Contacts of the helix formed by residues 2496 - 2511 (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 VAL2496 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2491B MET 5.4 4.0 - - - +
2492B SER* 5.6 5.8 - - - +
2494B SER 3.6 4.9 + - - +
2495B PHE* 1.3 87.5 - - - +
2497B PRO* 1.3 71.7 - - + +
2498B ASP* 2.9 32.6 + - + +
2499B HIS* 3.2 37.3 + - + +
2550B ALA* 4.6 10.3 - - + -
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Residues in contact with PRO2497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2475B LEU* 6.3 2.7 - - + -
2495B PHE* 4.4 8.5 - - + +
2496B VAL* 1.3 89.7 - - + +
2498B ASP* 1.3 59.5 + - - +
2499B HIS 3.2 0.9 - - - -
2500B LYS* 3.2 10.5 + - + +
2501B ALA* 2.9 25.2 + - - +
2550B ALA* 3.9 14.4 - - + +
2551B LEU* 4.0 27.1 - - + +
2554B TYR* 3.5 37.4 - - + -
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Residues in contact with ASP2498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2428B ALA* 5.7 0.2 - - - -
2496B VAL* 2.9 23.8 + - + +
2497B PRO* 1.3 75.5 - - - +
2499B HIS* 1.3 67.3 + - - +
2501B ALA* 3.3 9.5 + - - +
2502B SER* 2.9 22.9 + - - -
2550B ALA* 5.9 1.6 - - - +
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Residues in contact with HIS2499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2424B MET* 3.1 50.6 - - + +
2425B SER* 3.2 14.4 + - - -
2428B ALA* 3.6 19.7 - - + -
2494B SER 5.6 1.6 - - - -
2495B PHE* 3.5 28.6 - + + -
2496B VAL* 3.2 34.2 + - + +
2497B PRO 3.2 0.2 - - - -
2498B ASP* 1.3 77.3 - - + +
2500B LYS* 1.3 56.9 + - - +
2502B SER* 3.1 3.3 + - - -
2503B MET* 2.9 38.3 + - + +
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Residues in contact with LYS2500 (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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2470B ILE 4.6 4.3 - - - +
2471B ILE* 3.3 40.0 + - + +
2473B LEU* 3.0 25.8 + - - -
2474B PRO 4.7 0.2 - - - -
2475B LEU* 4.2 28.6 - - + +
2495B PHE* 4.3 17.9 - - + -
2497B PRO* 3.2 12.0 + - + +
2499B HIS* 1.3 79.1 - - - +
2501B ALA* 1.3 58.9 + - - +
2503B MET* 3.2 7.9 + - + +
2504B VAL* 2.9 34.7 + - - +
2526B GLY 4.7 8.7 + - - -
2527B PHE* 5.6 3.8 - - - +
2554B TYR* 3.3 35.7 - - + +
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Residues in contact with ALA2501 (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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2497B PRO 2.9 13.4 + - - +
2498B ASP* 3.5 14.4 - - - +
2500B LYS* 1.3 76.8 - - - +
2502B SER* 1.3 56.9 + - - +
2504B VAL* 3.1 8.3 - - + +
2505B LEU* 2.9 40.0 + - + +
2554B TYR* 3.4 19.2 - - + -
2557B LEU* 5.3 11.2 - - + -
2558B ALA* 5.7 2.0 - - + -
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Residues in contact with SER2502 (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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2428B ALA* 4.2 28.0 - - - -
2431B ILE* 5.0 1.8 - - - -
2432B ASP* 4.4 16.5 - - - -
2498B ASP 2.9 13.7 + - - -
2499B HIS 3.4 9.2 - - - -
2501B ALA* 1.3 76.0 - - - +
2503B MET* 1.3 60.4 + - - +
2505B LEU* 3.3 9.7 + - - +
2506B PHE* 2.9 30.5 + - - +
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Residues in contact with MET2503 (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* 6.2 4.3 - - + -
2428B ALA* 5.1 5.2 - - - -
2431B ILE* 4.1 32.5 - - + -
2466B ASP 5.4 0.7 - - - +
2467B LEU* 5.2 10.5 - - + +
2470B ILE* 3.8 33.0 - - + +
2471B ILE* 3.8 21.1 - - + -
2495B PHE* 6.4 0.4 - - + -
2499B HIS* 2.9 31.3 + - + +
2500B LYS* 3.2 8.7 + - - +
2502B SER* 1.3 80.2 - - - +
2504B VAL* 1.3 57.4 + - - +
2506B PHE* 3.3 9.8 + - + +
2507B LEU* 2.9 29.6 + - - +
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Residues in contact with VAL2504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2471B ILE* 3.7 11.9 - - + -
2500B LYS 2.9 15.0 + - - +
