Contacts of the strand formed by residues 130 - 140 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A LEU* 4.4 19.1 - - + -
111A VAL 3.7 4.5 - - - +
112A LEU* 4.7 3.4 - - + +
113A ASN* 3.1 10.3 + - - +
126A LEU* 3.5 19.5 - - + +
127A TYR* 3.4 26.1 + - + +
128A ASN 4.8 0.7 - - - +
129A ALA* 1.3 75.5 - - - +
131A GLU* 1.3 60.4 + - - +
132A TRP 3.6 25.4 - - - +
133A VAL* 4.1 6.5 - - + -
173A PRO* 3.5 34.8 - - + +
178A LEU* 5.2 2.7 - - + -
205A LEU* 3.6 34.1 - - + -
132B TRP* 6.2 0.2 - - - -
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 2.7 27.1 + - - +
112A LEU 3.9 11.6 - - - +
113A ASN* 3.3 23.4 + - - +
130A ILE* 1.3 75.4 - - - +
132A TRP* 1.3 71.5 + - + +
172A ARG* 3.2 40.6 + - - +
173A PRO* 3.8 5.7 - - - +
225A GLY* 5.3 2.4 - - - -
128D ASN* 2.9 32.7 + - - +
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Residues in contact with TRP 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ALA 4.0 0.2 - - - +
110A LEU* 3.5 4.3 - - - -
111A VAL* 2.9 46.0 + - + +
130A ILE* 3.6 5.4 - - - +
131A GLU* 1.3 99.3 - - + +
133A VAL* 1.3 65.2 + - - +
134A LEU* 4.2 11.7 - - + -
170A ALA* 3.6 30.5 - - + -
171A GLN 3.4 20.6 - - - -
172A ARG* 3.3 39.7 - - + -
124D ASP 5.5 2.2 - - - -
127D TYR* 4.6 17.0 - + + -
128D ASN* 2.8 38.1 - - + +
173D PRO* 4.9 9.0 - - + -
174D ALA* 3.7 34.5 - - + -
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ILE* 4.1 10.5 - - + -
109A ALA 3.4 3.4 - - - -
110A LEU* 3.8 15.0 - - + -
130A ILE* 4.1 9.0 - - + -
132A TRP* 1.3 76.2 - - - +
134A LEU* 1.3 65.0 + - - +
171A GLN* 2.8 37.4 + - - +
173A PRO* 4.0 17.7 - - + -
176A LEU* 3.6 33.7 - - + -
178A LEU* 4.0 22.4 - - + -
252A ILE* 4.4 11.4 - - + -
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ILE* 3.8 2.9 - - - +
109A ALA* 2.8 56.7 + - + +
111A VAL* 3.9 27.4 - - + -
132A TRP* 4.2 8.7 - - + -
133A VAL* 1.3 77.6 - - - +
135A PRO* 1.3 74.7 - - + +
166A ILE* 4.0 22.9 - - + -
167A GLY 4.4 2.7 - - - +
169A PRO 4.4 4.5 - - - +
170A ALA* 3.9 24.9 - - + -
227A ILE* 5.0 2.9 - - + -
252A ILE* 4.2 5.6 - - - -
124D ASP* 4.8 7.0 - - + +
127D TYR* 3.9 22.4 - - + -
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Residues in contact with PRO 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLU 3.9 5.2 - - - +
108A ILE* 5.0 0.4 - - - -
134A LEU* 1.3 90.5 - - + +
136A ALA* 1.3 60.2 + - - +
166A ILE* 3.8 1.9 - - - +
167A GLY 2.9 26.9 + - - -
168A GLY 3.5 26.9 - - - +
169A PRO 3.9 10.1 - - - +
249A ILE* 3.8 17.3 - - + -
252A ILE* 3.8 16.3 - - + +
253A GLY 3.9 2.0 - - - -
254A SER 3.7 25.1 - - - +
255A VAL* 3.7 14.1 - - + -
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ALA* 3.5 4.3 - - - +
107A GLU* 2.8 40.8 + - + +
109A ALA* 4.1 10.3 - - + -
135A PRO* 1.3 77.0 - - - +
137A LEU* 1.3 59.7 + - - +
164A TYR* 5.6 0.2 - - + -
165A VAL 3.2 13.2 - - - +
166A ILE* 4.4 5.4 - - + -
229A LEU* 3.9 28.3 - - + -
249A ILE* 4.8 0.3 - - - +
255A VAL* 3.7 11.5 - - - +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ILE* 4.2 14.8 - - + -
105A GLU 3.4 9.0 - - - +
106A ALA* 4.2 1.8 - - - -
107A GLU* 5.3 0.2 - - - -
136A ALA* 1.3 77.7 - - - +
138A GLU* 1.3 60.3 + - - +
139A VAL 4.0 0.2 - - - -
164A TYR* 3.3 6.8 - - - +
165A VAL* 2.9 43.5 + - + +
185A MET* 4.0 19.7 - - - -
245A PHE* 4.5 10.5 - - + +
246A GLU 5.3 0.4 - - - -
247A ALA* 3.9 27.8 - - + +
255A VAL* 3.8 22.9 - - + +
256A ALA* 4.0 2.7 - - - -
257A ALA* 3.9 35.9 - - + +
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Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LYS* 3.1 49.2 + - - +
82A LEU* 5.0 1.4 - - + +
86A MET* 5.6 0.7 - - - +
104A ILE* 3.2 4.2 - - - -
105A GLU* 2.8 41.7 + - + +
107A GLU* 3.1 32.8 - - + +
137A LEU* 1.3 72.3 - - - +
139A VAL* 1.3 64.0 + - - +
140A VAL* 3.4 15.6 + - - +
161A CYS* 3.7 15.9 - - - +
162A GLY 4.6 1.2 + - - -
163A VAL 3.8 10.5 - - - +
164A TYR* 4.2 1.8 - - + -
229A LEU* 3.8 17.9 - - + +
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Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ILE* 4.3 7.2 - - + -
99A VAL* 4.1 15.0 - - + -
102A PRO* 4.0 23.3 - - + -
103A ARG 3.3 11.7 - - - +
104A ILE* 3.5 18.6 - - + -
138A GLU* 1.3 71.8 - - - +
140A VAL* 1.3 57.5 + - - +
162A GLY* 3.2 7.8 + - - -
163A VAL* 2.9 51.5 + - + +
165A VAL* 4.7 8.1 - - + -
257A ALA* 5.9 0.2 - - + -
259A PHE* 3.9 27.1 - - + -
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Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LYS* 4.0 1.6 - - - +
99A VAL* 3.7 2.0 - - - +
101A GLN 4.0 0.2 - - - +
102A PRO* 3.3 5.4 - - - +
103A ARG* 2.7 55.0 + - + +
105A GLU* 3.7 18.2 - - - +
138A GLU* 3.4 22.1 + - + +
139A VAL* 1.3 75.8 - - - +
141A GLY* 1.3 58.3 + - - +
147A TRP* 3.6 21.3 - - + -
160A SER 3.2 16.6 - - - +
162A GLY 4.1 0.4 - - - +
236A MET* 3.9 12.8 - - + -
1264A PO4 3.5 20.6 - - - +
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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