Contacts of the strand formed by residues 129 - 132 (chain H) in PDB entry 6GYS
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 LEU 129 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118H LEU* 4.8 12.1 - - + -
119H GLU 3.4 22.9 - - - +
120H TRP* 3.4 49.1 - - + +
121H THR* 3.4 5.1 - - - +
128H ARG* 1.3 74.4 - - - +
130H ALA* 1.3 63.9 + - - +
141H TRP* 3.3 22.2 - - - +
142H TYR* 2.5 28.5 + - + +
143H THR* 4.2 0.2 - - - +
144H PHE* 4.6 9.0 - - + +
147H TYR* 4.6 27.4 - - + -
168H ILE* 3.7 22.2 - - + -
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Residues in contact with ALA 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118H LEU* 3.4 10.3 - - - +
119H GLU* 2.8 37.9 + - + +
121H THR* 3.7 20.6 - - + -
123H LEU* 5.4 3.4 - - + -
129H LEU* 1.3 79.7 - - - +
131H TYR* 1.3 60.9 + - - +
132H PHE* 4.2 21.5 - - + -
138H LEU* 5.5 2.7 - - + -
140H VAL 3.2 10.8 - - - +
141H TRP* 5.1 1.3 - - + -
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Residues in contact with TYR 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H ASP* 2.9 25.3 + - - -
26H GLY* 3.8 9.2 - - - -
28H PHE* 3.6 22.9 - + - -
104H PHE* 4.5 14.8 - + + -
115H ILE* 3.4 28.3 - - + +
116H ASP 3.2 29.1 + - - -
117H ALA 4.6 1.6 - - - -
118H LEU* 3.7 20.9 - - + -
130H ALA* 1.3 74.0 - - - +
132H PHE* 1.3 84.3 + - - +
133H ASN* 4.2 4.5 - - + -
134H LYS* 5.3 3.8 + - - -
138H LEU* 3.3 5.5 - - - -
139H GLU* 3.1 37.8 + - + -
140H VAL* 3.3 18.2 + - + +
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Residues in contact with PHE 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H TYR* 3.7 29.2 - + + -
116H ASP 4.5 1.9 - - - +
117H ALA* 4.6 7.6 + - - +
119H GLU* 3.3 19.2 + - - +
121H THR* 5.7 0.9 - - - -
130H ALA* 4.2 16.5 + - + -
131H TYR* 1.3 106.5 + - - +
133H ASN* 1.3 69.6 + - - +
134H LYS* 5.5 2.1 + - - -
136H SER* 3.5 32.8 - - - -
137H MET 3.3 1.8 - - - -
138H LEU* 3.5 30.3 - - + -
169H GLN* 5.9 1.3 - - - +
171H ASN* 5.6 0.9 - - - -
174H ASN* 3.3 35.0 - - - -
40L ARG* 5.2 1.3 - - - -
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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