Contacts of the strand formed by residues 130 - 140 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B LEU* 4.4 18.4 - - + -
111B VAL 3.7 4.5 - - - +
112B LEU* 4.7 4.3 - - + +
113B ASN* 3.4 8.1 + - - +
126B LEU* 3.5 18.2 - - + +
127B TYR* 3.4 20.0 + - + +
128B ASN 4.8 0.7 - - - +
129B ALA* 1.3 77.2 - - - +
131B GLU* 1.3 60.7 + - - +
132B TRP 3.6 24.9 - - - +
133B VAL* 4.1 5.4 - - + -
173B PRO* 3.4 36.5 - - + +
178B LEU* 5.1 2.9 - - + -
205B LEU* 3.5 39.9 - - + -
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ASN* 2.8 35.1 + - - +
111B VAL* 2.6 27.9 + - - +
112B LEU 3.8 12.5 - - - +
113B ASN* 3.9 22.9 - - - +
129B ALA 3.5 1.8 + - - -
130B ILE* 1.3 75.0 - - - +
132B TRP* 1.3 71.3 + - + +
172B ARG* 3.2 39.7 + - - +
173B PRO* 3.8 5.6 - - - +
225B GLY* 5.3 2.3 - - - -
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Residues in contact with TRP 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ASP 5.3 3.1 - - - -
127A TYR* 4.4 16.2 - + + -
128A ASN* 2.7 40.8 - - + +
173A PRO* 4.8 9.4 - - + -
174A ALA* 3.8 28.3 - - + -
109B ALA 3.9 0.2 - - - +
110B LEU* 3.5 3.5 - - - -
111B VAL* 2.9 46.4 + - + -
130B ILE* 3.6 6.1 - - - +
131B GLU* 1.3 98.8 - - + +
133B VAL* 1.3 64.0 + - - +
134B LEU* 4.2 12.6 - - + -
170B ALA* 3.6 30.1 - - + -
171B GLN 3.4 20.2 - - - -
172B ARG* 3.3 44.9 - - + -
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ILE* 4.2 10.3 - - + -
109B ALA 3.3 3.1 - - - -
110B LEU* 3.8 15.0 - - + -
130B ILE* 4.1 9.2 - - + -
132B TRP* 1.3 74.6 - - - +
134B LEU* 1.3 62.8 + - - +
171B GLN* 2.8 37.1 + - - +
173B PRO* 4.0 18.4 - - + -
176B LEU* 3.6 34.8 - - + -
178B LEU* 4.0 21.1 - - + -
252B ILE* 4.3 13.2 - - + -
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ASP* 4.6 10.1 - - + -
127A TYR* 3.7 33.4 - - + -
108B ILE* 3.8 2.4 - - - +
109B ALA* 2.8 54.4 + - + +
111B VAL* 3.9 26.5 - - + -
132B TRP* 4.2 7.2 - - + -
133B VAL* 1.3 78.4 - - - +
135B PRO* 1.3 74.2 - - + +
166B ILE* 3.9 23.1 - - + -
167B GLY 4.4 2.5 - - - +
169B PRO 4.4 4.7 - - - +
170B ALA* 3.8 14.8 - - + -
227B ILE* 5.0 0.7 - - + -
252B ILE* 4.2 5.6 - - - -
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Residues in contact with PRO 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLU 3.9 5.2 - - - +
108B ILE* 5.0 0.4 - - - -
134B LEU* 1.3 91.7 - - + +
136B ALA* 1.3 60.6 + - - +
166B ILE* 3.8 2.3 - - - +
167B GLY 2.9 26.5 + - - -
168B GLY 3.6 28.7 - - - +
169B PRO 3.9 12.6 - - - +
249B ILE* 3.8 21.5 - - + -
252B ILE* 3.8 17.2 - - + -
253B GLY* 4.0 2.2 - - - -
254B SER 3.7 17.7 - - - +
255B VAL* 3.8 10.5 - - + -
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ALA* 3.6 5.2 - - - +
107B GLU* 2.8 38.8 + - + +
109B ALA* 4.1 10.1 - - + -
135B PRO* 1.3 76.4 - - - +
137B LEU* 1.3 62.4 + - - +
164B TYR* 5.6 0.2 - - + -
165B VAL 3.2 12.8 - - - +
166B ILE* 4.5 5.2 - - + -
229B LEU* 3.9 28.5 - - + -
249B ILE* 4.7 0.3 - - - +
255B VAL* 3.7 11.9 - - - +
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ILE* 4.2 13.7 - - + -
105B GLU 3.4 8.5 - - - +
106B ALA* 4.3 1.1 - - - -
136B ALA* 1.3 80.6 - - - +
138B GLU* 1.3 59.9 + - - +
139B VAL 4.0 0.2 - - - -
164B TYR* 3.3 6.6 - - - +
165B VAL* 2.9 42.4 + - + +
185B MET* 3.9 20.0 - - - -
245B PHE* 4.5 11.0 - - + +
246B GLU 5.3 0.2 - - - -
247B ALA* 3.8 29.4 - - + +
255B VAL* 3.8 18.6 - - + +
256B ALA* 4.1 6.5 - - - -
257B ALA* 3.9 36.6 - - + +
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LYS* 3.0 49.9 + - - +
82B LEU* 5.1 1.5 - - + +
86B MET* 5.7 0.5 - - - +
103B ARG 3.6 0.2 - - - +
104B ILE* 3.2 4.1 - - - -
105B GLU* 2.8 41.0 + - + +
107B GLU* 3.0 35.1 - - - +
136B ALA 4.2 0.4 - - - -
137B LEU* 1.3 72.9 - - - +
139B VAL* 1.3 62.3 + - - +
140B VAL* 3.5 15.8 + - - +
161B CYS* 3.7 15.8 - - - -
162B GLY 4.7 1.0 + - - -
163B VAL 3.8 9.6 - - - +
164B TYR* 4.2 1.1 - - + -
229B LEU* 3.8 17.9 - - + -
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ILE* 4.4 7.6 - - + -
99B VAL* 4.1 15.3 - - + -
102B PRO* 4.0 23.6 - - + -
103B ARG 3.2 11.7 - - - +
104B ILE* 3.5 19.3 - - + -
138B GLU* 1.3 70.0 - - - +
140B VAL* 1.3 57.3 + - - +
162B GLY* 3.2 8.5 + - - -
163B VAL* 2.9 52.6 + - + +
165B VAL* 4.7 9.0 - - + -
239B VAL* 4.9 0.2 - - + -
259B PHE* 3.8 25.8 - - + -
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LYS* 4.0 2.9 - - - +
99B VAL* 3.7 2.0 - - - +
101B GLN 4.0 0.3 - - - +
102B PRO* 3.4 4.9 - - - +
103B ARG* 2.7 56.2 + - + +
105B GLU* 3.7 25.6 - - - +
138B GLU* 3.5 19.4 + - + +
139B VAL* 1.3 74.8 - - - +
141B GLY* 1.3 58.9 + - - +
147B TRP* 3.6 22.2 - - + -
160B SER* 3.2 18.8 - - - +
162B GLY 4.2 0.4 - - - +
236B MET* 3.9 12.8 - - + -
1263B PO4 3.9 12.1 - - - +
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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