Contacts of the strand formed by residues 130 - 140 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110M LEU* 4.4 18.4 - - + -
111M VAL 3.7 4.7 - - - +
112M LEU* 4.7 4.3 - - + +
113M ASN* 3.2 6.9 + - - +
126M LEU* 3.5 18.4 - - + +
127M TYR* 3.3 20.1 + - + +
128M ASN 4.8 0.7 - - - +
129M ALA* 1.3 77.4 - - - +
131M GLU* 1.3 60.8 + - - +
132M TRP 3.7 24.9 - - - +
133M VAL* 4.1 5.8 - - + -
173M PRO* 3.5 34.1 - - + +
178M LEU* 5.1 3.1 - - + -
205M LEU* 3.5 40.4 - - + -
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Residues in contact with GLU 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111M VAL* 2.7 28.0 + - - +
112M LEU 3.9 11.4 - - - +
113M ASN* 3.2 25.0 + - - +
129M ALA 3.5 0.6 + - - -
130M ILE* 1.3 73.5 - - - +
132M TRP* 1.3 69.7 + - + +
172M ARG* 3.2 38.6 + - - +
173M PRO* 3.8 5.8 - - - +
225M GLY* 5.3 2.3 - - - -
128O ASN* 2.8 36.4 + - - +
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Residues in contact with TRP 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109M ALA 3.9 0.2 - - - +
110M LEU* 3.5 4.2 - - - -
111M VAL* 2.9 42.0 + - + +
130M ILE* 3.7 5.9 - - - +
131M GLU* 1.3 99.2 - - + +
133M VAL* 1.3 62.7 + - - +
134M LEU* 4.2 16.4 - - + -
170M ALA* 3.7 29.2 - - + -
171M GLN 3.4 20.4 - - - -
172M ARG* 3.3 44.0 - - + -
124O ASP 5.3 2.2 - - - -
127O TYR* 4.4 16.4 - + + -
128O ASN* 2.8 40.1 - - + +
130O ILE 6.1 0.2 - - - -
173O PRO* 4.8 10.1 - - + -
174O ALA* 3.7 29.8 - - + -
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Residues in contact with VAL 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108M ILE* 4.2 10.8 - - + -
109M ALA 3.4 3.4 - - - -
110M LEU* 3.8 15.0 - - + -
130M ILE* 4.1 9.2 - - + -
132M TRP* 1.3 74.6 - - - +
134M LEU* 1.3 64.3 + - - +
171M GLN* 2.8 37.4 + - - +
173M PRO* 4.0 18.4 - - + -
176M LEU* 3.6 33.4 - - + -
178M LEU* 4.0 21.3 - - + -
252M ILE* 4.3 11.9 - - + -
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Residues in contact with LEU 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108M ILE* 3.8 2.4 - - - +
109M ALA* 2.8 52.6 + - + +
111M VAL* 3.9 26.5 - - + -
132M TRP* 4.2 7.9 - - + -
133M VAL* 1.3 78.5 - - - +
135M PRO* 1.3 73.0 - - + +
166M ILE* 3.9 22.7 - - + -
167M GLY 4.5 2.2 - - - +
169M PRO 4.4 4.7 - - - +
170M ALA* 3.8 14.1 - - + -
227M ILE* 5.0 1.1 - - + -
252M ILE* 4.2 5.6 - - - -
124O ASP* 4.7 9.0 - - + -
127O TYR* 3.7 34.1 - - + -
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Residues in contact with PRO 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107M GLU 3.9 5.6 - - - +
108M ILE* 5.0 0.4 - - - -
134M LEU* 1.3 90.0 - - + +
136M ALA* 1.3 59.6 + - - +
166M ILE* 3.8 1.7 - - - +
167M GLY 2.9 26.9 + - - -
168M GLY 3.5 22.7 - - - +
169M PRO 3.9 12.6 - - - +
249M ILE* 3.8 19.7 - - + -
252M ILE* 3.8 17.9 - - + -
253M GLY 3.9 2.5 - - - -
254M SER 3.7 25.1 - - - +
255M VAL* 3.8 10.8 - - + -
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Residues in contact with ALA 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106M ALA* 3.6 4.9 - - - +
107M GLU* 2.8 38.9 + - + +
109M ALA* 4.1 10.1 - - + -
135M PRO* 1.3 75.6 - - - +
137M LEU* 1.3 63.6 + - - +
164M TYR* 5.6 0.4 - - + -
165M VAL 3.2 13.5 - - - +
166M ILE* 4.4 4.9 - - + -
229M LEU* 3.9 28.0 - - + -
249M ILE* 4.7 0.2 - - - +
255M VAL* 3.7 12.1 - - - +
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Residues in contact with LEU 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104M ILE* 4.2 13.5 - - + -
105M GLU 3.4 8.5 - - - +
106M ALA* 4.3 1.3 - - - -
107M GLU* 5.3 0.2 - - - -
136M ALA* 1.3 78.4 - - - +
138M GLU* 1.3 61.1 + - - +
164M TYR* 3.3 5.9 - - - +
165M VAL* 2.9 43.5 + - + +
185M MET* 4.0 19.1 - - - -
245M PHE* 4.4 11.0 - - + +
246M GLU 5.2 0.2 - - - -
247M ALA* 3.8 29.6 - - + +
255M VAL* 3.7 19.2 - - + +
256M ALA* 4.0 6.5 - - - -
257M ALA* 3.9 36.3 - - + +
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Residues in contact with GLU 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60M LYS* 3.1 50.0 + - - +
82M LEU* 5.0 1.4 - - + +
86M MET* 5.7 0.5 - - - +
103M ARG 3.6 0.2 - - - +
104M ILE* 3.2 3.4 - - - -
105M GLU* 2.8 42.1 + - + +
107M GLU* 3.1 34.0 - - - +
136M ALA 4.2 0.2 - - - -
137M LEU* 1.3 72.4 - - - +
139M VAL* 1.3 64.1 + - - +
140M VAL* 3.5 15.4 + - - +
161M CYS* 3.7 15.4 - - - -
162M GLY 4.7 1.4 + - - -
163M VAL 3.8 10.0 - - - +
164M TYR* 4.2 1.8 - - + -
229M LEU* 3.8 17.3 - - + -
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Residues in contact with VAL 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94M ILE* 4.4 8.1 - - + -
99M VAL* 4.1 15.3 - - + -
102M PRO* 4.0 24.2 - - + -
103M ARG 3.2 11.2 - - - +
104M ILE* 3.5 19.5 - - + -
138M GLU* 1.3 70.2 - - - +
140M VAL* 1.3 58.6 + - - +
162M GLY* 3.2 8.5 + - - -
163M VAL* 2.9 51.2 + - + +
165M VAL* 4.7 8.5 - - + -
259M PHE* 3.8 25.4 - - + -
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Residues in contact with VAL 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60M LYS* 4.0 5.2 - - - +
99M VAL* 3.7 2.0 - - - +
101M GLN 4.0 0.2 - - - +
102M PRO* 3.4 4.9 - - - +
103M ARG* 2.7 55.5 + - + +
105M GLU* 3.7 24.9 - - - +
138M GLU* 3.5 20.2 + - - +
139M VAL* 1.3 75.6 - - - +
141M GLY* 1.3 58.2 + - - +
147M TRP* 3.7 21.5 - - + -
160M SER* 3.2 16.8 - - - +
162M GLY 4.2 0.9 - - - +
236M MET* 3.9 13.2 - - - -
1262M PO4 4.0 11.4 - - - +
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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