Contacts of the strand formed by residues 130 - 140 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110P LEU* 4.4 21.1 - - + -
111P VAL 3.7 4.5 - - - +
112P LEU* 4.7 4.3 - - + +
113P ASN* 3.2 6.5 + - - +
126P LEU* 3.6 18.6 - - + +
127P TYR* 3.3 19.8 + - + +
128P ASN 4.8 1.0 - - - +
129P ALA* 1.3 76.0 - - - +
131P GLU* 1.3 60.7 + - - +
132P TRP 3.7 24.7 - - - +
133P VAL* 4.2 5.6 - - + -
173P PRO* 3.5 35.5 - - + +
178P LEU* 5.1 2.9 - - + -
205P LEU* 3.5 39.7 - - + -
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Residues in contact with GLU 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111P VAL* 2.6 32.0 + - - +
112P LEU 3.9 7.3 - - - +
113P ASN* 3.2 25.4 + - - +
129P ALA 3.5 0.6 + - - -
130P ILE* 1.3 74.1 - - - +
132P TRP* 1.3 70.0 + - + +
172P ARG* 3.2 38.8 + - - +
173P PRO* 3.8 6.0 - - - +
225P GLY* 5.3 2.3 - - - -
128S ASN* 2.8 36.1 + - - +
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Residues in contact with TRP 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110P LEU* 3.5 3.8 - - - -
111P VAL* 2.9 43.0 + - + -
130P ILE* 3.7 5.5 - - - +
131P GLU* 1.3 98.6 - - + +
133P VAL* 1.3 63.7 + - - +
134P LEU* 4.2 16.3 - - + +
170P ALA* 3.6 27.8 - - + -
171P GLN 3.4 21.1 - - - -
172P ARG* 3.3 44.0 - - - -
124S ASP 5.4 3.6 - - - -
127S TYR* 4.4 15.0 - + + -
128S ASN* 2.7 40.5 - - + +
173S PRO* 4.9 8.7 - - + -
174S ALA* 3.8 28.9 - - + -
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Residues in contact with VAL 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108P ILE* 4.2 11.0 - - + -
109P ALA 3.4 2.9 - - - -
110P LEU* 3.8 15.0 - - + -
130P ILE* 4.2 9.0 - - + -
132P TRP* 1.3 75.7 - - - +
134P LEU* 1.3 63.2 + - - +
171P GLN* 2.8 39.7 + - - +
173P PRO* 4.0 18.2 - - + -
176P LEU* 3.6 33.7 - - + -
178P LEU* 4.0 21.3 - - + -
252P ILE* 4.3 11.7 - - + -
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Residues in contact with LEU 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108P ILE* 3.8 2.1 - - - -
109P ALA* 2.8 60.9 + - + +
111P VAL* 3.9 26.7 - - + -
132P TRP* 4.2 8.5 - - + -
133P VAL* 1.3 77.0 - - - +
135P PRO* 1.4 72.7 - - + +
166P ILE* 3.9 23.3 - - + -
167P GLY 4.3 2.2 - - - +
169P PRO 4.4 4.5 - - - +
170P ALA* 3.9 15.7 - - + -
227P ILE* 5.0 0.9 - - + -
252P ILE* 4.1 5.2 - - - -
124S ASP* 4.8 8.1 - - + +
127S TYR* 3.8 33.0 - - + -
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Residues in contact with PRO 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107P GLU 3.9 5.2 - - - +
108P ILE* 5.0 0.7 - - - -
134P LEU* 1.4 91.3 - - + +
136P ALA* 1.3 59.7 + - - +
166P ILE* 3.8 1.9 - - - +
167P GLY 2.9 27.0 + - - -
168P GLY 3.6 21.8 - - - +
169P PRO 3.9 13.0 - - - +
249P ILE* 3.7 22.9 - - + -
252P ILE* 3.7 17.4 - - + -
253P GLY 3.9 2.2 - - - -
254P SER 3.7 24.7 - - - +
255P VAL* 3.8 9.6 - - + -
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Residues in contact with ALA 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106P ALA* 3.6 4.3 - - - +
107P GLU* 2.8 41.3 + - + +
109P ALA* 4.1 10.8 - - + -
135P PRO* 1.3 76.6 - - - +
137P LEU* 1.3 61.9 + - - +
164P TYR* 5.6 0.2 - - + -
165P VAL 3.2 11.9 - - - +
166P ILE* 4.5 5.6 - - + -
229P LEU* 3.8 28.0 - - + -
249P ILE* 4.7 0.5 - - - +
255P VAL* 3.7 11.2 - - - +
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Residues in contact with LEU 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104P ILE* 4.2 13.7 - - + -
105P GLU 3.4 8.5 - - - +
106P ALA* 4.3 1.6 - - - -
136P ALA* 1.3 79.3 - - - +
138P GLU* 1.3 59.8 + - - +
139P VAL 4.1 0.4 - - - -
164P TYR* 3.3 6.3 - - - +
165P VAL* 2.9 43.5 + - + +
185P MET* 4.0 19.3 - - - -
245P PHE* 4.5 11.2 - - + +
247P ALA* 3.8 29.6 - - + +
255P VAL* 3.8 24.0 - - + +
256P ALA* 4.1 2.2 - - - -
257P ALA* 4.0 34.1 - - + +
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Residues in contact with GLU 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60P LYS* 3.1 47.5 + - - +
82P LEU* 5.1 1.2 - - + +
86P MET* 5.7 0.3 - - - +
103P ARG 3.5 0.2 - - - +
104P ILE* 3.2 4.0 - - - -
105P GLU* 2.8 41.2 + - + +
107P GLU* 3.1 33.1 - - - +
136P ALA 4.2 0.4 - - - -
137P LEU* 1.3 73.8 - - - +
139P VAL* 1.3 62.6 + - - +
140P VAL* 3.5 16.1 + - - +
161P CYS* 3.6 17.5 - - - -
162P GLY 4.6 1.0 + - - -
163P VAL 3.8 10.3 - - - +
164P TYR* 4.2 1.3 - - + -
229P LEU* 3.8 18.3 - - + +
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Residues in contact with VAL 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94P ILE* 4.4 7.4 - - + -
99P VAL* 4.1 14.8 - - + -
102P PRO* 4.0 23.6 - - + -
103P ARG 3.2 11.9 - - - +
104P ILE* 3.5 19.3 - - + -
138P GLU* 1.3 70.4 - - - +
140P VAL* 1.3 58.4 + - - +
162P GLY* 3.2 8.3 + - - -
163P VAL* 2.9 50.8 + - + +
165P VAL* 4.7 7.9 - - + -
239P VAL* 4.9 0.2 - - + -
257P ALA* 5.9 0.2 - - + -
259P PHE* 3.8 26.2 - - + -
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Residues in contact with VAL 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60P LYS* 4.0 1.3 - - - +
99P VAL* 3.7 2.3 - - - +
101P GLN 4.0 0.2 - - - +
102P PRO* 3.4 4.2 - - - +
103P ARG* 2.7 55.8 + - + +
105P GLU* 3.8 11.7 - - - +
138P GLU* 3.5 19.7 + - + +
139P VAL* 1.3 74.9 - - - +
141P GLY* 1.3 59.0 + - - +
147P TRP* 3.7 22.2 - - + -
160P SER* 3.2 18.2 - - - +
162P GLY 4.2 0.9 - - - +
236P MET* 3.9 13.2 - - + -
1263P PO4 3.2 27.4 - - - +
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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