2501B ALA* 3.1 20.9 - - - +
2503B MET* 1.3 75.7 - - - +
2505B LEU* 1.3 57.4 + - - +
2507B LEU* 3.8 8.9 - - + +
2508B ASP* 2.9 30.8 + - - +
2527B PHE* 3.5 39.0 - - + -
2554B TYR* 3.9 9.2 - - + +
2558B ALA* 3.7 29.6 - - + +
2559B VAL* 4.7 1.6 - - + -
2562B LEU* 5.2 9.6 - - + +
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Residues in contact with LEU2505 (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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2337B ARG* 6.3 0.9 - - - +
2432B ASP* 6.5 1.8 - - + -
2501B ALA* 2.9 28.1 + - + +
2502B SER* 3.7 7.6 - - - +
2504B VAL* 1.3 78.5 - - - +
2506B PHE* 1.3 57.5 + - - +
2508B ASP* 3.3 6.0 + - + +
2509B ARG* 2.9 44.5 + - + +
2558B ALA* 3.8 24.9 - - + -
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Residues in contact with PHE2506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2431B ILE* 3.5 46.2 - - + +
2432B ASP* 5.4 1.8 - - - +
2434B LEU* 4.6 3.8 - - + -
2435B GLY* 3.5 28.0 - - - -
2458B LEU* 5.2 8.7 - - + -
2459B ARG* 6.1 0.2 - - - -
2462B VAL* 4.0 31.2 - - + -
2463B PRO 5.2 0.2 - - - -
2467B LEU* 4.8 16.4 - - + -
2502B SER 2.9 17.4 + - - +
2503B MET* 3.6 9.2 - - + +
2505B LEU* 1.3 76.6 - - - +
2507B LEU* 1.3 60.9 + - - +
2509B ARG* 3.1 4.4 + - - +
2510B VAL* 2.9 67.6 + - + +
2511B TYR* 5.1 3.8 - + - -
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Residues in contact with LEU2507 (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* 4.6 15.3 - - + -
2467B LEU* 4.4 24.0 - - + -
2468B VAL* 5.5 2.2 - - + +
2471B ILE* 4.9 15.0 - - + -
2503B MET 2.9 18.3 + - - +
2504B VAL* 3.8 7.6 - - + +
2506B PHE* 1.3 81.5 - - - +
2508B ASP* 1.3 57.7 + - - +
2510B VAL* 4.7 2.2 - - - -
2511B TYR* 3.4 9.4 + - + +
2512B GLY* 2.6 38.5 + - - +
2519B LEU* 5.3 11.9 - - + -
2527B PHE* 6.3 4.9 - - + -
2562B LEU* 4.4 24.7 - - + -
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Residues in contact with ASP2508 (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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2504B VAL 2.9 18.7 + - - +
2505B LEU* 3.9 6.7 - - + +
2507B LEU* 1.3 79.0 - - - +
2509B ARG* 1.3 62.0 + - + +
2512B GLY* 3.4 26.3 - - - -
2558B ALA* 6.6 0.2 - - + -
2562B LEU* 4.1 24.2 - - + -
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Residues in contact with ARG2509 (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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2341B PHE* 4.3 21.8 - - - -
2344B GLY 5.1 2.6 + - - -
2346B SER* 3.8 9.8 + - - -
2435B GLY* 2.7 31.4 + - - +
2436B ARG* 2.8 29.4 + - - +
2438B ALA* 3.0 25.1 + - + +
2440B GLU* 3.5 38.5 - - + +
2455B ARG* 5.4 3.3 + - - -
2505B LEU* 2.9 29.1 + - + +
2506B PHE* 3.1 3.8 + - - +
2508B ASP* 1.3 82.5 - - + +
2510B VAL* 1.3 65.0 + - + +
2511B TYR 3.5 0.4 - - - -
2512B GLY 5.0 1.6 + - - -
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Residues in contact with VAL2510 (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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2435B GLY* 3.9 8.3 - - - +
2438B ALA* 3.7 18.8 - - + -
2455B ARG* 3.6 23.9 + - - +
2458B LEU* 3.6 31.4 - - + +
2459B ARG* 5.7 4.0 - - + +
2506B PHE* 2.9 60.5 + - + +
2507B LEU* 4.7 0.4 - - - -
2509B ARG* 1.3 76.9 - - - +
2511B TYR* 1.3 86.9 + - + +
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Residues in contact with TYR2511 (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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2459B ARG* 3.1 40.9 + - + +
2462B VAL 3.9 17.3 - - - -
2463B PRO* 3.8 8.6 - - - +
2464B LEU* 3.6 54.1 + - + -
2506B PHE* 5.1 2.9 - + - -
2507B LEU* 3.4 7.9 + - + +
2509B ARG 5.1 0.2 - - - -
2510B VAL* 1.3 108.1 - - + +
2512B GLY* 1.3 68.3 + - - +
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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