Contacts of the strand formed by residues 130 - 140 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110S LEU* 4.4 19.5 - - + -
111S VAL 3.7 4.7 - - - +
112S LEU* 4.7 3.6 - - + +
113S ASN* 3.2 8.8 + - - +
126S LEU* 3.5 18.8 - - + +
127S TYR* 3.3 20.3 + - + +
128S ASN 3.5 0.9 - - - +
129S ALA* 1.3 75.3 - - - +
131S GLU* 1.3 60.9 + - - +
132S TRP 3.6 24.7 - - - +
133S VAL* 4.1 6.1 - - + -
173S PRO* 3.4 36.2 - - + +
178S LEU* 5.1 2.7 - - + -
205S LEU* 3.6 39.7 - - + -
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Residues in contact with GLU 131 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128R ASN* 2.9 33.5 + - - +
111S VAL* 2.7 26.5 + - - +
112S LEU 3.9 11.8 - - - +
113S ASN* 3.2 25.7 + - - +
129S ALA 3.6 0.4 + - - -
130S ILE* 1.3 73.0 - - - +
132S TRP* 1.3 70.4 + - + +
172S ARG* 3.2 39.4 + - - +
173S PRO* 3.8 6.0 - - - +
225S GLY* 5.3 2.1 - - - -
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Residues in contact with TRP 132 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124R ASP 5.5 2.2 - - - -
127R TYR* 4.6 16.4 - - + -
128R ASN* 2.7 38.4 - - + +
173R PRO* 4.9 9.2 - - + -
174R ALA* 3.7 34.3 - - + -
110S LEU* 3.5 4.2 - - - -
111S VAL* 3.0 46.0 + - + +
130S ILE* 3.6 5.8 - - - +
131S GLU* 1.3 99.4 - - + +
133S VAL* 1.3 64.3 + - - +
134S LEU* 4.2 12.6 - - + -
170S ALA* 3.6 29.6 - - + -
171S GLN 3.3 20.6 - - - -
172S ARG* 3.3 39.5 - - - -
173S PRO* 5.0 0.2 - - - -
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Residues in contact with VAL 133 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108S ILE* 4.2 10.8 - - + -
109S ALA 3.4 3.4 - - - -
110S LEU* 3.8 14.8 - - + -
130S ILE* 4.1 9.0 - - + -
132S TRP* 1.3 74.8 - - - +
134S LEU* 1.3 64.5 + - - +
171S GLN* 2.9 37.1 + - - +
173S PRO* 4.0 18.4 - - + -
176S LEU* 3.6 35.2 - - + -
178S LEU* 4.0 22.0 - - + -
252S ILE* 4.4 11.7 - - + -
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Residues in contact with LEU 134 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124R ASP* 4.8 5.8 - - + -
127R TYR* 3.8 32.8 - - + -
108S ILE* 3.8 2.1 - - - +
109S ALA* 2.8 58.2 + - + +
111S VAL* 3.9 27.1 - - + -
132S TRP* 4.2 8.1 - - + -
133S VAL* 1.3 78.7 - - - +
135S PRO* 1.4 76.0 - - + +
166S ILE* 3.9 22.0 - - + -
167S GLY 4.3 2.7 - - - +
169S PRO 4.3 4.7 - - - +
170S ALA* 3.9 15.0 - - + -
227S ILE* 5.1 3.4 - - + -
252S ILE* 4.2 4.9 - - - -
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Residues in contact with PRO 135 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107S GLU 3.9 4.9 - - - +
108S ILE* 5.0 0.7 - - - -
134S LEU* 1.4 91.0 - - + +
136S ALA* 1.3 59.5 + - - +
166S ILE* 3.8 1.7 - - - +
167S GLY* 2.9 27.4 + - - -
168S GLY 3.6 30.1 - - - +
169S PRO 3.9 12.8 - - - +
249S ILE* 3.8 17.7 - - + -
252S ILE* 3.8 16.6 - - + +
253S GLY 3.9 2.2 - - - -
254S SER 3.7 16.8 - - - +
255S VAL* 3.8 13.9 - - + +
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Residues in contact with ALA 136 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106S ALA* 3.6 4.7 - - - +
107S GLU* 2.8 37.3 + - + +
109S ALA* 4.1 10.5 - - + -
134S LEU 3.7 0.2 + - - -
135S PRO* 1.3 75.6 - - - +
137S LEU* 1.3 62.9 + - - +
164S TYR* 5.6 0.4 - - + -
165S VAL 3.1 13.0 - - - +
166S ILE* 4.5 5.8 - - + -
229S LEU* 3.9 27.6 - - + -
249S ILE* 4.6 0.5 - - - +
255S VAL* 3.7 11.3 - - - +
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Residues in contact with LEU 137 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104S ILE* 4.2 13.5 - - + -
105S GLU 3.4 8.7 - - - +
106S ALA* 4.3 1.3 - - - -
107S GLU* 5.3 0.2 - - - -
136S ALA* 1.3 78.2 - - - +
138S GLU* 1.3 60.2 + - - +
164S TYR* 3.3 5.9 - - - +
165S VAL* 2.9 44.1 + - + +
185S MET* 3.9 19.5 - - - -
245S PHE* 4.4 11.4 - - + +
246S GLU 5.3 0.2 - - - -
247S ALA* 3.8 29.2 - - + +
255S VAL* 3.8 18.6 - - + +
256S ALA 4.0 5.6 - - - -
257S ALA* 3.9 36.3 - - + +
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Residues in contact with GLU 138 (chain S).
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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60S LYS* 3.1 48.8 + - - +
82S LEU* 5.0 0.7 - - + +
86S MET* 5.6 0.5 - - - +
103S ARG 3.6 0.2 - - - +
104S ILE* 3.2 4.0 - - - -
105S GLU* 2.8 40.9 + - + +
107S GLU* 3.1 33.7 - - + +
136S ALA 4.2 0.2 - - - -
137S LEU* 1.3 73.9 - - - +
139S VAL* 1.3 62.9 + - - +
140S VAL* 3.4 16.3 + - - +
161S CYS* 3.7 15.4 - - - -
162S GLY 4.6 1.4 + - - -
163S VAL 3.8 10.0 - - - +
164S TYR* 4.2 1.8 - - + -
229S LEU* 3.8 19.1 - - + -
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Residues in contact with VAL 139 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94S ILE* 4.3 7.4 - - + -
99S VAL* 4.1 14.6 - - + -
102S PRO* 4.0 24.0 - - + -
103S ARG 3.3 11.0 - - - +
104S ILE* 3.5 19.1 - - + -
138S GLU* 1.3 69.0 - - - +
140S VAL* 1.3 60.6 + - - +
162S GLY* 3.2 8.3 + - - -
163S VAL* 2.9 52.4 + - + +
165S VAL* 4.7 9.0 - - + -
259S PHE* 3.9 25.8 - - + -
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Residues in contact with VAL 140 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60S LYS* 4.0 3.1 - - - +
99S VAL* 3.7 1.8 - - - +
101S GLN 4.0 0.3 - - - +
102S PRO* 3.3 4.3 - - - +
103S ARG* 2.7 55.9 + - + +
105S GLU* 3.8 11.2 - - - +
138S GLU* 3.4 21.7 + - - +
139S VAL* 1.3 74.3 - - - +
141S GLY* 1.3 59.2 + - - +
147S TRP* 3.6 22.0 - - + -
160S SER* 3.2 17.7 - - - +
162S GLY 4.1 0.4 - - - +
236S MET* 3.9 13.0 - - + -
1262S PO4 3.7 25.4 - - - +
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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