Contacts of the strand formed by residues 130 - 140 (chain E) in PDB entry 2WQT
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 ILE 130 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110E LEU* 4.4 18.6 - - + -
111E VAL 3.7 4.5 - - - +
112E LEU* 4.7 3.6 - - + +
113E ASN* 3.4 8.2 + - - +
126E LEU* 3.5 19.5 - - + +
127E TYR* 3.4 20.6 + - + +
128E ASN 4.8 0.7 - - - +
129E ALA* 1.3 78.1 - - - +
131E GLU* 1.3 61.5 + - - +
132E TRP 3.6 25.1 - - - +
133E VAL* 4.1 5.4 - - + -
173E PRO* 3.5 35.1 - - + +
178E LEU* 5.2 2.7 - - + -
205E LEU* 3.6 39.9 - - + -
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Residues in contact with GLU 131 (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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128B ASN* 2.9 34.7 + - - +
111E VAL* 2.6 28.6 + - - +
112E LEU 3.9 11.8 - - - +
113E ASN* 3.9 23.1 - - + +
129E ALA 3.6 1.8 + - - -
130E ILE* 1.3 74.2 - - - +
132E TRP* 1.3 70.4 + - + +
172E ARG* 3.2 40.1 + - - +
173E PRO* 3.8 6.0 - - - +
225E GLY* 5.3 2.3 - - - -
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Residues in contact with TRP 132 (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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124B ASP 5.5 3.1 - - - -
127B TYR* 4.5 15.0 - + + -
128B ASN* 2.7 40.7 - - + +
173B PRO* 4.9 9.0 - - + -
174B ALA* 3.8 30.7 - - + -
110E LEU* 3.5 4.9 - - - -
111E VAL* 2.9 45.2 + - + -
130E ILE* 3.6 6.0 - - - +
131E GLU* 1.3 100.7 - - + +
133E VAL* 1.3 64.0 + - - +
134E LEU* 4.2 11.9 - - + -
170E ALA* 3.7 28.3 - - + -
171E GLN 3.4 20.6 - - - -
172E ARG* 3.3 44.0 - - + -
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Residues in contact with VAL 133 (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 ILE* 4.2 10.8 - - + -
109E ALA 3.4 3.1 - - - -
110E LEU* 3.8 15.3 - - + -
130E ILE* 4.1 9.2 - - + -
132E TRP* 1.3 75.9 - - - +
134E LEU* 1.3 63.4 + - - +
171E GLN* 2.8 36.6 + - - +
173E PRO* 4.0 17.9 - - + -
176E LEU* 3.6 33.9 - - + -
178E LEU* 4.0 22.2 - - + -
252E ILE* 4.3 11.8 - - + +
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Residues in contact with LEU 134 (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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124B ASP* 4.8 5.8 - - + -
127B TYR* 3.8 32.5 - - + -
108E ILE* 3.8 2.8 - - - +
109E ALA* 2.8 53.7 + - + +
111E VAL* 3.9 26.9 - - + -
132E TRP* 4.3 8.3 - - + -
133E VAL* 1.3 78.7 - - - +
135E PRO* 1.3 74.6 - - + +
166E ILE* 3.9 22.9 - - + -
167E GLY 4.3 2.0 - - - +
169E PRO 4.4 4.7 - - - +
170E ALA* 3.8 15.5 - - + -
227E ILE* 5.0 3.1 - - + -
252E ILE* 4.1 5.4 - - - -
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Residues in contact with PRO 135 (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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107E GLU 3.9 5.2 - - - +
108E ILE* 5.0 0.4 - - - -
134E LEU* 1.3 90.6 - - + +
136E ALA* 1.3 59.9 + - - +
166E ILE* 3.8 2.1 - - - +
167E GLY 2.9 27.0 + - - -
168E GLY 3.6 22.4 - - - +
169E PRO 3.9 12.1 - - - +
249E ILE* 3.8 21.1 - - + -
252E ILE* 3.7 17.2 - - + -
253E GLY 3.9 8.3 - - - -
254E SER 3.7 18.8 - - - +
255E VAL* 3.8 10.5 - - + -
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Residues in contact with ALA 136 (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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106E ALA* 3.6 4.7 - - - +
107E GLU* 2.8 39.9 + - + +
109E ALA* 4.1 10.3 - - + -
134E LEU 3.8 0.2 + - - -
135E PRO* 1.3 75.8 - - - +
137E LEU* 1.3 61.0 + - - +
164E TYR* 5.6 0.2 - - + -
165E VAL 3.2 12.6 - - - +
166E ILE* 4.4 5.6 - - + -
229E LEU* 3.9 28.0 - - + -
249E ILE* 4.8 0.5 - - - +
255E VAL* 3.7 11.7 - - - +
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Residues in contact with LEU 137 (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 ILE* 4.2 14.1 - - + -
105E GLU 3.4 8.1 - - - +
106E ALA* 4.3 1.1 - - - -
107E GLU* 5.3 0.2 - - - -
136E ALA* 1.3 78.2 - - - +
138E GLU* 1.3 60.7 + - - +
139E VAL 4.0 0.2 - - - -
164E TYR* 3.3 6.2 - - - +
165E VAL* 2.9 43.3 + - + +
185E MET* 3.9 20.4 - - - -
245E PHE* 4.4 12.1 - - + +
247E ALA* 3.8 27.8 - - + +
255E VAL* 3.8 22.4 - - + +
256E ALA* 4.1 1.8 - - - -
257E ALA* 3.9 35.2 - - + +
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Residues in contact with GLU 138 (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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60E LYS* 3.1 48.2 + - - +
82E LEU* 5.0 1.2 - - + +
86E MET* 5.6 0.9 - - - +
104E ILE* 3.2 3.4 - - - -
105E GLU* 2.8 42.1 + - + +
107E GLU* 3.1 33.1 - - + +
136E ALA 4.2 0.4 + - - -
137E LEU* 1.3 73.9 - - - +
139E VAL* 1.3 64.0 + - - +
140E VAL* 3.4 16.2 + - - +
161E CYS* 3.7 17.0 - - - +
162E GLY 4.7 1.2 + - - -
163E VAL 3.8 9.4 - - - +
164E TYR* 4.2 1.3 - - + -
229E LEU* 3.8 18.4 - - + -
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Residues in contact with VAL 139 (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 ILE* 4.4 7.4 - - + -
99E VAL* 4.1 15.0 - - + -
102E PRO* 4.0 24.2 - - + -
103E ARG 3.2 11.0 - - - +
104E ILE* 3.5 18.4 - - + -
138E GLU* 1.3 71.1 - - - +
140E VAL* 1.3 58.4 + - - +
162E GLY* 3.2 8.5 + - - -
163E VAL* 2.9 52.1 + - + +
165E VAL* 4.7 8.5 - - + -
239E VAL* 4.9 0.2 - - + -
259E PHE* 3.8 26.0 - - + -
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Residues in contact with VAL 140 (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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60E LYS* 4.1 0.4 - - - +
99E VAL* 3.7 2.2 - - - +
101E GLN 4.0 0.3 - - - +
102E PRO* 3.3 4.5 - - - +
103E ARG* 2.7 56.7 + - + +
105E GLU* 3.7 19.1 - - - +
138E GLU* 3.4 19.4 + - + +
139E VAL* 1.3 75.5 - - - +
141E GLY* 1.3 58.0 + - - +
147E TRP* 3.7 21.3 - - + -
160E SER 3.2 16.8 - - - +
162E GLY 4.2 0.4 - - - +
236E MET* 3.9 13.0 - - - -
1262E PO4 3.7 23.1 - - - +
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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