Contacts of the helix formed by residues 2468 - 2476 (chain B) in PDB entry 1V9P
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 ASP2468 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2429B LEU* 3.9 15.6 - - + +
2437B ALA* 6.0 2.7 - - - -
2438B ILE* 3.6 11.2 - - - -
2466B VAL* 3.4 7.5 - - - +
2467B ARG* 1.3 95.9 + - - +
2469B VAL* 1.3 67.3 + - - +
2470B ALA* 3.6 9.2 + - - +
2471B ASP* 3.0 23.7 + - - +
2472B LEU* 3.9 0.5 + - - +
2570B LEU* 3.4 18.2 - - + +
2573B ARG* 2.8 44.2 + - - -
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Residues in contact with VAL2469 (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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2437B ALA* 4.2 13.6 - - + +
2438B ILE* 3.9 11.2 - - + +
2441B TYR* 3.3 49.8 - - + -
2468B ASP* 1.3 73.0 - - - +
2470B ALA* 1.3 64.9 + - - +
2472B LEU* 2.9 27.7 + - + +
2473B TYR* 3.6 6.3 - - - -
2512B ALA 5.5 0.7 - - - +
2513B LEU* 4.6 4.7 - - + -
2570B LEU* 3.6 29.8 - - + -
2574B LEU* 3.6 20.0 - - + -
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Residues in contact with ALA2470 (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 ASP* 3.3 12.1 + - - +
2469B VAL* 1.3 80.5 - - - +
2471B ASP* 1.3 62.2 + - - +
2472B LEU 3.0 1.1 + - - -
2473B TYR* 3.2 18.8 + - - +
2474B HIS* 3.8 16.6 + - + +
2570B LEU* 4.4 3.8 - - + -
2573B ARG* 3.7 33.4 - - + +
2574B LEU* 3.3 26.5 - - + +
2577B ALA* 4.8 2.1 - - + +
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Residues in contact with ASP2471 (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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2465B LEU 4.2 6.3 - - - +
2466B VAL* 3.7 12.6 - - + -
2467B ARG* 3.1 53.7 + - - +
2468B ASP* 3.0 24.6 + - - +
2470B ALA* 1.3 78.2 - - - +
2472B LEU* 1.3 60.7 + - - +
2473B TYR 3.2 0.8 + - - -
2474B HIS* 3.5 24.9 + - - +
2475B LEU* 3.6 17.2 + - - +
2573B ARG* 4.5 7.0 + - - -
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Residues in contact with LEU2472 (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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2438B ILE* 3.8 20.0 - - + +
2441B TYR* 4.1 21.8 - - + -
2442B ALA* 5.6 0.4 - - + -
2449B ILE* 4.5 9.9 - - + -
2452B LEU* 3.6 37.0 - - + -
2460B LEU* 4.8 2.5 - - + -
2466B VAL* 3.9 21.1 - - + -
2468B ASP 4.5 2.2 - - - +
2469B VAL* 2.9 21.0 + - - +
2471B ASP* 1.3 79.5 - - - +
2473B TYR* 1.3 63.6 + - + +
2474B HIS 3.4 0.2 - - - -
2475B LEU* 3.1 32.5 - - + +
2498B ILE* 3.6 23.3 - - + +
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Residues in contact with TYR2473 (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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2441B TYR* 2.8 38.5 + + - -
2447B MET* 4.9 0.2 - - - +
2449B ILE* 4.4 3.0 - - + +
2469B VAL 3.6 21.1 - - - -
2470B ALA* 3.2 10.0 + - - +
2472B LEU* 1.3 84.8 - - + +
2474B HIS* 1.3 57.2 + - - +
2475B LEU 3.0 5.6 + - - -
2476B ARG* 3.3 26.4 + - - +
2498B ILE* 3.3 28.9 - - + -
2501B SER* 3.2 18.4 + - - -
2502B LYS* 3.6 30.7 + - + +
2574B LEU* 4.7 0.9 - - + -
2577B ALA* 3.8 25.4 - - + +
2579B VAL* 3.5 27.4 - - + +
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Residues in contact with HIS2474 (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 ALA* 3.9 16.3 + - + -
2471B ASP* 3.5 23.1 + - - +
2472B LEU 3.4 0.2 - - - -
2473B TYR* 1.3 76.1 - - - +
2475B LEU* 1.3 55.7 + - - +
2476B ARG* 2.8 48.4 + - - +
2477B LYS* 4.4 5.2 + - - +
2480B LEU* 5.1 4.7 - - - +
2573B ARG* 5.2 15.2 + - - +
2576B GLU* 5.6 6.4 + - + +
2577B ALA* 4.5 21.1 - - + +
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Residues in contact with LEU2475 (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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2452B LEU* 5.6 0.9 - - + -
2460B LEU* 4.7 8.5 - - + -
2465B LEU* 3.7 38.1 - - + +
2466B VAL* 4.2 4.5 - - + -
2471B ASP 3.6 7.2 + - - +
2472B LEU* 3.1 38.1 - - + +
2473B TYR 3.0 0.4 - - - -
2474B HIS* 1.3 76.9 - - - +
2476B ARG* 1.3 65.5 + - - +
2477B LYS* 2.6 21.1 + - - +
2480B LEU* 4.4 15.3 - - + -
2481B LEU* 4.2 29.0 - - + +
2495B LEU* 4.2 8.3 - - + +
2498B ILE* 4.0 18.8 - - + -
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Residues in contact with ARG2476 (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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2473B TYR* 3.3 19.2 + - - +
2474B HIS* 2.8 39.6 + - - +
2475B LEU* 1.3 74.9 - - - +
2477B LYS* 1.3 65.5 + - + +
2478B GLU* 3.1 10.6 - - - +
2495B LEU* 3.1 25.3 - - - +
2502B LYS* 5.2 9.1 - - - +
2576B GLU 5.4 1.6 + - - -
2577B ALA* 5.0 11.3 + - - +
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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