Contacts of the helix formed by residues 2496 - 2511 (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 VAL2496 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2491H MET 5.4 4.0 - - - +
2492H SER* 5.6 5.2 - - - +
2494H SER 3.6 4.4 + - - +
2495H PHE* 1.3 86.8 - - - +
2497H PRO* 1.3 70.3 - - + +
2498H ASP* 2.9 32.1 + - + +
2499H HIS* 3.2 37.6 + - + +
2550H ALA* 4.6 11.2 - - + -
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Residues in contact with PRO2497 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2475H LEU* 6.3 2.9 - - + -
2495H PHE* 4.4 8.1 - - + +
2496H VAL* 1.3 88.5 - - + +
2498H ASP* 1.3 60.2 + - - +
2499H HIS 3.2 0.7 - - - -
2500H LYS* 3.2 10.2 + - + +
2501H ALA* 2.9 23.9 + - - +
2550H ALA* 3.9 14.1 - - + +
2551H LEU* 4.0 26.5 - - + +
2554H TYR* 3.5 37.9 - - + -
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Residues in contact with ASP2498 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2428H ALA* 5.7 0.4 - - - -
2496H VAL* 2.9 22.9 + - + +
2497H PRO* 1.3 74.7 - - - +
2499H HIS* 1.3 67.2 + - + +
2501H ALA* 3.3 9.4 + - - +
2502H SER* 2.9 23.4 + - - -
2550H ALA* 5.9 1.9 - - - +
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Residues in contact with HIS2499 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2424H MET* 3.1 51.2 - - + +
2425H SER* 3.2 14.0 + - - -
2428H ALA* 3.6 19.5 - - + -
2494H SER 5.6 1.8 - - - -
2495H PHE* 3.5 28.0 - + + -
2496H VAL* 3.2 35.7 + - + +
2498H ASP* 1.3 77.0 - - + +
2500H LYS* 1.3 57.3 + - - +
2502H SER* 3.1 3.6 + - - -
2503H MET* 2.9 38.6 + - + +
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Residues in contact with LYS2500 (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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2470H ILE 4.6 4.5 - - - +
2471H ILE* 3.3 39.3 + - + +
2473H LEU* 3.0 25.4 + - - -
2474H PRO* 4.9 0.2 - - - +
2475H LEU* 4.2 29.0 - - + +
2495H PHE* 4.3 18.0 - - + -
2497H PRO* 3.2 11.8 + - + +
2499H HIS* 1.3 77.6 - - - +
2501H ALA* 1.3 59.1 + - - +
2503H MET* 3.2 8.2 + - + +
2504H VAL* 2.9 34.8 + - - +
2526H GLY 4.7 8.2 + - - -
2527H PHE* 5.6 4.5 - - - +
2554H TYR* 3.3 35.9 - - + +
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Residues in contact with ALA2501 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2497H PRO 2.9 14.4 + - - +
2498H ASP* 3.5 14.4 - - - +
2499H HIS 3.2 0.2 - - - -
2500H LYS* 1.3 76.4 - - - +
2502H SER* 1.3 56.5 + - - +
2504H VAL* 3.1 9.1 - - - +
2505H LEU* 2.9 40.5 + - + +
2554H TYR* 3.4 18.7 - - + -
2557H LEU* 5.3 11.9 - - + -
2558H ALA* 5.7 1.8 - - + -
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Residues in contact with SER2502 (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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2428H ALA* 4.2 27.6 - - - -
2431H ILE* 5.0 2.2 - - - +
2432H ASP* 4.4 15.6 - - - +
2498H ASP 2.9 13.8 + - - -
2499H HIS 3.1 8.9 + - - -
2501H ALA* 1.3 76.8 - - - +
2503H MET* 1.3 60.3 + - - +
2505H LEU* 3.3 9.6 + - - +
2506H PHE* 2.9 30.9 + - - +
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Residues in contact with MET2503 (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* 6.2 4.0 - - + -
2428H ALA* 5.1 4.7 - - - -
2431H ILE* 4.1 33.2 - - + -
2466H ASP 5.4 0.4 - - - +
2467H LEU* 5.2 10.5 - - + +
2470H ILE* 3.8 33.4 - - + +
2471H ILE* 3.8 21.3 - - + +
2495H PHE* 6.4 0.4 - - + -
2499H HIS* 2.9 32.8 + - + +
2500H LYS* 3.2 8.9 + - + +
2502H SER* 1.3 79.1 - - - +
2504H VAL* 1.3 57.7 + - - +
2506H PHE* 3.3 9.8 + - + +
2507H LEU* 2.9 29.7 + - - +
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Residues in contact with VAL2504 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2471H ILE* 3.7 11.9 - - + -
