Contacts of the helix formed by residues 2484 - 2488 (chain A) in PDB entry 2NQC
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 ASP2484 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2483A GLY* 1.3 70.7 - - - -
2485A PRO* 1.3 67.0 - - - +
2486A GLY* 2.8 18.4 + - - -
2487A LEU* 3.0 38.1 + - + +
2513A ALA* 2.8 30.0 + - - +
2557A TYR* 4.1 3.3 - - - -
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Residues in contact with PRO2485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2483A GLY 3.5 10.3 - - - +
2484A ASP* 1.3 86.8 - - - +
2486A GLY* 1.3 60.9 + - - +
2487A LEU 3.1 1.8 + - - -
2488A VAL* 3.2 18.2 + - + +
2557A TYR* 3.7 39.7 - - + +
2558A GLY 5.8 0.4 - - - +
2561A GLN* 3.8 42.6 - - + +
2562A HIS 4.4 8.7 - - - +
2563A ILE* 3.9 14.6 - - + +
2564A VAL 4.5 1.0 + - - -
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Residues in contact with GLY2486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2484A ASP* 2.8 11.8 + - - -
2485A PRO* 1.3 81.0 - - - +
2487A LEU* 1.3 66.0 + - - +
2488A VAL 3.4 2.8 + - - +
2561A GLN* 5.5 1.3 - - - +
2564A VAL* 4.6 20.4 - - - +
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Residues in contact with LEU2487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2484A ASP* 3.0 37.1 + - + +
2486A GLY* 1.3 82.3 - - - +
2488A VAL* 1.3 61.9 + - - +
2489A SER* 3.8 3.3 + - - -
2509A ASN* 4.1 5.0 - - - +
2512A ASN* 3.6 42.9 + - + +
2513A ALA* 3.8 9.9 + - - +
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Residues in contact with VAL2488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2484A ASP 3.9 0.4 - - - +
2485A PRO 3.2 17.7 + - - +
2486A GLY 4.8 2.3 - - - +
2487A LEU* 1.3 78.1 - - - +
2489A SER* 1.3 62.2 + - - +
2508A VAL* 3.6 30.5 - - + -
2509A ASN 3.5 7.2 - - - +
2510A THR* 4.2 6.7 - - + -
2513A ALA* 3.6 22.7 - - + -
2518A LEU* 4.9 2.2 - - + -
2557A TYR* 3.6 30.1 - - + -
2563A ILE* 3.7 30.7 - - + +
2564A VAL* 4.6 9.0 + - - +
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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