Contacts of the strand formed by residues 1109 - 1113 (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 PHE1109 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714B ILE* 4.0 1.1 - - - -
715B PRO* 3.4 6.5 - - + +
716B THR* 3.0 31.4 - - - -
717B ASN 5.3 0.7 - - - -
718B PHE* 3.8 22.2 - + - -
911B VAL* 4.4 9.6 - - + -
915B VAL* 3.7 28.5 - - + -
919B ASN* 4.9 8.1 - - - -
1067B TYR* 4.0 14.4 - - - -
1105B THR* 4.1 0.2 - - - -
1106B GLN* 2.9 52.1 + - + +
1107B ARG 3.3 1.8 + - - -
1108B ASN* 1.3 80.0 - - - +
1110B TYR* 1.3 73.7 + - - +
1111B GLU* 3.0 19.4 + - + -
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Residues in contact with TYR1110 (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 15.7 - - + +
715B PRO 2.6 19.1 + - - +
716B THR* 3.7 28.6 - - + +
1073B LYS* 4.7 9.2 + - + -
1075B PHE* 3.7 39.3 - + - -
1096B VAL* 4.5 10.0 - - + +
1098B ASN* 5.2 5.5 + - - +
1103B PHE* 5.0 6.6 - - - -
1105B THR* 4.0 15.5 - - + -
1109B PHE* 1.3 80.9 - - - +
1111B GLU* 1.3 60.9 + - - +
1112B PRO* 3.7 38.3 - - + +
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Residues in contact with GLU1111 (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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1123A SER* 4.5 10.0 - - - -
912B THR* 3.7 12.0 - - - +
914B ASN* 3.2 23.7 + - - +
915B VAL* 5.0 3.8 - - - +
918B GLU* 4.2 12.6 - - - +
1105B THR* 3.4 18.1 - - - +
1106B GLN* 3.5 31.1 + - - +
1109B PHE* 3.0 15.3 + - + -
1110B TYR* 1.3 73.2 - - - +
1112B PRO* 1.3 71.4 - - + +
1113B GLN* 3.5 22.0 + - + +
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Residues in contact with PRO1112 (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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1103B PHE* 3.9 31.4 - - + -
1105B THR* 3.4 8.9 - - + -
1110B TYR* 3.7 37.9 - - + +
1111B GLU* 1.3 89.6 - - + +
1113B GLN* 1.3 62.9 + - - +
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Residues in contact with GLN1113 (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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1121A PHE* 5.8 6.1 - - - -
1123A SER* 5.8 5.3 - - - -
1092B GLU 5.8 0.2 - - - +
1103B PHE* 3.2 25.6 - - - +
1104B VAL* 3.2 35.2 + - + +
1105B THR* 4.8 1.9 - - - -
1106B GLN* 5.3 2.9 - - - +
1111B GLU* 3.8 22.2 + - + +
1112B PRO* 1.3 78.3 - - - +
1114B ILE* 1.3 71.8 + - - +
1115B ILE 3.5 0.3 + - - -
1119B ASN* 5.4 6.9 - - - +
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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