Contacts of the strand formed by residues 94 - 100 (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 ARG 94 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E THR* 6.1 5.0 - - - +
92E ALA 3.7 9.4 + - - +
93E ASP* 1.3 82.0 - - - +
95E TRP* 1.3 63.4 + - - +
96E ARG* 3.9 7.0 + - + +
152E GLN 4.9 1.6 + - - -
154E SER* 4.2 9.7 + - - -
166E GLU* 2.7 44.2 + - - +
167E ALA* 3.4 19.8 - - - +
168E PRO* 4.0 25.5 - - + +
169E MET* 4.4 3.6 - - - -
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Residues in contact with TRP 95 (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* 1.3 73.2 - - - +
96E ARG* 1.3 64.7 + - - +
97E VAL* 3.5 40.3 - - + +
118E VAL* 4.4 8.5 - - + -
142E TYR* 4.3 18.4 - + + -
143E THR 4.7 7.9 + - - -
144E LEU* 3.6 28.7 - - + -
145E PRO* 3.3 31.1 - - + +
148E VAL* 5.1 2.9 - - + -
153E VAL* 5.4 0.7 - - + -
165E VAL* 4.0 24.5 - - + -
166E GLU* 2.9 28.8 - - - +
167E ALA* 2.8 27.2 + - + +
169E MET* 3.9 20.5 - - - +
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Residues in contact with ARG 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E ARG* 3.9 6.7 + - + +
95E TRP* 1.3 84.4 + - - +
97E VAL* 1.3 73.9 + - - +
98E SER* 4.7 10.7 + - - -
164E THR* 3.5 34.0 + - + +
165E VAL 3.2 9.9 - - - +
166E GLU* 3.9 14.2 + - + +
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Residues in contact with VAL 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E TRP* 3.5 36.6 - - + +
96E ARG* 1.3 84.1 - - - +
98E SER* 1.3 61.8 + - - +
99E LEU* 6.4 0.4 - - + -
142E TYR* 3.9 42.4 - - + -
163E LEU 4.1 0.3 - - - +
164E THR* 3.5 6.3 - - - +
165E VAL* 2.9 48.3 + - + +
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Residues in contact with SER 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E ARG* 4.7 11.0 + - - -
97E VAL* 1.3 77.0 - - - +
99E LEU* 1.3 65.8 + - - +
142E TYR* 4.3 7.4 + - - -
162E THR* 3.2 23.2 - - - +
163E LEU 3.5 4.7 + - - -
164E THR* 4.0 8.4 + - - +
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Residues in contact with LEU 99 (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* 6.4 0.4 - - + -
98E SER* 1.3 78.2 + - - +
100E ASP* 1.3 72.1 + - + +
101E VAL* 3.7 22.1 + - + -
120E ILE* 4.4 15.3 - - + -
138E PHE* 4.2 18.4 - - + -
140E ARG* 4.1 35.9 - - + +
142E TYR* 4.3 10.5 - - + +
162E THR* 3.4 6.1 - - - -
163E LEU* 2.7 46.1 + - + +
165E VAL* 6.5 0.9 - - + -
131F HIS* 6.3 2.7 - - + -
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Residues in contact with ASP 100 (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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99E LEU* 1.3 84.5 - - + +
101E VAL* 1.3 75.1 + - - +
102E ASN* 3.1 29.0 + - - +
160E GLU 4.6 2.4 - - - +
161E GLY 3.4 8.4 - - - +
162E THR* 4.5 7.9 - - + +
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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