Contacts of the strand formed by residues 162 - 168 (chain F) in PDB entry 6GJH
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 THR 162 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98F SER* 3.9 27.6 - - - -
99F LEU 3.6 9.4 - - - +
100F ASP* 4.9 4.2 + - - +
156F SER 3.6 2.4 - - - +
157F LEU* 3.6 3.7 - - - +
158F SER* 2.9 37.1 + - - -
160F GLU* 4.9 6.4 + - - +
161F GLY* 1.3 76.5 + - - +
163F LEU* 1.3 61.4 + - - +
164F THR* 3.7 9.9 + - - +
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Residues in contact with LEU 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F VAL 3.9 0.9 - - - +
98F SER* 3.2 1.4 - - - -
99F LEU* 2.7 51.9 + - + +
101F VAL* 4.0 15.5 - - + -
109F LEU* 4.8 17.5 - - + -
111F VAL* 4.1 11.0 - - + -
120F ILE* 3.7 41.5 - - + -
155F SER* 4.2 11.0 - - - -
156F SER* 3.7 27.8 - - - +
157F LEU* 3.8 10.4 - - + +
161F GLY 3.9 0.2 + - - -
162F THR* 1.3 71.2 - - - +
164F THR* 1.3 59.8 + - - +
165F VAL* 4.1 7.3 + - + +
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Residues in contact with THR 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F ARG* 4.0 18.7 + - - +
96F ARG* 4.0 14.8 - - + -
97F VAL 3.4 9.2 - - - +
98F SER* 3.3 18.3 + - - +
154F SER 3.7 1.2 - - - +
155F SER* 3.3 4.5 - - - -
156F SER* 3.1 39.7 + - - +
162F THR* 3.7 9.9 + - - +
163F LEU* 1.3 71.9 - - - +
165F VAL* 1.3 64.5 + - - +
166F GLU* 4.3 12.1 - - - +
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Residues in contact with VAL 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F TRP* 4.0 16.4 - - + +
96F ARG* 3.3 4.3 - - - +
97F VAL* 2.9 43.5 + - + +
99F LEU* 6.5 0.2 - - + -
111F VAL* 4.5 6.7 - - + -
118F VAL* 4.3 13.9 - - + -
120F ILE* 4.0 26.2 - - + -
153F VAL* 3.6 26.2 - - + -
154F SER 3.4 4.3 - - - +
155F SER* 4.1 12.8 - - - -
163F LEU* 4.2 12.1 - - + +
164F THR* 1.3 76.2 - - - +
166F GLU* 1.3 63.6 + - - +
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Residues in contact with GLU 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F ARG* 3.0 38.3 + - - +
95F TRP* 3.3 6.1 - - - +
96F ARG* 3.7 47.8 + - + -
152F GLN 3.8 0.5 - - - +
153F VAL* 3.3 5.1 - - - +
154F SER* 2.9 39.5 + - - +
164F THR* 4.3 9.7 - - + +
165F VAL* 1.3 73.9 - - - +
167F ALA* 1.3 64.1 + - - +
145G PRO* 5.7 0.2 - - - +
146G PRO* 3.3 27.5 - - - +
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Residues in contact with ALA 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F ARG* 3.4 10.7 - - - +
95F TRP* 2.7 50.8 + - + +
144F LEU* 5.6 1.6 - - + -
148F VAL* 5.2 9.6 - - + -
149F ASP 5.2 2.7 - - - +
152F GLN 3.8 8.1 - - - +
153F VAL* 4.0 18.2 - - + -
166F GLU* 1.3 80.1 - - - +
168F PRO* 1.3 72.3 - - + +
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Residues in contact with PRO 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F ASP 3.7 9.6 - - - +
94F ARG* 3.8 21.5 - - - +
95F TRP* 5.4 0.3 - - - +
148F VAL* 4.2 19.8 - - - +
149F ASP 5.3 2.7 + - - +
152F GLN* 3.4 47.1 - - + +
167F ALA* 1.3 90.6 - - + +
169F MET* 1.3 69.1 + - - +
170F PRO 4.0 0.3 - - - -
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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