Contacts of the strand formed by residues 1102 - 1106 (chain A) in PDB entry 6ZGI
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 TRP1102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1076A THR* 4.0 7.6 - - - -
1077A THR 3.9 11.7 - - - -
1078A ALA* 3.7 35.7 - - + -
1081A ILE* 4.7 5.2 - - + -
1095A PHE* 4.2 9.0 - - + -
1096A VAL* 3.2 36.8 - - - -
1097A SER* 3.7 20.6 + - - -
1100A THR 4.9 4.4 - - - -
1101A HIS* 1.3 80.4 - - - +
1103A PHE* 1.3 71.3 + - - +
1113A GLN 4.7 0.3 - - - +
1114A ILE* 5.3 0.5 - - - -
1115A ILE* 4.2 16.6 + - + +
1133A VAL* 4.2 23.8 - - + +
1134A ASN 5.1 3.5 + - - -
1135A ASN* 3.8 42.4 - - + +
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Residues in contact with PHE1103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095A PHE* 3.4 7.3 - - - +
1096A VAL* 2.9 42.0 + - + +
1098A ASN* 4.4 13.9 - - + -
1101A HIS* 3.9 24.0 - + + -
1102A TRP* 1.3 83.1 - - - +
1104A VAL* 1.3 61.2 + - - +
1110A TYR* 4.7 7.9 - - - -
1112A PRO* 3.9 22.0 - - + -
1113A GLN 3.3 31.9 - - - +
1114A ILE* 4.6 11.9 - - + -
1115A ILE* 4.1 7.3 - - - +
1K NAG 3.8 38.4 - - - -
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Residues in contact with VAL1104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090A PRO* 4.3 11.2 - - + -
1093A GLY* 4.4 3.6 - - - +
1094A VAL 3.3 17.3 - - - +
1095A PHE* 3.8 23.8 - - + -
1103A PHE* 1.3 76.3 - - - +
1105A THR* 1.3 70.2 + - - +
1111A GLU 3.9 1.0 - - - +
1113A GLN* 3.1 36.4 + - + +
1115A ILE* 4.1 8.4 - - + +
1119A ASN* 3.1 39.7 - - - +
1120A THR* 5.8 0.4 - - + -
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Residues in contact with THR1105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714A ILE* 5.0 5.4 - - + -
1093A GLY* 2.9 9.4 - - - -
1094A VAL* 2.9 53.4 + - + +
1096A VAL* 4.3 19.7 - - + -
1104A VAL* 1.3 76.5 - - - +
1106A GLN* 1.3 70.4 + - - +
1109A PHE 3.3 6.2 + - - -
1110A TYR* 3.8 10.1 - - + -
1111A GLU 3.1 36.5 + - - -
1112A PRO* 4.6 3.4 - - - -
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Residues in contact with GLN1106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714A ILE* 4.3 2.1 - - - +
910A GLY 4.2 7.2 - - - +
911A VAL* 4.0 10.9 - - - +
912A THR* 3.3 45.9 + - + +
915A VAL* 4.7 2.0 - - - +
1092A GLU 4.8 4.5 - - - +
1093A GLY* 4.5 5.2 - - - -
1094A VAL* 4.8 0.4 - - - -
1105A THR* 1.3 92.4 + - - +
1107A ARG* 1.3 64.4 + - - +
1108A ASN 4.7 1.2 + - - +
1109A PHE* 2.9 57.7 + - - +
1111A GLU* 3.7 27.7 + - + +
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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