Contacts of the strand formed by residues 2090 - 2093 (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 CYS2090 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2080D ILE* 3.8 26.7 - - + -
2083D ALA* 3.9 15.7 - - - -
2084D GLN* 4.0 15.2 - - - +
2088D LYS 3.9 2.9 + - - -
2089D THR* 1.3 80.8 - - - +
2091D ALA* 1.3 60.5 + - - +
2113D ASN 4.2 3.8 + - - +
2114D LEU* 3.4 19.5 - - + +
2115D LEU* 3.0 27.8 + - - +
2138D VAL* 4.1 2.5 - - - -
2140D VAL* 3.1 32.5 - - - +
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Residues in contact with ALA2091 (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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2080D ILE* 4.7 0.9 - - - +
2090D CYS* 1.3 75.6 - - - +
2092D PHE* 1.3 60.0 + - - +
2093D ILE* 4.2 4.3 - - + -
2114D LEU* 4.2 2.2 - - - -
2115D LEU* 3.2 19.1 - - + +
2132D LEU* 3.7 29.8 - - + -
2138D VAL* 3.9 10.9 - - + +
2140D VAL 2.9 6.6 + - - +
2141D ILE* 3.3 9.3 - - + -
2142D VAL* 3.0 28.4 + - - +
3026D ILE* 5.4 1.1 - - + -
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Residues in contact with PHE2092 (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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2073D THR* 4.1 9.0 - - + -
2076D THR* 3.5 26.0 - - + -
2077D LEU* 4.0 13.5 - - + -
2080D ILE* 3.9 15.3 - - + -
2091D ALA* 1.3 73.7 - - - +
2093D ILE* 1.3 65.0 + - - +
2094D ASP* 3.6 33.5 + - + -
2099D LEU* 3.6 25.8 - - + -
2114D LEU* 3.8 23.1 - - + -
2115D LEU 2.7 8.3 + - - +
2116D CYS* 3.3 3.7 - - - -
2117D SER 3.0 24.3 + - - +
2142D VAL* 3.6 15.0 - - + -
2144D ASP* 3.5 32.3 - - + -
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Residues in contact with ILE2093 (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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2091D ALA* 4.9 1.6 - - + -
2092D PHE* 1.3 79.7 - - - +
2094D ASP* 1.3 59.5 + - - +
2095D ALA* 3.1 6.1 + - + +
2116D CYS* 6.1 0.2 - - - -
2117D SER* 3.6 13.2 - - - +
2119D PRO* 3.8 29.4 - - + -
2125D ALA* 4.0 17.7 - - + -
2128D ILE* 3.9 27.4 - - + -
2129D CYS* 4.1 5.8 - - - -
2132D LEU* 4.7 7.0 - - + -
2141D ILE* 4.0 21.5 - - + -
2142D VAL 2.7 18.7 + - - +
2143D VAL* 3.6 19.0 - - + +
2144D ASP* 2.9 27.7 + - - +
3026D ILE* 5.4 1.1 - - + -
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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