Contacts of the helix formed by residues 2502 - 2510 (chain B) in PDB entry 1CVU
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 GLU2502 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2163B MET* 3.4 25.5 - - + +
2171B LEU* 4.0 6.3 - - + +
2452B ILE* 4.0 11.5 - - - +
2455B SER* 5.4 3.7 - - - -
2456B ARG* 2.6 54.3 + - - +
2461B GLN 5.6 0.2 - - - -
2463B LEU* 3.9 2.0 - - - +
2495B TYR* 2.6 29.9 + - + +
2501B MET* 1.3 79.7 - - - +
2503B LEU* 1.3 62.0 + - - +
2504B TYR 3.6 0.2 - - - -
2505B PRO* 3.4 16.4 - - + +
2506B ALA* 3.0 28.8 + - - +
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Residues in contact with LEU2503 (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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2380B GLU* 4.7 9.9 - - + +
2383B THR* 4.8 7.6 - - + -
2384B LEU* 5.8 1.8 - - + +
2460B TYR* 4.3 22.0 - - + -
2461B GLN 4.9 3.9 + - - +
2462B SER 4.7 0.2 - - - -
2463B LEU* 3.9 24.3 - - + +
2466B TYR* 4.0 44.0 - - + -
2502B GLU* 1.3 72.7 - - - +
2504B TYR* 1.3 64.5 + - - +
2506B ALA* 3.3 3.2 + - - +
2507B LEU* 2.9 40.7 + - + +
2521B THR* 4.2 25.1 - - + -
2525B LEU* 4.3 10.8 - - + -
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Residues in contact with TYR2504 (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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2182B LEU* 4.3 12.1 - - + -
2383B THR* 3.8 29.8 - - + +
2384B LEU* 5.4 1.3 - - - -
2386B HIS* 3.6 33.9 + - + +
2388B HIS* 4.2 5.0 - - - +
2440B VAL* 5.1 0.3 - - - +
2448B ALA* 3.5 24.5 - - - +
2451B SER* 3.3 33.5 + - - +
2452B ILE* 3.8 17.7 - - + +
2455B SER* 4.4 10.7 - - - +
2502B GLU* 4.7 0.2 - - - +
2503B LEU* 1.3 76.9 - - - +
2505B PRO* 1.3 75.1 - - + +
2507B LEU* 3.1 22.2 + - + +
2508B LEU* 3.4 35.8 + - + +
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Residues in contact with PRO2505 (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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2177B VAL* 4.1 17.0 - - + -
2181B VAL* 6.0 0.2 - - + -
2182B LEU* 4.1 18.1 - - + +
2452B ILE* 4.5 20.6 - - + -
2491B LEU* 5.7 0.4 - - + -
2495B TYR* 4.1 9.6 - - - +
2501B MET* 4.0 13.7 - - + -
2502B GLU* 3.4 33.2 - - + +
2504B TYR* 1.3 101.0 - - + +
2506B ALA* 1.3 61.4 + - - +
2508B LEU* 3.0 14.0 + - - +
2509B VAL* 3.1 15.2 + - - +
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Residues in contact with ALA2506 (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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2463B LEU* 3.7 33.7 - - + -
2481B LEU* 4.1 10.3 - - + +
2501B MET* 3.5 15.1 - - + +
2502B GLU 3.0 19.7 + - - +
2503B LEU 3.4 4.5 - - - +
2505B PRO* 1.3 81.6 - - - +
2507B LEU* 1.3 57.3 + - - +
2509B VAL* 4.6 1.3 - - - +
2510B GLU* 2.8 36.7 + - - +
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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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2384B LEU* 3.6 37.2 - - + +
2435B ALA* 3.8 15.8 + - - +
2503B LEU* 2.9 36.0 + - + +
2504B TYR* 3.1 14.8 + - + +
2506B ALA* 1.3 78.8 - - + +
2508B LEU* 1.3 65.4 + - + +
2509B VAL 3.3 0.6 + - - -
2510B GLU* 3.9 11.7 + - - +
2519B GLY 5.5 0.3 + - - -
2521B THR* 3.6 20.9 - - + +
2522B MET* 3.5 56.7 - - + +
2525B LEU* 5.6 1.3 - - + -
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Residues in contact with LEU2508 (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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2182B LEU* 4.0 14.3 - - + +
2384B LEU 6.0 0.2 - - - +
2386B HIS 4.3 10.1 - - - +
2389B PRO* 3.9 9.4 - - + -
2434B VAL* 3.4 44.0 - - + +
2435B ALA* 4.3 0.9 - - - -
2437B GLY* 2.8 26.9 + - - -
2438B ARG 4.6 0.3 + - - -
2440B VAL* 3.5 29.8 - - + -
2504B TYR* 3.4 42.6 + - + +
2505B PRO 3.0 8.7 + - - +
2507B LEU* 1.3 82.6 - - + +
2509B VAL* 1.3 60.1 + - - +
2510B GLU 3.7 0.2 - - - -
2522B MET* 4.9 3.4 - - + -
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Residues in contact with VAL2509 (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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2181B VAL* 3.6 44.2 - - + +
2182B LEU* 4.6 1.8 - - + -
2436B GLY 4.1 9.5 - - - +
2437B GLY* 3.9 4.9 - - - -
2481B LEU* 4.1 11.9 - - + -
2482B THR* 3.5 35.9 - - + +
2487B MET* 3.9 15.7 - - - +
2491B LEU* 3.8 13.9 - - + -
2501B MET* 5.0 0.9 - - + -
2505B PRO 3.1 13.9 + - - +
2506B ALA* 4.1 3.4 - - - +
2508B LEU* 1.3 77.1 - - - +
2510B GLU* 1.3 71.0 + - - +
2511B LYS 3.5 1.2 + - - -
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Residues in contact with GLU2510 (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 ALA* 3.5 2.8 - - + +
2436B GLY 3.1 18.7 + - - -
2463B LEU* 6.3 0.2 - - - -
2475B TYR* 2.6 30.6 + - - +
2481B LEU* 3.5 18.4 - - + +
2506B ALA 2.8 16.9 + - - +
2507B LEU* 4.1 12.2 - - - +
2508B LEU 3.7 1.2 - - - -
2509B VAL* 1.3 77.2 - - - +
2511B LYS* 1.3 74.2 + - + +
2512B PRO* 3.0 5.0 - - - +
2519B GLY* 3.3 22.2 + - - +
2520B GLU* 3.8 9.4 + - - +
2521B THR* 2.8 39.4 + - - -
2522B MET* 4.0 2.4 + - - +
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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