Contacts of the strand formed by residues 130 - 140 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110C LEU* 4.4 19.1 - - + -
111C VAL 3.7 4.9 - - - +
112C LEU* 4.7 4.3 - - + +
113C ASN* 3.6 8.8 + - - -
126C LEU* 3.6 19.1 - - + +
127C TYR* 3.3 21.1 + - + +
128C ASN 4.8 1.0 - - - +
129C ALA* 1.3 76.7 - - - +
131C GLU* 1.3 61.6 + - - +
132C TRP 3.7 25.1 - - - +
133C VAL* 4.1 5.6 - - + -
173C PRO* 3.5 36.1 - - + +
178C LEU* 5.1 2.9 - - + -
205C LEU* 3.5 39.5 - - + -
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Residues in contact with GLU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C VAL* 2.7 27.3 + - - +
112C LEU 3.9 11.3 - - - +
113C ASN* 3.9 25.0 - - - +
129C ALA 3.6 1.6 + - - -
130C ILE* 1.3 74.7 - - - +
132C TRP* 1.3 71.5 + - + +
172C ARG* 3.3 39.5 + - - +
173C PRO* 3.8 6.6 - - - +
225C GLY* 5.3 2.4 - - - -
128E ASN* 2.9 33.3 + - - +
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Residues in contact with TRP 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C ALA 3.9 0.3 - - - +
110C LEU* 3.5 4.2 - - - -
111C VAL* 2.9 47.0 + - + +
130C ILE* 3.7 5.3 - - - +
131C GLU* 1.3 100.1 - - + +
133C VAL* 1.3 64.0 + - - +
134C LEU* 4.3 11.7 - - + -
170C ALA* 3.6 29.8 - - + -
171C GLN 3.4 20.6 - - - -
172C ARG* 3.3 44.6 - - + -
124E ASP 5.4 2.2 - - - -
127E TYR* 4.4 17.7 - + + -
128E ASN* 2.8 38.6 - - + +
173E PRO* 4.9 9.4 - - + -
174E ALA* 3.8 29.2 - - + -
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Residues in contact with VAL 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ILE* 4.2 10.5 - - + -
109C ALA 3.4 3.4 - - - -
110C LEU* 3.8 14.8 - - + -
130C ILE* 4.1 9.9 - - + -
132C TRP* 1.3 76.2 - - - +
134C LEU* 1.3 63.8 + - - +
171C GLN* 2.8 37.5 + - - +
173C PRO* 4.0 18.2 - - + -
176C LEU* 3.6 33.4 - - + -
178C LEU* 4.0 22.0 - - + -
252C ILE* 4.4 11.9 - - + -
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ILE* 3.8 1.9 - - - -
109C ALA* 2.8 53.0 + - + +
111C VAL* 3.9 26.5 - - + -
132C TRP* 4.3 8.7 - - + -
133C VAL* 1.3 79.1 - - - +
135C PRO* 1.3 74.3 - - + +
166C ILE* 3.9 23.3 - - + -
167C GLY 4.4 2.0 - - - +
169C PRO 4.3 4.7 - - - +
170C ALA* 3.8 14.8 - - + -
227C ILE* 5.1 1.1 - - + -
252C ILE* 4.2 5.4 - - - -
124E ASP* 4.8 8.7 - - + +
127E TYR* 3.8 33.0 - - + -
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Residues in contact with PRO 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C GLU 3.9 4.9 - - - +
108C ILE* 5.0 0.4 - - - -
134C LEU* 1.3 92.0 - - + +
136C ALA* 1.3 60.1 + - - +
166C ILE* 3.8 2.1 - - - +
167C GLY* 2.9 27.0 + - - -
168C GLY 3.6 23.1 - - - +
169C PRO 3.9 13.2 - - - +
249C ILE* 3.8 17.3 - - + -
252C ILE* 3.8 17.2 - - + +
253C GLY 3.9 2.2 - - - -
254C SER 3.7 24.5 - - - +
255C VAL* 3.8 13.9 - - + -
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C ALA* 3.6 4.3 - - - +
107C GLU* 2.8 38.6 + - + +
109C ALA* 4.1 11.0 - - + -
135C PRO* 1.3 76.4 - - - +
137C LEU* 1.3 63.2 + - - +
164C TYR* 5.6 0.4 - - + -
165C VAL 3.2 12.6 - - - +
166C ILE* 4.4 5.2 - - + -
229C LEU* 3.9 26.9 - - + -
249C ILE* 4.7 0.5 - - - +
255C VAL* 3.7 11.6 - - - +
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Residues in contact with LEU 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ILE* 4.2 12.8 - - + -
105C GLU 3.4 8.7 - - - +
106C ALA* 4.3 0.9 - - - -
107C GLU* 5.3 0.2 - - - -
136C ALA* 1.3 78.7 - - - +
138C GLU* 1.3 60.1 + - - +
139C VAL 4.1 0.4 - - - -
164C TYR* 3.3 5.9 - - - +
165C VAL* 2.9 42.2 + - + +
185C MET* 3.8 28.9 - - - -
229C LEU* 5.7 0.4 - - - -
245C PHE* 4.3 11.4 - - + +
247C ALA* 3.8 21.5 - - + +
255C VAL* 3.8 17.9 - - + +
256C ALA 4.1 6.3 - - - -
257C ALA* 3.9 36.3 - - + +
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Residues in contact with GLU 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LYS* 3.1 49.4 + - - +
82C LEU* 5.0 1.2 - - + +
86C MET* 5.7 0.5 - - - +
104C ILE* 3.2 4.3 - - - -
105C GLU* 2.8 42.1 + - + +
107C GLU* 3.1 33.2 - - + +
136C ALA 4.2 0.2 - - - -
137C LEU* 1.3 73.4 - - - +
139C VAL* 1.3 63.0 + - - +
140C VAL* 3.5 16.1 + - - +
161C CYS* 3.7 15.4 - - - -
162C GLY 4.6 1.4 + - - -
163C VAL 3.8 9.9 - - - +
164C TYR* 4.2 0.9 - - + -
229C LEU* 3.8 17.5 - - + -
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Residues in contact with VAL 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ILE* 4.3 7.2 - - + -
99C VAL* 4.1 14.1 - - + -
102C PRO* 4.0 24.2 - - + -
103C ARG 3.2 11.9 - - - +
104C ILE* 3.5 18.8 - - + -
138C GLU* 1.3 70.3 - - - +
140C VAL* 1.3 59.5 + - - +
162C GLY* 3.2 8.3 + - - -
163C VAL* 2.9 52.2 + - + +
165C VAL* 4.7 8.5 - - + -
259C PHE* 3.8 26.0 - - + -
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Residues in contact with VAL 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LYS* 4.0 4.7 - - - +
99C VAL* 3.7 2.2 - - - +
101C GLN 4.0 0.2 - - - +
102C PRO* 3.3 5.2 - - - +
103C ARG* 2.7 56.2 + - + +
105C GLU* 3.7 16.2 - - - +
138C GLU* 3.5 20.8 + - + +
139C VAL* 1.3 74.1 - - - +
141C GLY* 1.3 58.3 + - - +
147C TRP* 3.6 22.9 - - + -
159C ALA 4.8 0.2 - - - +
160C SER* 3.2 17.0 - - - +
162C GLY 4.2 0.7 - - - +
236C MET* 3.9 12.6 - - + -
1262C PO4 3.5 19.3 - - - +
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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