Contacts of the strand formed by residues 1097 - 1102 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261I SER* 2.8 40.2 + - - -
263I VAL* 4.0 14.1 - - + -
267I ASN* 3.2 28.5 - - - -
268I ARG* 3.4 23.7 - - + +
1068J TYR* 3.3 17.3 - + - -
1075J GLU* 4.1 14.1 - - - -
1089J ARG 3.4 6.1 - - - +
1090J GLU* 4.8 2.6 - - - +
1094J GLU* 3.1 27.6 + - + +
1095J ILE 3.3 0.6 - - - -
1096J GLU* 1.4 92.2 - - + +
1098J TRP* 1.3 68.4 + - - +
1108J TYR* 4.0 31.2 - - + -
1109J VAL 3.6 17.9 - - - -
1110J PRO* 3.7 30.1 - - + -
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Residues in contact with TRP1098 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019J PHE* 4.2 4.5 - + - -
1054J MET* 3.2 57.4 - - + -
1055J GLY* 4.4 2.7 - - - -
1062J ILE* 4.6 1.8 - - + -
1086J ILE* 3.8 33.2 - - + -
1088J HIS 3.6 8.1 - - - +
1089J ARG* 3.1 60.8 + - + +
1090J GLU* 6.2 0.2 - - - -
1091J ASP* 5.1 1.6 + - - -
1095J ILE 3.3 18.9 + - - -
1097J TRP* 1.3 77.8 - - - +
1099J TRP* 1.3 61.0 + - - +
1100J ALA 3.5 1.8 + - - -
1108J TYR* 3.3 6.0 - - - -
1109J VAL* 2.8 37.5 + - + +
1111J ARG* 3.6 28.9 - - + +
1114J LEU* 3.8 15.9 - - + -
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Residues in contact with TRP1099 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1074J ASP* 3.8 14.4 - - + -
1086J ILE* 3.8 2.6 - - - +
1087J ILE* 2.9 49.7 + - + -
1088J HIS* 2.9 35.3 + + + +
1090J GLU* 4.4 4.7 - - - +
1098J TRP* 1.3 68.9 - - - +
1100J ALA* 1.3 58.7 + - - +
1106J GLU* 3.1 42.9 + - + +
1107J GLY* 3.7 24.7 - - - -
1108J TYR* 3.5 53.8 - + + -
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Residues in contact with ALA1100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076J LEU* 3.5 11.7 - - + +
1084J MET* 4.0 10.8 - - + -
1085J THR 3.4 7.6 - - - +
1086J ILE* 3.7 13.2 - - + -
1087J ILE* 4.3 4.0 - - - -
1098J TRP 3.5 0.8 + - - -
1099J TRP* 1.3 75.0 - - - +
1101J ARG* 1.3 60.8 + - - +
1106J GLU* 3.2 5.4 - - - +
1107J GLY 2.8 38.9 + - - +
1109J VAL* 3.7 27.1 - - + -
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Residues in contact with ARG1101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084J MET* 3.1 5.7 - - - +
1085J THR* 2.8 36.6 + - - +
1087J ILE* 3.8 21.8 - - + -
1100J ALA* 1.3 72.5 - - - +
1102J LEU* 1.3 61.6 + - - +
1103J ASN 3.8 19.8 + - - +
1104J ASP* 3.2 29.4 + - - +
1105J LYS 3.5 10.3 - - - +
1106J GLU* 3.4 28.7 + - + +
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Residues in contact with LEU1102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076J LEU* 3.8 21.9 - - + +
1077J PRO 3.5 21.5 - - - +
1078J MET* 4.9 1.1 - - - -
1082J ASP* 3.3 40.6 - - + +
1083J CYS 3.3 24.7 - - - +
1084J MET* 4.0 11.2 - - + +
1101J ARG* 1.3 72.4 - - - +
1103J ASN* 1.4 73.4 + - + +
1104J ASP 3.2 3.3 + - - -
1105J LYS* 3.0 22.9 + - - +
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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