Contacts of the strand formed by residues 2061 - 2065 (chain D) 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 ILE2061 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2060D ARG* 1.3 74.4 - - - +
2062D VAL* 1.3 65.6 + - - +
2175D MET* 4.1 12.8 - - - +
2178D LEU* 4.9 3.4 - - + -
2179D ALA* 4.4 20.9 - - + +
2182D LEU* 3.7 29.2 - - + -
2189D LEU* 3.4 7.9 - - + +
2191D PHE* 3.7 17.7 - - + -
2215D LEU* 3.7 28.9 - - + -
2218D TYR* 4.1 31.8 + - + +
2219D ALA* 3.3 4.0 - - - -
2220D SER* 2.7 34.4 + - - -
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Residues in contact with VAL2062 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2056D LEU* 3.9 26.9 - - + -
2057D PRO* 4.0 11.0 - - + -
2061D ILE* 1.3 83.9 - - - +
2063D GLU* 1.3 65.0 + - - +
2064D ILE* 4.3 6.5 - - + -
2188D LEU* 3.8 19.5 - - + -
2189D LEU 2.9 11.1 + - - +
2190D ILE* 3.4 18.9 - - + +
2191D PHE* 2.7 35.0 + - - +
2219D ALA* 4.6 0.4 - - - -
2221D VAL* 3.4 29.8 - - + +
2223D LEU* 4.6 1.1 - - + -
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Residues in contact with GLU2063 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2062D VAL* 1.3 75.4 - - - +
2064D ILE* 1.3 67.5 + - - +
2065D TYR* 4.3 5.5 - - + -
2191D PHE 3.3 9.0 - - - +
2193D ASN* 3.1 31.7 - - + +
2209D THR* 3.2 15.2 + - - +
2215D LEU* 3.4 35.5 - - + +
2216D LYS 4.6 0.3 + - - -
2219D ALA* 4.3 2.2 - - + +
2221D VAL 3.0 7.9 + - - +
2222D ARG* 2.5 46.9 + - - +
2223D LEU* 2.7 31.9 + - - +
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Residues in contact with ILE2064 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2056D LEU* 5.6 1.3 - - + -
2062D VAL* 4.6 2.7 - - + -
2063D GLU* 1.3 77.5 - - - +
2065D TYR* 1.3 62.1 + - - +
2072D LYS* 4.3 14.8 - - + +
2075D LEU* 3.7 29.2 - - + -
2076D THR* 4.1 11.2 - - - +
2190D ILE* 3.6 29.2 - - + -
2191D PHE 2.9 8.1 + - - +
2192D ILE* 3.4 10.3 - - + +
2193D ASN 2.8 26.1 + - - +
2223D LEU* 3.4 29.6 - - + +
2225D ILE* 3.8 27.4 - - + -
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Residues in contact with TYR2065 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2063D GLU* 4.3 7.6 - - + -
2064D ILE* 1.3 74.3 - - - +
2066D GLY* 1.3 63.4 + - - +
2072D LYS* 3.9 5.4 - - - -
2193D ASN* 3.3 20.6 - - + +
2194D GLN 4.8 2.2 - - - +
2195D ILE* 4.3 11.9 - - + -
2207D GLU* 5.4 1.8 - - - -
2209D THR* 3.9 20.4 - - - +
2222D ARG* 3.7 42.9 + - + -
2223D LEU 2.9 18.9 + - - +
2224D ASP* 3.5 30.1 + - + -
2225D ILE* 2.9 27.0 + - - +
2226D ARG* 4.6 5.2 - - - -
2247D VAL* 3.5 27.7 - - + +
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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