - - +
2499F HIS 3.2 0.4 - - - -
2500F LYS* 3.2 9.7 + - + +
2501F ALA* 2.9 24.1 + - - +
2550F ALA* 3.9 13.5 - - + +
2551F LEU* 4.0 27.4 - - + +
2554F TYR* 3.5 39.1 - - + -
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Residues in contact with ASP2498 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2428F ALA* 5.7 0.4 - - - -
2496F VAL* 2.9 23.9 + - + +
2497F PRO* 1.3 76.2 - - - +
2499F HIS* 1.3 66.2 + - + +
2501F ALA* 3.3 9.1 + - - +
2502F SER* 2.9 23.7 + - - -
2550F ALA* 5.9 1.6 - - - +
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Residues in contact with HIS2499 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2424F MET* 3.1 51.5 - - + +
2425F SER* 3.2 14.9 + - - -
2428F ALA* 3.6 19.1 - - + -
2494F SER 5.6 1.3 - - - -
2495F PHE* 3.5 27.2 - + + -
2496F VAL* 3.2 35.7 + - + +
2497F PRO 3.2 0.2 - - - -
2498F ASP* 1.3 76.5 - - + +
2500F LYS* 1.3 58.7 + - - +
2502F SER* 3.1 3.6 + - - -
2503F MET* 2.9 38.2 + - + +
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Residues in contact with LYS2500 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2470F ILE 4.6 4.5 - - - +
2471F ILE* 3.3 39.2 + - + +
2473F LEU* 3.0 24.8 + - - -
2474F PRO 4.7 0.2 - - - -
2475F LEU* 4.2 27.9 - - + +
2495F PHE* 4.3 18.8 - - + -
2497F PRO* 3.2 12.2 + - + +
2499F HIS* 1.3 78.9 - - - +
2501F ALA* 1.3 57.7 + - - +
2503F MET* 3.2 8.2 + - + +
2504F VAL* 2.9 35.0 + - - +
2526F GLY 4.7 7.8 + - - -
2527F PHE* 5.6 3.8 - - - +
2554F TYR* 3.3 35.9 - - + +
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Residues in contact with ALA2501 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2497F PRO 2.9 14.2 + - - +
2498F ASP* 3.5 13.9 - - - +
2499F HIS 3.2 0.2 - - - -
2500F LYS* 1.3 76.0 - - - +
2502F SER* 1.3 57.0 + - - +
2504F VAL* 3.1 8.8 - - + +
2505F LEU* 2.9 39.5 + - + +
2554F TYR* 3.4 18.9 - - + -
2557F LEU* 5.3 12.1 - - + -
2558F ALA* 5.7 1.8 - - + +
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Residues in contact with SER2502 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2428F ALA* 4.2 27.4 - - - -
2431F ILE* 5.0 2.0 - - - -
2432F ASP* 4.4 16.8 - - - -
2498F ASP 2.9 13.3 + - - -
2499F HIS 3.1 8.9 + - - -
2501F ALA* 1.3 77.1 - - - +
2503F MET* 1.3 60.0 + - - +
2505F LEU* 3.3 10.1 + - - +
2506F PHE* 2.9 30.8 + - - +
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Residues in contact with MET2503 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2377F LEU* 6.2 3.6 - - + -
2428F ALA* 5.1 4.7 - - - -
2431F ILE* 4.1 32.8 - - + -
2466F ASP 5.4 0.7 - - - +
2467F LEU* 5.2 10.9 - - + +
2470F ILE* 3.8 34.3 - - + +
2471F ILE* 3.8 20.8 - - + +
2495F PHE* 6.4 0.4 - - + -
2499F HIS* 2.9 31.9 + - + +
2500F LYS* 3.2 9.4 + - - +
2502F SER* 1.3 80.6 - - - +
2504F VAL* 1.3 57.6 + - - +
2506F PHE* 3.3 8.5 + - + +
2507F LEU* 2.9 29.7 + - - +
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Residues in contact with VAL2504 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2471F ILE* 3.7 11.7 - - + -
2500F LYS 2.9 15.4 + - - +
2501F ALA* 3.1 20.6 - - - +
2503F MET* 1.3 76.0 - - - +
2505F LEU* 1.3 56.0 + - - +
2507F LEU* 3.8 10.3 - - + +
2508F ASP* 2.9 31.7 + - - +
2527F PHE* 3.5 38.4 - - + -
2554F TYR* 3.9 9.2 - - + +
2558F ALA* 3.7 30.1 - - + +
2559F VAL* 4.7 2.0 - - + -
