Contacts of the helix formed by residues 2173 - 2182 (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 ASP2173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2171B LEU 3.6 2.0 + - - -
2172B PRO* 1.3 72.7 - - - +
2174B SER* 1.3 65.6 + - - +
2175B LYS* 2.6 40.7 + - - +
2176B GLU* 3.2 27.5 + - + +
2177B VAL* 3.2 20.1 + - - +
2449B LYS* 5.2 1.2 - - - -
2456B ARG* 4.8 0.9 - - - +
2494B LEU* 5.1 0.6 - - - +
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Residues in contact with SER2174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2172B PRO 3.2 4.8 + - - -
2173B ASP* 1.3 73.2 + - - +
2175B LYS* 1.3 59.8 + - - +
2177B VAL* 3.8 7.5 - - - +
2178B LEU* 2.8 31.1 + - - +
2449B LYS* 3.1 26.4 + - - -
2452B ILE* 3.6 19.3 - - - +
2453B ASP* 2.7 28.5 + - - -
2456B ARG* 3.6 14.1 + - - +
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Residues in contact with LYS2175 (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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2173B ASP* 2.6 22.7 + - - +
2174B SER* 1.3 75.1 + - - +
2176B GLU* 1.3 58.0 + - + +
2178B LEU* 3.2 9.5 - - + +
2179B GLU* 2.9 66.3 + - + +
2449B LYS* 4.2 17.9 - - + +
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Residues in contact with GLU2176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2173B ASP* 3.2 30.8 + - + +
2175B LYS* 1.3 78.3 - - - +
2177B VAL* 1.3 60.1 + - - +
2179B GLU* 3.9 14.6 - - - +
2180B LYS* 2.9 68.4 + - - +
2494B LEU* 3.7 23.2 - - + +
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Residues in contact with VAL2177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2172B PRO* 4.1 12.3 - - + +
2173B ASP 3.2 17.9 + - - +
2174B SER* 3.8 6.7 - - - +
2176B GLU* 1.3 74.8 - - - +
2178B LEU* 1.3 66.9 + - - +
2181B VAL* 3.1 40.6 + - + +
2182B LEU* 3.6 3.6 + - + +
2452B ILE* 4.4 9.2 - - + -
2456B ARG* 4.6 1.6 - - - +
2491B LEU* 4.7 2.0 - - + -
2494B LEU* 4.1 18.8 - - + -
2495B TYR* 3.7 34.3 - - + +
2505B PRO* 4.1 19.3 - - + -
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Residues in contact with LEU2178 (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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2174B SER 2.8 19.1 + - - +
2175B LYS* 3.2 12.6 - - + +
2177B VAL* 1.3 76.3 - - - +
2179B GLU* 1.3 54.2 + - + +
2182B LEU* 2.8 48.0 + - + +
2183B LEU* 2.8 36.7 + - + -
2440B VAL* 5.1 0.4 - - + -
2445B GLN* 3.7 41.1 - - + +
2448B ALA* 4.1 19.7 - - + -
2449B LYS* 4.5 21.3 - - + +
2452B ILE* 4.5 1.7 - - + +
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Residues in contact with GLU2179 (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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2175B LYS* 2.9 51.3 + - + +
2176B GLU* 3.9 15.3 - - - +
2178B LEU* 1.3 76.4 - - + +
2180B LYS* 1.3 56.2 + - + +
2181B VAL 3.3 0.3 + - - -
2183B LEU* 3.9 25.2 - - + +
2185B ARG* 2.5 39.2 + - - +
2445B GLN* 5.3 2.4 - - - +
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Residues in contact with LYS2180 (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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2176B GLU* 2.9 56.7 + - - +
2177B VAL 4.3 0.9 - - - +
2179B GLU* 1.3 74.8 - - + +
2181B VAL* 1.3 67.8 + - + +
2185B ARG* 2.9 4.3 + - - +
2438B ARG* 2.9 30.7 + - - -
2490B GLU* 2.9 37.9 + - + +
2494B LEU* 4.5 15.1 - - + +
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Residues in contact with VAL2181 (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* 3.1 27.7 + - + +
2180B LYS* 1.3 84.0 - - + +
2182B LEU* 1.3 65.9 + - + +
2438B ARG* 2.7 29.8 + - - +
2487B MET* 3.5 42.6 - - + +
2490B GLU* 4.3 9.6 - - + -
2491B LEU* 3.9 25.1 - - + -
2494B LEU* 5.7 1.6 - - + -
2505B PRO* 6.0 0.4 - - + -
2509B VAL* 3.6 22.7 - - + +
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Residues in contact with LEU2182 (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* 3.9 11.9 - - + +
2178B LEU* 2.8 34.9 + - + +
2181B VAL* 1.3 86.9 - - + +
2183B LEU* 1.3 65.4 + - - +
2438B ARG* 3.6 1.8 - - - +
2439B ASN 3.0 7.1 + - - -
2440B VAL* 3.0 29.2 + - + +
2448B ALA* 4.8 4.5 - - + -
2452B ILE* 4.0 27.4 - - + -
2504B TYR* 4.3 18.2 - - + -
2505B PRO* 4.1 20.6 - - + +
2508B LEU* 4.0 29.6 - - + +
2509B VAL* 4.6 3.1 - - + -
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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