Contacts of the strand formed by residues 130 - 140 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110G LEU* 4.4 19.7 - - + -
111G VAL 3.7 4.9 - - - +
112G LEU* 4.7 4.0 - - + +
113G ASN* 3.2 9.6 + - - +
126G LEU* 3.5 19.7 - - + +
127G TYR* 3.3 19.8 + - + +
128G ASN 4.8 0.9 - - - +
129G ALA* 1.3 73.6 - - - +
131G GLU* 1.3 60.8 + - - +
132G TRP 3.6 24.9 - - - +
133G VAL* 4.1 5.8 - - + -
173G PRO* 3.5 36.1 - - + +
178G LEU* 5.2 2.5 - - + -
205G LEU* 3.5 39.7 - - + -
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Residues in contact with GLU 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F ASN* 2.9 34.1 + - - +
111G VAL* 2.6 30.1 + - - +
112G LEU 3.9 8.6 - - - +
113G ASN* 3.2 25.0 + - - +
129G ALA 3.5 0.6 + - - -
130G ILE* 1.3 74.8 - - - +
132G TRP* 1.3 70.8 + - + +
172G ARG* 3.3 39.9 + - - +
173G PRO* 3.8 5.9 - - - +
225G GLY* 5.3 2.4 - - - -
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Residues in contact with TRP 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F ASP 5.5 2.0 - - - -
127F TYR* 4.6 16.8 - - + -
128F ASN* 2.8 39.3 - - + +
173F PRO* 4.8 9.2 - - + -
174F ALA* 3.7 33.9 - - + -
110G LEU* 3.4 4.0 - - - -
111G VAL* 2.9 46.2 + - + +
130G ILE* 3.6 5.8 - - - +
131G GLU* 1.3 101.2 - - + +
133G VAL* 1.3 63.6 + - - +
134G LEU* 4.2 12.6 - - + -
170G ALA* 3.6 28.0 - - + -
171G GLN 3.4 21.5 - - - -
172G ARG* 3.3 39.7 - - - -
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Residues in contact with VAL 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G ILE* 4.2 10.3 - - + -
109G ALA 3.4 2.9 - - - -
110G LEU* 3.8 14.8 - - + -
130G ILE* 4.1 8.5 - - + -
132G TRP* 1.3 76.1 - - - +
134G LEU* 1.3 63.1 + - - +
170G ALA 4.0 0.2 - - - -
171G GLN* 2.9 38.3 + - - +
173G PRO* 4.0 18.4 - - + -
176G LEU* 3.6 34.3 - - + -
178G LEU* 4.0 21.8 - - + -
252G ILE* 4.3 12.5 - - + +
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Residues in contact with LEU 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F ASP* 4.9 6.3 - - + +
127F TYR* 3.8 33.4 - - + -
108G ILE* 3.8 2.4 - - - +
109G ALA* 2.8 54.3 + - + +
111G VAL* 3.9 26.5 - - + -
132G TRP* 4.2 8.7 - - + -
133G VAL* 1.3 77.5 - - - +
135G PRO* 1.3 75.5 - - + +
166G ILE* 4.0 22.4 - - + -
167G GLY 4.4 2.9 - - - +
169G PRO 4.4 4.3 - - - +
170G ALA* 3.8 15.3 - - + -
227G ILE* 5.0 3.4 - - + -
252G ILE* 4.1 5.8 - - - -
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Residues in contact with PRO 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G GLU 3.9 4.7 - - - +
108G ILE* 5.0 0.2 - - - -
134G LEU* 1.3 90.7 - - + +
136G ALA* 1.3 60.5 + - - +
166G ILE* 3.8 2.1 - - - +
167G GLY 2.9 27.0 + - - -
168G GLY 3.5 25.4 - - - +
169G PRO 3.9 9.2 - - - +
249G ILE* 3.8 17.9 - - + -
252G ILE* 3.8 14.3 - - + +
253G GLY 3.8 5.2 - - - -
254G SER 3.6 24.2 - - - +
255G VAL* 3.8 13.9 - - + -
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Residues in contact with ALA 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G ALA* 3.6 5.2 - - - +
107G GLU* 2.8 38.6 + - + +
109G ALA* 4.1 10.3 - - + -
135G PRO* 1.3 75.4 - - - +
137G LEU* 1.3 64.6 + - - +
164G TYR* 5.6 0.4 - - + -
165G VAL 3.2 11.9 - - - +
166G ILE* 4.5 5.6 - - + -
229G LEU* 3.9 27.4 - - + -
249G ILE* 4.8 0.2 - - - +
255G VAL* 3.7 10.8 - - - +
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Residues in contact with LEU 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G ILE* 4.2 12.8 - - + -
105G GLU 3.4 7.9 - - - +
106G ALA* 4.3 0.7 - - - -
107G GLU* 5.3 0.2 - - - -
136G ALA* 1.3 76.5 - - - +
138G GLU* 1.3 60.2 + - - +
139G VAL 4.1 0.2 - - - -
164G TYR* 3.4 6.6 - - - +
165G VAL* 2.9 42.9 + - + +
185G MET* 3.8 21.1 - - + -
245G PHE* 4.2 11.2 - - + +
247G ALA* 3.5 30.7 - - + +
255G VAL* 3.7 18.8 - - + +
256G ALA 4.0 6.3 - - - -
257G ALA* 3.9 36.6 - - + +
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Residues in contact with GLU 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G LYS* 3.1 50.1 + - - +
82G LEU* 5.0 1.1 - - + +
86G MET* 5.6 0.7 - - - +
104G ILE* 3.2 4.2 - - - -
105G GLU* 2.8 42.2 + - + +
107G GLU* 3.1 32.0 - - - +
136G ALA 4.2 0.2 - - - -
137G LEU* 1.3 73.3 - - - +
139G VAL* 1.3 63.7 + - - +
140G VAL* 3.4 15.5 + - - +
161G CYS* 3.7 15.6 - - - -
162G GLY 4.7 1.2 + - - -
163G VAL 3.8 10.3 - - - +
164G TYR* 4.2 2.2 - - + -
229G LEU* 3.8 17.9 - - + -
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Residues in contact with VAL 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G ILE* 4.3 8.3 - - + -
99G VAL* 4.1 15.0 - - + -
102G PRO* 4.0 20.9 - - + -
103G ARG 3.2 11.0 - - - +
104G ILE* 3.5 18.4 - - + -
138G GLU* 1.3 69.6 - - - +
140G VAL* 1.3 60.3 + - - +
162G GLY* 3.2 8.3 + - - -
163G VAL* 2.9 51.9 + - + +
165G VAL* 4.7 9.2 - - + -
257G ALA* 5.8 0.4 - - + -
259G PHE* 3.9 28.7 - - + -
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Residues in contact with VAL 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G LYS* 4.0 3.1 - - - +
99G VAL* 3.7 3.0 - - - +
101G GLN 4.0 0.2 - - - +
102G PRO* 3.3 4.9 - - - +
103G ARG* 2.7 55.5 + - + +
105G GLU* 3.7 17.0 - - - +
138G GLU* 3.4 19.5 + - + +
139G VAL* 1.3 75.0 - - - +
141G GLY* 1.3 59.4 + - - +
147G TRP* 3.6 22.0 - - + -
160G SER* 3.2 17.0 - - - +
162G GLY 4.2 0.2 - - - +
236G MET* 3.9 13.0 - - + -
1263G PO4 3.4 21.8 - - - +
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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