Contacts of the strand formed by residues 1097 - 1102 (chain B) in PDB entry 4A63
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 TRP1097 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A SER* 2.8 31.7 + - - -
263A VAL* 3.8 19.3 - - + -
267A ASN* 3.4 17.5 - - - -
268A ARG* 3.5 22.6 - - + +
1068B TYR* 3.4 27.8 - + - -
1075B GLU* 4.2 13.2 - - - -
1089B ARG 3.3 6.2 - - - +
1090B GLU* 4.7 3.6 - - - +
1094B GLU* 3.1 33.8 + - + +
1095B ILE 3.3 0.4 - - - -
1096B GLU* 1.4 103.4 - - + +
1098B TRP* 1.4 66.6 + - - +
1108B TYR* 4.0 28.8 - - + -
1109B VAL* 3.5 27.4 - - - -
1110B PRO* 3.6 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1098 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019B PHE* 4.1 11.9 - + - -
1054B MET* 3.4 52.9 - - + -
1055B GLY* 4.3 3.4 - - - -
1086B ILE* 3.8 26.7 - - + -
1088B HIS 3.4 7.4 - - - +
1089B ARG* 3.2 61.3 + - + +
1091B ASP* 5.2 1.4 + - - -
1095B ILE 3.4 18.2 + - - -
1097B TRP* 1.4 78.6 - - - +
1099B TRP* 1.3 61.9 + - - +
1100B ALA 3.5 1.9 + - - -
1108B TYR* 3.3 6.7 - - - -
1109B VAL* 3.0 35.7 + - + +
1111B ARG* 3.6 27.8 - - + +
1114B LEU* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1099 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074B ASP* 3.8 13.7 - - + -
1086B ILE* 3.7 2.9 - - - +
1087B ILE* 2.8 54.0 + - + -
1088B HIS* 2.7 33.6 + - + +
1090B GLU* 4.7 4.2 - - - +
1098B TRP* 1.3 68.4 - - - +
1100B ALA* 1.3 54.7 + - - +
1106B GLU* 3.2 48.5 + - + +
1107B GLY* 3.5 24.9 - - - -
1108B TYR* 3.5 51.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076B LEU* 3.7 10.0 - - + +
1084B MET* 4.2 11.2 - - + -
1085B THR 3.4 8.1 - - - +
1086B ILE* 3.7 22.0 - - + -
1087B ILE* 4.1 4.3 - - - -
1099B TRP* 1.3 75.1 + - - +
1101B ARG* 1.3 61.7 + - - +
1106B GLU* 3.2 8.5 - - - +
1107B GLY 2.8 32.2 + - - +
1109B VAL* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084B MET* 3.1 5.5 - - - +
1085B THR* 2.8 36.0 + - - +
1087B ILE* 3.8 22.9 - - + -
1100B ALA* 1.3 73.4 - - - +
1102B LEU* 1.3 60.5 + - - +
1103B ASN 4.2 5.1 + - - +
1104B ASP 5.9 0.4 - - - +
1105B LYS 3.5 6.7 - - - +
1106B GLU* 3.9 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076B LEU* 3.8 19.7 - - + +
1077B PRO* 3.4 22.2 - - + +
1078B MET* 4.9 1.1 - - - -
1082B ASP* 3.4 39.3 - - + +
1083B CYS 3.3 23.1 - - - +
1084B MET* 3.9 15.0 - - + +
1101B ARG* 1.3 72.7 - - - +
1103B ASN* 1.4 73.3 + - + +
1104B ASP 3.2 3.5 + - - -
1105B LYS* 3.0 23.4 + - - +
----------------------------------------------------------
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