Contacts of the strand formed by residues 1112 - 1115 (chain E) 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 PHE1112 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008E PHE* 3.5 28.9 - + - -
1036E PHE* 3.7 17.7 - + + -
1048E TYR* 3.9 15.9 - + - -
1053E PHE* 3.8 31.2 - + - -
1063E GLN* 3.4 4.7 - - - +
1064E GLY 3.0 34.5 + - - +
1065E GLY* 3.5 21.1 - - - -
1098E LEU* 3.6 22.2 - - + -
1099E SER 3.3 15.7 - - - +
1100E MET* 4.6 1.6 - - - -
1101E ALA* 3.7 5.4 - - - +
1110E SER 3.5 14.6 - - - +
1111E GLN* 1.3 76.6 - - - +
1113E PHE* 1.3 68.6 + - - +
1114E ILE* 4.3 8.1 - - + -
1129E PHE* 4.5 4.9 - - + -
1158E ILE* 4.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060E PHE* 5.4 0.2 - + - -
1061E MET* 3.7 36.1 - - + -
1062E CYS 3.2 11.2 - - - +
1063E GLN* 4.1 4.3 - - + -
1092E HIS* 3.9 3.6 - + - -
1097E ILE 3.5 2.3 - - - +
1098E LEU* 3.5 4.5 - - - +
1099E SER* 2.9 56.9 + - - +
1100E MET 3.6 20.4 - - - -
1101E ALA* 4.0 6.5 - - - -
1112E PHE* 1.3 79.5 - - - +
1114E ILE* 1.3 62.2 + - - +
1115E CYS* 3.7 20.2 - - - -
1122E LEU* 3.6 33.2 - - + -
1126E HIS* 3.9 10.1 - + - -
104K PRO* 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008E PHE* 5.1 0.4 - - + -
1020E VAL* 5.5 1.1 - - + -
1022E PHE* 3.7 32.1 - - + -
1053E PHE* 4.1 24.2 - - + -
1061E MET* 3.3 4.8 - - - +
1062E CYS* 2.9 34.0 + - + +
1096E GLY* 4.1 7.0 - - - +
1097E ILE 3.3 3.1 - - - -
1098E LEU* 4.3 4.3 - - + -
1112E PHE* 4.3 11.4 - - + -
1113E PHE* 1.3 75.7 - - - +
1115E CYS* 1.3 70.4 + - - +
1116E THR* 4.1 3.1 - - - +
1132E VAL* 3.9 23.8 - - + -
1139E VAL* 4.1 27.1 - - + -
1142E MET* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060E PHE 3.7 7.2 - - - +
1061E MET* 4.1 1.3 - - - -
1092E HIS* 4.1 8.1 - - - -
1094E GLY 3.7 11.0 - - - +
1096E GLY* 2.7 28.3 + - - -
1097E ILE* 2.9 29.0 + - - +
1099E SER* 5.3 0.2 - - - -
1113E PHE* 3.7 23.1 - - - -
1114E ILE* 1.3 73.1 - - - +
1116E THR* 1.3 60.3 + - - +
1117E ALA 3.4 17.3 - - - +
1119E THR* 3.5 25.6 - - - -
1136E MET* 3.8 3.3 - - - +
----------------------------------------------------------
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