Contacts of the strand formed by residues 162 - 168 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98E SER* 3.2 26.5 - - - +
99E LEU 3.4 12.1 - - - +
100E ASP* 4.5 7.0 + - - +
156E SER 3.7 1.6 - - - +
157E LEU* 3.4 3.8 - - - +
158E SER* 2.9 40.3 + - - -
160E GLU* 4.3 9.4 + - - +
161E GLY* 1.3 78.5 - - - +
163E LEU* 1.3 62.8 + - - +
164E THR* 4.5 6.0 + - - +
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Residues in contact with LEU 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E VAL 4.1 0.3 - - - +
98E SER* 3.5 3.5 + - - -
99E LEU* 2.7 45.5 + - + +
101E VAL* 3.9 18.8 - - + -
109E LEU* 4.9 16.6 - - + -
111E VAL* 4.3 14.6 - - + -
120E ILE* 3.9 29.2 - - + -
155E SER* 4.0 16.4 - - - +
156E SER 3.6 22.7 - - - +
157E LEU* 3.9 10.9 - - + +
161E GLY 4.0 0.8 + - - -
162E THR* 1.3 72.8 - - - +
164E THR* 1.3 61.2 + - - +
165E VAL* 4.2 14.2 + - + +
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Residues in contact with THR 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ARG* 3.5 36.7 + - + +
97E VAL 3.5 9.0 - - - +
98E SER* 4.0 7.1 + - - -
155E SER* 3.0 24.8 - - - -
156E SER* 3.0 25.5 + - - +
162E THR* 4.0 6.3 + - - +
163E LEU* 1.3 74.9 + - - +
165E VAL* 1.3 70.4 + - - +
166E GLU* 4.7 16.2 - - + +
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Residues in contact with VAL 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E TRP* 4.0 8.7 - - + -
96E ARG* 3.2 3.5 - - - +
97E VAL* 2.9 48.7 + - + +
99E LEU* 6.5 0.9 - - + -
111E VAL* 4.3 6.5 - - + -
118E VAL* 4.2 14.6 - - + -
120E ILE* 4.5 15.9 - - + -
153E VAL* 3.6 23.8 - - + -
154E SER 3.4 11.4 - - - +
155E SER* 4.0 10.3 - - - -
163E LEU* 4.3 19.1 - - + +
164E THR* 1.3 77.9 - - - +
166E GLU* 1.3 64.6 + - - +
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Residues in contact with GLU 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E ARG* 2.7 43.4 + - + +
95E TRP* 2.9 23.1 - - - +
96E ARG* 3.9 13.5 + - + +
152E GLN 3.9 0.2 - - - +
153E VAL* 3.5 2.3 - - - +
154E SER* 2.9 42.0 + - - +
155E SER* 5.8 0.2 - - - -
156E SER* 5.6 2.3 + - - -
164E THR* 4.7 14.3 - - + +
165E VAL* 1.3 76.7 - - - +
167E ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E ARG* 3.4 8.7 - - - +
95E TRP* 2.8 40.5 + - + +
144E LEU* 5.1 0.2 - - + -
148E VAL* 3.8 25.4 - - + -
152E GLN 3.8 9.6 - - - +
153E VAL* 3.9 14.6 - - + -
166E GLU* 1.3 76.9 - - - +
168E PRO* 1.3 72.5 - - + +
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Residues in contact with PRO 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E ALA* 4.8 8.5 - - + +
93E ASP 3.6 9.6 - - - +
94E ARG* 4.0 24.9 - - + +
148E VAL* 4.1 17.5 - - - +
149E ASP* 4.7 3.4 + - + -
152E GLN* 3.6 35.7 - - + +
167E ALA* 1.3 89.4 - - + +
169E MET* 1.3 67.9 + - - +
170E PRO* 4.0 1.4 - - - +
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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