Contacts of the strand formed by residues 1097 - 1100 (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 ILE1097 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025E PHE* 5.5 2.7 - - + -
1091E LYS 4.2 5.4 - - - +
1092E HIS* 4.2 7.6 - - + -
1093E THR* 3.8 22.0 - - - +
1094E GLY 2.9 35.0 + - - +
1095E PRO 3.4 1.3 + - - +
1096E GLY* 1.3 75.3 - - - +
1098E LEU* 1.3 66.2 + - - +
1099E SER* 4.5 0.2 - - - -
1113E PHE 3.5 1.6 - - - +
1114E ILE* 3.3 4.3 - - - -
1115E CYS* 2.9 45.5 + - - -
1128E VAL* 3.6 34.3 - - + -
1130E GLY 3.7 8.1 - - - +
1131E LYS* 4.4 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1098 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022E PHE* 4.3 18.4 - - + -
1024E LEU* 3.7 21.3 - - + -
1036E PHE* 3.7 21.1 - - + -
1096E GLY 3.4 2.2 + - - +
1097E ILE* 1.3 72.5 - - - +
1099E SER* 1.3 60.4 + - - +
1112E PHE* 3.6 33.0 - - + -
1113E PHE 3.5 5.8 - - - +
1114E ILE* 4.3 9.4 - - + +
1128E VAL* 3.6 3.6 - - - +
1129E PHE* 3.1 54.7 + - + -
1130E GLY* 2.6 25.5 + - - +
1131E LYS* 4.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1099 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092E HIS* 3.1 34.2 + - - -
1097E ILE* 4.0 2.7 - - - -
1098E LEU* 1.3 75.9 - - - +
1100E MET* 1.3 62.3 + - - +
1112E PHE* 3.3 5.2 - - - +
1113E PHE* 2.9 48.1 + - - -
1126E HIS* 3.4 12.0 - - - +
1127E VAL 3.1 16.4 + - - -
1128E VAL* 4.1 4.5 - - - -
1129E PHE* 3.4 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1100 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032E THR* 3.8 17.0 - - + +
1035E ASN* 4.2 11.9 - - - +
1036E PHE* 5.4 3.6 - - - -
1048E TYR* 5.6 0.9 - - - -
1083E PHE* 4.3 1.6 - - + -
1099E SER* 1.3 76.2 + - - +
1101E ALA* 1.3 54.4 + - - +
1102E ASN* 4.2 1.0 + - - -
1108E ASN* 3.2 44.4 - - + +
1109E GLY 3.8 26.2 - - - +
1110E SER* 4.3 3.8 - - - +
1111E GLN 3.6 18.4 - - - +
1112E PHE* 4.6 2.9 - - - -
1113E PHE* 3.6 1.5 - - - -
1126E HIS* 2.6 35.9 + - - +
1127E VAL* 2.9 14.9 + - + +
1129E PHE* 3.5 31.4 - - + -
----------------------------------------------------------
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