2562F LEU* 5.2 9.8 - - + +
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Residues in contact with LEU2505 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2337F ARG* 6.3 0.9 - - - +
2432F ASP* 6.5 1.8 - - + -
2501F ALA* 2.9 26.8 + - + +
2502F SER* 3.7 8.1 - - - +
2504F VAL* 1.3 77.3 - - - +
2506F PHE* 1.3 56.4 + - - +
2508F ASP* 3.3 6.3 + - + +
2509F ARG* 2.9 45.0 + - + +
2558F ALA* 3.8 24.7 - - + -
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Residues in contact with PHE2506 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2431F ILE* 3.5 46.7 - - + +
2432F ASP* 5.4 2.2 - - - +
2434F LEU* 4.6 3.8 - - + -
2435F GLY* 3.5 27.1 - - - -
2458F LEU* 5.2 7.6 - - + -
2459F ARG* 6.1 0.2 - - - -
2462F VAL* 4.0 31.9 - - + -
2467F LEU* 4.8 17.5 - - + -
2502F SER 2.9 17.8 + - - +
2503F MET* 3.6 9.2 - - + +
2505F LEU* 1.3 76.4 - - - +
2507F LEU* 1.3 61.5 + - - +
2509F ARG* 3.1 4.8 + - - +
2510F VAL* 2.9 68.7 + - + +
2511F TYR* 5.1 3.6 - + - -
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Residues in contact with LEU2507 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2464F LEU* 4.6 14.4 - - + -
2467F LEU* 4.4 23.1 - - + -
2468F VAL* 5.5 2.5 - - + +
2471F ILE* 4.9 15.3 - - + -
2503F MET 2.9 17.7 + - - +
2504F VAL* 3.8 6.7 - - + +
2505F LEU 3.3 0.2 - - - -
2506F PHE* 1.3 81.8 - - - +
2508F ASP* 1.3 57.1 + - - +
2510F VAL* 4.7 2.5 - - - -
2511F TYR* 3.4 8.1 + - + +
2512F GLY* 2.6 39.0 + - - +
2519F LEU* 5.3 12.1 - - + -
2527F PHE* 6.3 5.2 - - + -
2562F LEU* 4.4 24.2 - - + -
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Residues in contact with ASP2508 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2504F VAL 2.9 17.5 + - - +
2505F LEU* 3.9 7.2 - - + +
2507F LEU* 1.3 79.4 - - - +
2509F ARG* 1.3 62.5 + - + +
2512F GLY* 3.4 25.1 - - - -
2558F ALA* 6.6 0.2 - - + -
2562F LEU* 4.1 24.5 - - + -
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Residues in contact with ARG2509 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2341F PHE* 4.3 21.2 - - - -
2344F GLY 5.1 2.6 + - - -
2346F SER* 3.8 10.1 + - - -
2435F GLY 2.7 31.2 + - - +
2436F ARG* 2.8 30.0 + - - +
2438F ALA* 3.0 24.1 + - - +
2440F GLU* 3.5 38.3 - - + +
2455F ARG* 5.4 3.5 + - - -
2505F LEU* 2.9 30.1 + - + +
2506F PHE* 3.1 4.2 + - - +
2508F ASP* 1.3 82.0 - - + +
2510F VAL* 1.3 64.3 + - + +
2511F TYR 3.5 0.6 - - - -
2512F GLY 5.0 1.2 + - - -
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Residues in contact with VAL2510 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2435F GLY* 3.9 8.3 - - - -
2438F ALA* 3.7 17.7 - - + -
2455F ARG* 3.6 24.8 + - - +
2458F LEU* 3.6 31.9 - - + +
2459F ARG* 5.7 4.0 - - + +
2506F PHE* 2.9 61.7 + - + +
2507F LEU* 4.7 0.2 - - - -
2509F ARG* 1.3 78.3 - - - +
2511F TYR* 1.3 83.6 + - + +
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Residues in contact with TYR2511 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2459F ARG* 3.1 41.0 + - + +
2462F VAL 3.9 17.5 - - - -
2463F PRO* 3.8 8.7 - - - +
2464F LEU* 3.6 53.3 + - + -
2506F PHE* 5.1 3.4 - + - -
2507F LEU* 3.4 7.7 + - + +
2510F VAL* 1.3 106.4 - - + +
2512F GLY* 1.3 68.9 + - - +
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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