Contacts of the strand formed by residues 2195 - 2197 (chain A) in PDB entry 3CMT
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 ILE2195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2065A TYR* 4.3 11.0 - - + -
2066A GLY* 3.6 34.7 + - - +
2067A PRO* 3.7 7.6 - - + -
2194A GLN* 1.3 76.0 - - - +
2196A ARG* 1.3 93.4 + - - +
2197A MET* 4.9 6.9 - - + +
2207A GLU* 3.8 27.8 - - + +
2208A THR 3.2 10.5 - - - +
2226A ARG* 3.2 31.4 - - - +
3213A ASN* 4.4 5.4 - - - +
3217A PHE* 3.6 19.5 - - + -
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Residues in contact with ARG2196 (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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2147A ALA* 4.5 5.3 + - - +
2194A GLN* 2.8 42.6 + - - +
2195A ILE* 1.3 95.9 + - - +
2197A MET* 1.3 64.1 + - - +
2207A GLU* 3.5 0.9 - - - -
2208A THR* 2.8 39.3 + - - +
2209A THR 5.3 1.3 - - - +
2210A THR* 4.6 17.5 + - + +
3172A SER* 3.3 25.5 + - - -
3213A ASN* 4.5 4.7 - - - +
3214A ALA* 3.7 23.3 - - - +
3217A PHE* 3.9 7.1 - - - -
3218A TYR* 4.1 8.1 + - - -
1008B C 6.4 0.2 - - + -
1009B C 3.9 28.8 + - + +
1010B T 3.3 21.3 - - - +
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Residues in contact with MET2197 (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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2195A ILE* 4.9 6.3 - - + +
2196A ARG* 1.3 77.2 - - - +
2198A LYS* 1.3 61.4 + - - +
2199A ILE* 4.6 0.3 - - - +
2206A PRO* 3.5 16.4 - - + +
2207A GLU* 4.1 27.1 - - + +
2208A THR* 4.3 1.6 - - - -
3213A ASN* 3.6 24.2 - - - +
1009B C 3.7 19.8 - - - +
1010B T 2.7 61.8 + - + +
1011B T 5.9 2.2 - - + -
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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