Contacts of the helix formed by residues 2496 - 2511 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2491D MET 5.4 4.0 - - - +
2492D SER* 5.6 4.7 - - - +
2494D SER 3.6 4.4 + - - +
2495D PHE* 1.3 87.6 - - - +
2497D PRO* 1.3 71.4 - - + +
2498D ASP* 2.9 32.5 + - + +
2499D HIS* 3.2 36.2 + - + +
2550D ALA* 4.6 10.1 - - + -
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Residues in contact with PRO2497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2475D LEU* 6.3 3.4 - - + -
2495D PHE* 4.4 7.6 - - + +
2496D VAL* 1.3 89.2 - - + +
2498D ASP* 1.3 59.9 + - - +
2499D HIS 3.2 0.9 - - - -
2500D LYS* 3.2 10.5 + - + +
2501D ALA* 2.9 24.5 + - - +
2550D ALA* 3.9 13.9 - - + +
2551D LEU* 4.0 27.6 - - + +
2554D TYR* 3.5 37.2 - - + -
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Residues in contact with ASP2498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2428D ALA* 5.7 0.7 - - - -
2496D VAL* 2.9 23.5 + - + +
2497D PRO* 1.3 76.2 - - - +
2499D HIS* 1.3 65.6 + - + +
2501D ALA* 3.3 9.1 + - - +
2502D SER* 2.9 23.6 + - - -
2550D ALA* 5.9 1.6 - - - +
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Residues in contact with HIS2499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2424D MET* 3.1 51.9 - - + +
2425D SER* 3.2 14.2 + - - -
2428D ALA* 3.6 19.3 - - + -
2494D SER 5.6 1.3 - - - -
2495D PHE* 3.5 27.7 - + + -
2496D VAL* 3.2 35.4 + - + +
2497D PRO 3.2 0.4 - - - -
2498D ASP* 1.3 77.4 - - + +
2500D LYS* 1.3 57.0 + - - +
2502D SER* 3.1 2.8 + - - -
2503D MET* 2.9 38.8 + - + +
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Residues in contact with LYS2500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2470D ILE 4.6 4.9 - - - +
2471D ILE* 3.3 40.4 + - + +
2473D LEU 3.0 24.9 + - - -
2474D PRO 4.7 0.2 - - - -
2475D LEU* 4.2 28.6 - - + +
2495D PHE* 4.3 19.4 - - + -
2497D PRO* 3.2 11.8 + - + +
2499D HIS* 1.3 79.0 - - - +
2501D ALA* 1.3 57.9 + - - +
2503D MET* 3.2 8.1 + - + +
2504D VAL* 2.9 34.7 + - - +
2526D GLY 4.7 8.2 + - - -
2527D PHE* 5.6 4.5 - - - +
2554D TYR* 3.3 36.3 - - + +
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Residues in contact with ALA2501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2497D PRO 2.9 14.0 + - - +
2498D ASP* 3.5 13.7 - - - +
2499D HIS 3.2 0.2 - - - -
2500D LYS* 1.3 77.0 - - - +
2502D SER* 1.3 56.0 + - - +
2504D VAL* 3.1 8.6 - - + +
2505D LEU* 2.9 39.0 + - + +
2554D TYR* 3.4 19.0 - - + -
2557D LEU* 5.3 12.3 - - + -
2558D ALA* 5.7 1.8 - - + -
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Residues in contact with SER2502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2428D ALA* 4.2 28.5 - - - -
2431D ILE* 5.0 2.0 - - - +
2432D ASP* 4.4 15.2 - - - -
2498D ASP 2.9 13.7 + - - -
2499D HIS 3.4 9.2 - - - -
2501D ALA* 1.3 77.3 - - - +
2503D MET* 1.3 60.0 + - - +
2505D LEU* 3.3 10.0 + - - +
2506D PHE* 2.9 31.4 + - - +
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Residues in contact with MET2503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2377D LEU* 6.2 3.8 - - + -
2428D ALA* 5.1 4.9 - - - -
2431D ILE* 4.1 31.9 - - + -
2466D ASP 5.4 0.4 - - - +
2467D LEU* 5.2 10.9 - - + +
2470D ILE* 3.8 32.8 - - + +
2471D ILE* 3.8 20.6 - - + -
2499D HIS* 2.9 31.1 + - + +
2500D LYS* 3.2 9.2 + - - +
2502D SER* 1.3 80.8 - - - +
2504D VAL* 1.3 58.2 + - - +
2506D PHE* 3.3 9.8 + - + +
2507D LEU* 2.9 29.0 + - - +
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Residues in contact with VAL2504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2471D ILE* 3.7 12.3 - - + -
2500D LYS 2.9 15.8 + - - +
