Contacts of the strand formed by residues 162 - 168 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98G SER* 4.2 12.6 - - - -
99G LEU 3.3 18.7 + - - +
100G ASP* 4.5 9.9 + - - +
156G SER 3.7 1.2 - - - +
157G LEU* 3.5 4.1 - - - +
158G SER* 3.0 36.7 + - - -
160G GLU* 5.2 4.5 - - - +
161G GLY* 1.3 77.2 + - - +
163G LEU* 1.3 69.7 + - - +
164G THR* 3.9 7.2 + - - +
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Residues in contact with LEU 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G VAL 4.0 0.5 - - - +
98G SER* 3.3 2.4 - - - -
99G LEU* 2.6 48.5 + - + +
101G VAL* 4.2 11.2 - - + -
109G LEU* 5.3 11.9 - - + -
111G VAL* 4.0 15.0 - - + -
120G ILE* 3.7 32.3 - - + -
155G SER* 4.0 17.0 - - - +
156G SER* 3.5 22.4 - - - +
157G LEU* 3.7 18.1 - - + +
161G GLY 4.0 0.4 + - - -
162G THR* 1.3 73.1 - - - +
164G THR* 1.3 60.4 + - - +
165G VAL* 4.2 13.8 + - + +
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Residues in contact with THR 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G ARG* 3.9 36.4 + - + +
97G VAL 3.4 10.5 - - - +
98G SER* 3.6 12.2 + - - +
154G SER 3.9 0.3 - - - +
155G SER* 3.1 4.9 - - - -
156G SER* 2.9 45.2 + - - +
162G THR* 3.9 8.0 + - - +
163G LEU* 1.3 74.1 - - - +
165G VAL* 1.3 65.8 + - - +
166G GLU* 4.4 11.8 - - + +
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Residues in contact with VAL 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G TRP* 4.0 13.4 - - + -
96G ARG* 3.3 2.6 - - - +
97G VAL* 2.9 44.7 + - + +
111G VAL* 4.5 5.8 - - + -
118G VAL* 4.3 11.9 - - + -
120G ILE* 3.9 27.6 - - + -
153G VAL* 3.6 23.8 - - + -
154G SER 3.4 10.8 - - - +
155G SER* 4.1 12.6 - - - -
163G LEU* 4.2 11.9 - - + +
164G THR* 1.3 77.6 - - - +
166G GLU* 1.3 63.3 + - - +
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Residues in contact with GLU 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G ARG* 3.4 37.3 + - + +
95G TRP* 2.9 20.4 - - - +
96G ARG* 3.4 32.4 + - + -
153G VAL* 3.7 1.9 - - - +
154G SER* 3.0 46.6 + - - +
156G SER* 5.5 1.9 + - - -
164G THR* 4.4 9.7 - - + +
165G VAL* 1.3 77.0 - - - +
167G ALA* 1.3 64.2 + - - +
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Residues in contact with ALA 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G ARG* 3.4 5.8 - - - -
95G TRP* 2.8 44.6 + - + +
144G LEU* 5.0 4.3 - - + -
148G VAL* 5.2 9.6 - - + -
149G ASP 5.2 2.2 - - - +
152G GLN 3.8 8.7 - - - +
153G VAL* 4.1 18.4 - - + -
166G GLU* 1.3 77.8 + - - +
168G PRO* 1.3 74.4 - - + +
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Residues in contact with PRO 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G ALA* 4.8 8.1 - - + +
93G ASP 3.5 9.9 - - - +
94G ARG* 4.4 7.4 - - + -
148G VAL* 4.1 17.9 - - - +
149G ASP* 4.8 3.8 + - + +
152G GLN* 3.4 38.4 - - + +
167G ALA* 1.3 85.2 - - + +
169G MET* 1.3 68.6 + - - +
170G PRO 4.0 0.2 - - - -
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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