Contacts of the strand formed by residues 110 - 114 (chain B) in PDB entry 5GGP
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 VAL 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B TYR* 3.3 6.5 - - - +
109B LYS* 1.3 79.5 - - - +
111B TYR* 1.3 63.1 + - - +
120B LEU* 3.8 12.6 - - + -
121B GLU* 3.5 1.8 - - - -
122B ASP* 3.0 40.5 + - + +
132B HIS* 3.6 30.1 - - + +
176B THR* 3.6 22.7 - - + +
177B VAL 3.3 35.2 - - - +
178B LYS* 3.5 10.3 - - + +
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Residues in contact with TYR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLU* 4.1 30.6 + - + -
103B VAL* 3.4 1.4 - - - -
104B TYR* 2.8 51.9 + - + +
109B LYS* 4.7 9.6 - - - -
110B VAL* 1.3 78.2 - - - +
112B VAL* 1.3 69.5 + - - +
113B ALA* 3.5 31.0 - - + +
118B THR* 3.8 23.2 + - + -
120B LEU* 3.3 13.5 - - - -
121B GLU* 4.0 26.0 - - - -
239B LEU* 5.3 1.8 - - + -
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Residues in contact with VAL 112 (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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101B VAL* 4.8 0.4 - - + -
102B GLU 3.2 9.0 - - - +
103B VAL* 4.2 5.2 - - + -
111B TYR* 1.3 82.6 - - - +
113B ALA* 1.3 71.4 + - - +
114B VAL* 4.3 5.2 - - + -
118B THR* 3.7 2.8 - - - +
119B VAL* 2.8 25.8 + - + -
120B LEU* 2.8 30.1 + - + +
134B ILE* 3.7 34.3 - - + -
174B ILE* 4.1 34.1 - - + -
176B THR* 4.2 11.2 - - + -
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Residues in contact with ALA 113 (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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100B ASP 4.4 0.2 - - - -
101B VAL* 3.3 5.9 - - - +
102B GLU* 2.9 38.7 + - + +
111B TYR* 3.5 29.1 - - + +
112B VAL* 1.3 75.1 - - - +
114B VAL* 1.3 66.4 + - - +
115B ASP 4.3 0.2 - - - -
116B GLY* 4.8 6.7 - - - +
117B THR 3.2 19.5 - - - +
118B THR* 4.3 1.3 - - - +
119B VAL 4.4 0.2 - - - +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.2 17.7 - - + -
100B ASP 3.3 7.6 - - - +
101B VAL* 4.4 6.7 - - + -
112B VAL* 4.3 4.3 - - + -
113B ALA* 1.3 80.1 - - - +
115B ASP* 1.3 80.5 + - + +
116B GLY 3.0 0.4 - - - -
117B THR* 2.9 23.7 + - - +
119B VAL* 4.2 19.7 - - + +
134B ILE* 6.0 0.4 - - + -
136B LEU* 4.2 24.2 - - + -
141B GLY 4.5 7.0 - - - +
143B VAL* 5.9 0.9 - - + -
174B ILE* 4.1 25.4 - - + -
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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