2501D ALA* 3.1 20.6 - - - +
2503D MET* 1.3 76.0 - - - +
2505D LEU* 1.3 57.7 + - - +
2507D LEU* 3.8 9.3 - - + +
2508D ASP* 2.9 30.8 + - - +
2527D PHE* 3.5 38.6 - - + -
2554D TYR* 3.9 8.5 - - + +
2558D ALA* 3.7 29.8 - - + +
2559D VAL* 4.7 1.8 - - + -
2562D LEU* 5.2 9.3 - - + +
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Residues in contact with LEU2505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2337D ARG* 6.3 1.1 - - - +
2432D ASP* 6.5 1.6 - - + -
2501D ALA* 2.9 27.5 + - + +
2502D SER* 3.7 7.9 - - - +
2504D VAL* 1.3 76.8 - - - +
2506D PHE* 1.3 57.7 + - - +
2508D ASP* 3.3 6.4 + - + +
2509D ARG* 2.9 44.4 + - + +
2558D ALA* 3.8 23.3 - - + -
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Residues in contact with PHE2506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2431D ILE* 3.5 45.8 - - + +
2432D ASP* 5.4 2.2 - - - +
2434D LEU* 4.6 3.8 - - + -
2435D GLY* 3.5 27.8 - - - -
2458D LEU* 5.2 7.6 - - + -
2459D ARG* 6.1 0.4 - - - -
2462D VAL* 4.0 32.3 - - + -
2467D LEU* 4.8 16.6 - - + -
2502D SER 2.9 17.4 + - - +
2503D MET* 3.6 9.4 - - + +
2505D LEU* 1.3 76.3 - - - +
2507D LEU* 1.3 60.3 + - - +
2509D ARG* 3.1 4.0 + - - +
2510D VAL* 2.9 67.9 + - + +
2511D TYR* 5.1 3.1 - + - -
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Residues in contact with LEU2507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2464D LEU* 4.6 15.3 - - + -
2467D LEU* 4.4 22.9 - - + -
2468D VAL* 5.5 2.7 - - + +
2471D ILE* 4.9 15.9 - - + -
2503D MET 2.9 16.8 + - - +
2504D VAL* 3.8 7.4 - - + +
2505D LEU 3.3 0.2 - - - -
2506D PHE* 1.3 81.7 - - - +
2508D ASP* 1.3 55.9 + - - +
2510D VAL* 4.7 2.2 - - - -
2511D TYR* 3.4 9.3 + - + +
2512D GLY* 2.6 38.6 + - - +
2519D LEU* 5.3 12.1 - - + -
2527D PHE* 6.3 4.5 - - + -
2562D LEU* 4.4 24.0 - - + -
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Residues in contact with ASP2508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2504D VAL 2.9 17.7 + - - +
2505D LEU* 3.9 7.2 - - + +
2507D LEU* 1.3 78.5 - - - +
2509D ARG* 1.3 62.6 + - + +
2512D GLY* 3.4 25.8 - - - -
2562D LEU* 4.1 24.0 - - + -
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Residues in contact with ARG2509 (chain D).
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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2341D PHE* 4.3 21.4 - - - -
2344D GLY 5.1 2.8 + - - -
2346D SER* 3.8 10.0 + - - -
2435D GLY* 2.7 30.9 + - - +
2436D ARG* 2.8 29.9 + - - +
2438D ALA* 3.0 24.7 + - + +
2440D GLU* 3.5 37.9 - - + +
2455D ARG* 5.4 3.6 + - - -
2505D LEU* 2.9 29.1 + - + +
2506D PHE* 3.1 3.8 + - - +
2508D ASP* 1.3 82.9 - - + +
2510D VAL* 1.3 64.3 + - + +
2511D TYR 3.8 0.7 + - - -
2512D GLY 5.0 1.0 + - - -
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Residues in contact with VAL2510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2435D GLY* 3.9 8.3 - - - -
2438D ALA* 3.7 17.9 - - + -
2455D ARG* 3.6 24.9 + - - +
2458D LEU* 3.6 31.4 - - + +
2459D ARG* 5.7 3.6 - - + +
2506D PHE* 2.9 61.7 + - + +
2507D LEU* 4.7 0.2 - - - -
2509D ARG* 1.3 77.1 - - - +
2511D TYR* 1.3 84.5 + - + +
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Residues in contact with TYR2511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2459D ARG* 3.1 40.1 + - + +
2462D VAL 3.9 17.3 - - - -
2463D PRO* 3.8 8.6 - - - +
2464D LEU* 3.6 53.1 + - + -
2506D PHE* 5.1 3.8 - + - -
2507D LEU* 3.4 7.9 + - + +
2509D ARG 5.1 0.2 - - - -
2510D VAL* 1.3 107.7 - - + +
2512D GLY* 1.3 68.1 + - - +
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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