Contacts of the strand formed by residues 117 - 129 (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 VAL 117 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112E LYS 3.7 0.5 - - - +
113E THR* 3.2 6.0 - - - +
114E LYS* 2.8 42.2 + - + +
115E ASP* 3.8 7.2 - - + +
116E GLY* 1.3 83.4 - - - +
118E VAL* 1.3 73.7 + - - +
119E GLU* 3.8 3.6 + - + +
141E LYS* 3.9 26.7 - - + -
142E TYR 3.3 12.8 - - - +
143E THR* 4.3 17.9 - - + +
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Residues in contact with VAL 118 (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* 4.4 7.9 - - + -
97E VAL* 6.3 0.2 - - + -
111E VAL* 4.0 22.7 - - + -
112E LYS 3.4 5.4 - - - +
113E THR* 4.3 9.2 - - - +
117E VAL* 1.3 74.4 - - - +
119E GLU* 1.3 61.7 + - - +
120E ILE* 3.8 20.8 - - + +
140E ARG 3.8 0.5 - - - +
141E LYS* 3.2 5.4 - - - -
142E TYR* 2.8 43.9 + - + +
144E LEU* 3.7 37.5 - - + -
153E VAL* 4.4 9.9 - - + -
165E VAL* 4.2 10.8 - - + -
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Residues in contact with GLU 119 (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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110E THR* 3.6 4.5 + - - +
111E VAL* 3.6 1.2 - - - -
112E LYS* 2.7 52.7 + - + +
114E LYS* 4.0 29.0 + - + +
117E VAL* 4.9 4.0 - - + +
118E VAL* 1.3 74.8 - - - +
120E ILE* 1.3 62.6 + - - +
121E THR* 3.6 14.6 + - - +
139E THR* 3.7 26.3 - - + +
140E ARG 3.5 3.6 - - - +
141E LYS* 4.0 21.2 - - + -
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Residues in contact with ILE 120 (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* 4.4 9.6 - - + -
109E LEU* 4.9 4.3 - - + -
110E THR 3.4 7.9 - - - +
111E VAL* 4.3 15.0 - - + -
118E VAL* 3.8 19.3 - - + +
119E GLU* 1.3 74.6 - - - +
121E THR* 1.3 64.2 + - - +
138E PHE* 3.7 23.9 - - + -
139E THR* 3.2 4.0 - - - +
140E ARG* 2.8 38.6 + - + +
142E TYR* 3.7 37.7 - - + -
163E LEU* 3.9 21.8 - - + -
165E VAL* 4.5 15.5 - - + -
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Residues in contact with THR 121 (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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108E GLU 3.7 0.9 - - - +
109E LEU* 3.3 5.6 - - - +
110E THR* 3.0 47.1 + - + +
112E LYS* 5.8 1.4 - - - +
119E GLU* 3.6 20.1 + - - +
120E ILE* 1.3 74.7 - - - +
122E GLY* 1.3 67.8 + - - +
123E LYS* 5.2 5.6 - - + -
138E PHE* 3.4 13.7 - - - +
139E THR* 3.4 16.1 + - - +
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Residues in contact with GLY 122 (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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104E PHE* 3.5 8.3 - - - -
108E GLU 3.4 7.9 - - - -
109E LEU* 4.0 7.2 - - - -
121E THR* 1.3 77.1 - - - +
123E LYS* 1.3 62.3 + - - +
137E CYS* 3.2 3.3 - - - +
138E PHE* 2.9 52.7 + - - +
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Residues in contact with LYS 123 (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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104E PHE* 3.4 5.0 - - - -
108E GLU* 3.2 28.9 + - - +
121E THR* 5.2 7.0 - - + -
122E GLY* 1.3 76.1 - - - +
124E HIS* 1.3 66.4 + - - +
125E GLU* 5.3 5.2 - - + +
136E ARG 3.4 11.1 + - - +
137E CYS* 4.2 19.8 - - + +
137F CYS* 5.0 3.6 - - - -
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Residues in contact with HIS 124 (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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103E HIS 3.6 15.7 - - - -
104E PHE* 3.6 25.1 - + + -
108E GLU* 3.2 33.0 - - - +
123E LYS* 1.3 77.4 + - - +
125E GLU* 1.3 72.0 + - - +
127E ARG* 3.4 27.1 + - + +
134E ILE* 3.6 24.2 - - + -
135E SER* 3.6 10.5 - - - -
136E ARG* 3.2 52.8 + - + +
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Residues in contact with GLU 125 (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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91D THR* 4.7 19.1 - - - +
108E GLU* 4.7 2.0 + - - -
123E LYS* 6.1 6.1 - - + +
124E HIS* 1.3 92.8 + - - +
126E GLU* 1.3 69.5 + - - +
127E ARG* 3.2 3.6 + - - +
135E SER* 4.0 2.9 - - - -
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Residues in contact with GLU 126 (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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125E GLU* 1.3 76.9 - - - +
127E ARG* 1.3 61.5 + - - +
133E TYR* 3.5 42.4 - - + +
134E ILE 3.3 11.9 - - - +
135E SER* 3.8 11.7 + - - +
139F THR* 5.5 3.8 - - - +
141F LYS* 3.0 34.8 + - - +
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Residues in contact with ARG 127 (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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103E HIS* 3.0 32.1 + - - +
104E PHE* 4.8 0.4 - - - +
105E ALA* 5.2 1.6 - - - +
108E GLU* 3.7 12.5 + - - -
124E HIS* 3.4 43.6 + - + +
125E GLU 4.2 2.0 - - - +
126E GLU* 1.3 74.7 - - - +
128E GLN* 1.3 70.1 + - - +
129E ASP* 5.7 2.0 - - - -
133E TYR* 3.2 9.9 - - - -
134E ILE* 2.9 45.2 + - + +
136E ARG* 4.0 11.9 - - - +
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Residues in contact with GLN 128 (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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127E ARG* 1.3 86.6 - - - +
129E ASP* 1.3 74.5 + - - +
132E GLY* 3.2 14.4 - - - +
133E TYR* 4.0 28.2 + - + -
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Residues in contact with ASP 129 (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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127E ARG* 5.6 2.5 - - + -
128E GLN* 1.3 86.9 + - - +
130E GLU* 1.3 66.5 + - - +
131E HIS* 3.0 10.1 + - - -
132E GLY* 2.8 35.5 + - - +
134E ILE* 4.1 12.6 - - + +
136E ARG* 5.1 4.5 + - - +
140F ARG* 3.0 35.2 + - - -
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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