Contacts of the strand formed by residues 1055 - 1057 (chain C) in PDB entry 1AWV
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 ARG1055 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053C PHE 3.2 1.0 - - - -
1054C HIS* 1.3 97.3 - - + +
1056C ILE* 1.3 57.7 + - - +
1057C ILE* 3.5 26.3 - - - +
1060C PHE* 4.7 0.6 - - - -
1061C MET* 3.8 15.5 - - + +
1062C CYS* 3.7 0.5 - - - -
1063C GLN* 2.7 65.4 + - + +
1149C ASN 4.3 7.7 + - - +
1150C GLY* 4.0 17.5 - - - -
101I HIS* 6.2 3.1 - - - -
102I VAL 5.3 2.5 - - - -
103I GLY* 4.1 6.8 - - - -
104I PRO* 2.7 30.7 + - - +
105I ILE* 4.3 14.1 - - - +
106I ALA* 5.4 0.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1056 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053C PHE* 3.9 21.8 - - + -
1055C ARG* 1.3 76.8 - - - +
1057C ILE* 1.3 62.2 + - - +
1061C MET 3.6 3.6 - - - +
1062C CYS* 3.8 21.3 - - + -
1142C MET* 3.8 13.7 - - + +
1143C GLU* 3.6 35.7 - - + +
1145C PHE* 5.3 0.2 - - + -
1146C GLY* 3.1 19.0 - - - +
1147C SER 3.3 2.8 + - - -
1150C GLY 2.6 26.0 + - - +
1152C THR* 3.7 18.7 - - + +
1156C ILE* 3.8 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1057 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055C ARG* 3.5 35.9 - - + +
1056C ILE* 1.3 72.7 - - - +
1058C PRO* 1.3 65.0 - - - +
1059C GLY 3.3 0.2 + - - -
1060C PHE* 2.8 44.5 + - + -
1061C MET* 2.9 31.3 + - + +
1143C GLU* 4.1 0.9 - - - +
1147C SER 3.7 3.8 - - - +
1148C ARG* 3.5 27.6 - - - +
1149C ASN* 4.2 2.5 - - - -
1150C GLY* 3.3 26.0 - - - +
106I ALA* 4.7 8.5 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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