Contacts of the strand formed by residues 1102 - 1106 (chain B) in PDB entry 6VSB
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076B THR* 3.9 6.5 - - + -
1077B THR* 3.6 35.7 - - - -
1078B ALA* 3.6 16.4 - - + -
1081B ILE* 4.3 4.7 - - + -
1095B PHE* 4.3 7.4 - - + -
1096B VAL 3.0 27.6 - - - -
1097B SER* 3.5 25.9 - - - -
1099B GLY 5.9 0.8 + - - -
1100B THR 3.8 15.5 + - - -
1101B HIS* 1.3 74.1 + - - +
1103B PHE* 1.3 76.0 + - - +
1115B ILE* 3.4 19.3 + - + +
1133B VAL* 3.6 32.9 - - + +
1134B ASN 4.8 1.9 + - - -
1135B ASN* 3.0 35.5 + - + +
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Residues in contact with PHE1103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095B PHE* 3.2 6.4 - - - +
1096B VAL* 2.8 43.0 + - + -
1098B ASN* 4.6 7.6 - - + -
1101B HIS* 3.7 38.4 - + + -
1102B TRP* 1.3 84.9 - - - +
1104B VAL* 1.3 66.0 + - - +
1110B TYR* 5.0 5.6 - - - -
1112B PRO* 3.9 30.7 - - + -
1113B GLN 3.2 25.1 - - - +
1114B ILE* 4.2 14.8 - - + -
1115B ILE* 3.7 7.0 - - - +
1L NAG 4.0 26.5 - - - -
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Residues in contact with VAL1104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090B PRO* 4.7 11.9 - - + -
1092B GLU 4.4 16.4 - - - +
1094B VAL 3.5 7.0 - - - +
1095B PHE* 3.5 42.4 - - + -
1103B PHE* 1.3 78.2 - - - +
1105B THR* 1.3 65.2 + - - +
1113B GLN* 3.2 43.4 + - + +
1114B ILE 5.5 0.2 - - - +
1115B ILE* 3.6 9.6 - - + -
1119B ASN* 3.7 27.1 - - + +
1120B THR* 4.7 0.2 - - + -
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Residues in contact with THR1105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714B ILE* 3.7 22.0 - - - +
1092B GLU 4.5 3.1 - - - -
1093B GLY* 3.2 4.0 - - - -
1094B VAL* 3.0 29.6 + - - +
1096B VAL* 4.0 13.1 - - + +
1104B VAL* 1.3 79.1 - - - +
1106B GLN* 1.3 69.8 + - - +
1109B PHE 4.1 1.0 + - - -
1110B TYR* 4.0 13.9 - - + -
1111B GLU 3.4 22.4 - - - +
1112B PRO* 3.4 29.8 - - + -
1113B GLN* 4.8 2.2 - - - -
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Residues in contact with GLN1106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714B ILE* 4.0 1.6 - - - +
910B GLY 4.6 13.7 - - - +
911B VAL* 5.1 0.4 - - - -
912B THR* 3.2 38.0 - - + +
915B VAL* 4.0 1.2 - - - +
1092B GLU 4.5 5.8 + - - +
1093B GLY* 4.2 6.5 - - - -
1105B THR* 1.3 81.9 + - - +
1107B ARG* 1.3 66.1 + - - +
1108B ASN 4.2 2.7 - - - +
1109B PHE* 2.9 65.6 + - + +
1111B GLU* 3.5 24.5 + - - +
1113B GLN* 5.3 3.5 + - - +
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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