Contacts of the strand formed by residues 1115 - 1117 (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 LEU1115 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1089D THR* 4.4 7.4 - - + -
1090D CYS 3.0 17.5 + - - +
1091D ALA* 3.2 12.5 - - + -
1092D PHE 2.7 29.5 + - - -
1113D ASN 3.3 6.7 + - - +
1114D LEU* 1.3 75.5 - - - +
1116D CYS* 1.3 54.2 + - - +
1132D LEU* 4.7 4.0 - - + -
1138D VAL* 4.2 16.2 - - + -
2010D LEU* 3.8 29.2 - - + -
2014D LEU* 3.7 35.2 - - + -
2026D ILE* 4.1 18.6 - - + -
2027D MET 3.8 7.9 - - - +
2028D ARG* 4.5 15.9 - - - +
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Residues in contact with CYS1116 (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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1092D PHE* 3.3 11.9 - - - +
1094D ASP* 4.8 3.1 - - - -
1099D LEU* 4.2 13.7 - - - -
1114D LEU* 4.2 2.5 - - + -
1115D LEU* 1.3 77.1 - - - +
1117D SER* 1.3 70.0 + - - +
2026D ILE* 3.7 3.9 - - - +
2027D MET* 2.7 48.1 + - + +
2029D LEU* 3.9 30.1 - - + +
2032D ASP* 5.3 1.4 - - - +
2035D MET* 3.5 29.7 - - + +
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Residues in contact with SER1117 (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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1092D PHE 2.9 6.5 + - - +
1093D ILE* 3.6 21.3 - - - -
1094D ASP* 2.8 27.0 + - - +
1116D CYS* 1.3 78.1 - - - +
1118D GLN* 1.3 64.4 + - - +
1119D PRO* 3.5 10.5 - - - +
1128D ILE* 3.5 18.3 - - - +
2025D SER 2.6 25.0 + - - -
2026D ILE* 4.2 12.5 - - - +
2035D MET* 5.8 0.2 - - - -
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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