2500H LYS 2.9 15.2 + - - +
2501H ALA* 3.1 20.4 - - - +
2503H MET* 1.3 75.7 - - - +
2505H LEU* 1.3 58.2 + - - +
2507H LEU* 3.8 9.2 - - + +
2508H ASP* 2.9 31.7 + - - +
2527H PHE* 3.5 37.9 - - + -
2554H TYR* 3.9 9.2 - - + +
2558H ALA* 3.7 29.8 - - + +
2559H VAL* 4.7 2.0 - - + -
2562H LEU* 5.2 9.6 - - + +
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Residues in contact with LEU2505 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2337H ARG* 6.3 1.1 - - - +
2432H ASP* 6.5 1.6 - - + -
2501H ALA* 2.9 27.3 + - + +
2502H SER* 3.7 8.3 - - - +
2504H VAL* 1.3 78.1 - - - +
2506H PHE* 1.3 56.0 + - - +
2508H ASP* 3.3 5.5 + - + +
2509H ARG* 2.9 44.5 + - + +
2558H ALA* 3.8 23.1 - - + -
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Residues in contact with PHE2506 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2431H ILE* 3.5 47.6 - - + +
2432H ASP* 5.4 1.5 - - - +
2434H LEU* 4.6 4.0 - - + -
2435H GLY* 3.5 27.1 - - - -
2458H LEU* 5.2 7.4 - - + -
2459H ARG* 6.1 0.4 - - - -
2462H VAL* 4.0 31.9 - - + -
2463H PRO 5.2 0.2 - - - -
2467H LEU* 4.8 15.9 - - + -
2502H SER 2.9 16.8 + - - +
2503H MET* 3.6 9.2 - - + +
2505H LEU* 1.3 77.8 - - - +
2507H LEU* 1.3 61.2 + - - +
2509H ARG* 3.1 4.0 + - - +
2510H VAL* 2.9 67.5 + - + +
2511H TYR* 5.1 3.8 - + - -
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Residues in contact with LEU2507 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2464H LEU* 4.6 15.0 - - + -
2467H LEU* 4.4 23.6 - - + -
2468H VAL* 5.5 2.7 - - + +
2471H ILE* 4.9 15.0 - - + -
2503H MET 2.9 16.4 + - - +
2504H VAL* 3.8 8.5 - - + +
2506H PHE* 1.3 81.9 - - - +
2508H ASP* 1.3 56.9 + - - +
2510H VAL* 4.7 2.5 - - - -
2511H TYR* 3.4 8.6 + - + +
2512H GLY* 2.6 38.0 + - - +
2519H LEU* 5.3 12.6 - - + -
2527H PHE* 6.3 5.4 - - + -
2562H LEU* 4.4 24.0 - - + -
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Residues in contact with ASP2508 (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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2504H VAL 2.9 17.9 + - - +
2505H LEU* 3.9 6.7 - - + +
2507H LEU* 1.3 79.2 - - + +
2509H ARG* 1.3 63.8 + - + +
2512H GLY* 3.4 26.1 - - - -
2558H ALA* 6.6 0.2 - - + -
2562H LEU* 4.1 23.8 - - + -
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Residues in contact with ARG2509 (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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2341H PHE* 4.3 21.1 - - - -
2344H GLY 5.1 2.8 + - - -
2346H SER* 3.8 9.8 + - - -
2435H GLY* 2.7 30.8 + - - +
2436H ARG* 2.8 29.9 + - - +
2438H ALA* 3.0 24.3 + - + +
2440H GLU* 3.5 38.0 - - + +
2455H ARG* 5.4 3.6 + - - -
2505H LEU* 2.9 30.8 + - + +
2506H PHE* 3.8 4.0 - - - +
2508H ASP* 1.3 81.3 - - + +
2510H VAL* 1.3 64.9 + - + +
2511H TYR 5.1 0.3 - - - -
2512H GLY 5.0 1.4 + - - -
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Residues in contact with VAL2510 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2435H GLY* 3.9 8.7 - - - +
2438H ALA* 3.7 17.5 - - + -
2455H ARG* 3.6 24.4 + - - +
2458H LEU* 3.6 32.5 - - + +
2459H ARG* 5.7 4.0 - - + +
2506H PHE* 2.9 60.5 + - + +
2507H LEU* 4.7 0.4 - - - -
2509H ARG* 1.3 77.6 - - - +
2511H TYR* 1.3 84.5 + - + +
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Residues in contact with TYR2511 (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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2459H ARG* 3.1 40.7 + - + +
2462H VAL 3.9 17.3 - - - -
2463H PRO* 3.8 8.8 - - - +
2464H LEU* 3.6 55.1 + - + -
2506H PHE* 5.1 3.6 - + - -
2507H LEU* 3.4 7.7 + - + +
2510H VAL* 1.3 106.2 - - + +
2512H GLY* 1.3 67.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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