Contacts of the strand formed by residues 130 - 140 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I LEU* 4.4 19.5 - - + -
111I VAL 3.7 5.2 - - - +
112I LEU* 4.7 4.3 - - + +
113I ASN* 3.3 6.3 + - - +
126I LEU* 3.6 19.1 - - + +
127I TYR* 3.3 20.9 + - + +
128I ASN 4.9 0.7 - - - +
129I ALA* 1.3 76.5 - - - +
131I GLU* 1.3 63.0 + - - +
132I TRP 3.6 24.2 - - - +
133I VAL* 4.1 5.6 - - + -
173I PRO* 3.4 35.4 - - + +
178I LEU* 5.2 2.5 - - + -
205I LEU* 3.6 40.2 - - + -
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Residues in contact with GLU 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H ASN* 3.1 32.1 + - - +
111I VAL* 2.6 27.0 + - - +
112I LEU 3.9 11.2 - - - +
113I ASN* 3.3 24.7 + - - +
129I ALA 3.5 0.4 + - - -
130I ILE* 1.3 76.5 - - - +
132I TRP* 1.3 70.9 + - + +
172I ARG* 3.2 40.2 + - - +
173I PRO* 3.8 4.7 - - - +
225I GLY* 5.3 2.8 - - - -
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Residues in contact with TRP 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H ASP 5.6 2.0 - - - -
127H TYR* 4.7 15.3 - + + -
128H ASN* 2.7 39.8 - - + +
173H PRO* 5.0 8.3 - - + -
174H ALA* 3.7 34.1 - - + -
109I ALA 3.9 0.2 - - - +
110I LEU* 3.5 3.8 - - - -
111I VAL* 3.0 44.0 + - + +
130I ILE* 3.6 6.1 - - - +
131I GLU* 1.3 99.8 - - + +
133I VAL* 1.3 63.2 + - - +
134I LEU* 4.2 15.7 - - + -
170I ALA* 3.7 27.8 - - + -
171I GLN 3.4 23.3 - - - -
172I ARG* 3.3 38.6 - - - -
173I PRO* 5.0 0.2 - - - -
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Residues in contact with VAL 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I ILE* 4.2 10.5 - - + -
109I ALA 3.4 2.9 - - - -
110I LEU* 3.8 14.4 - - + -
130I ILE* 4.1 9.0 - - + -
132I TRP* 1.3 77.0 - - - +
134I LEU* 1.3 63.1 + - - +
170I ALA 4.0 0.2 - - - -
171I GLN* 2.9 37.6 + - - +
173I PRO* 4.0 18.4 - - + -
176I LEU* 3.6 33.9 - - + -
178I LEU* 4.0 21.8 - - + -
252I ILE* 4.3 11.2 - - + -
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Residues in contact with LEU 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H ASP* 4.8 6.1 - - + +
127H TYR* 3.9 23.6 - - + -
108I ILE* 3.8 2.8 - - - +
109I ALA* 2.8 54.3 + - + +
111I VAL* 3.9 25.8 - - + -
132I TRP* 4.2 8.5 - - + -
133I VAL* 1.3 79.4 - - - +
135I PRO* 1.4 75.0 - - + +
166I ILE* 4.0 22.7 - - + -
167I GLY 4.4 2.2 - - - +
169I PRO 4.4 4.3 - - - +
170I ALA* 3.9 24.2 - - + -
227I ILE* 5.0 3.4 - - + -
252I ILE* 4.1 5.8 - - - -
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Residues in contact with PRO 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I GLU 3.9 5.2 - - - +
108I ILE* 5.0 0.2 - - - -
134I LEU* 1.4 91.9 - - + +
136I ALA* 1.3 58.8 + - - +
166I ILE* 3.8 2.1 - - - +
167I GLY 2.9 26.9 + - - -
168I GLY 3.5 26.7 - - - +
169I PRO 3.9 9.2 - - - +
249I ILE* 3.8 20.9 - - + -
252I ILE* 3.8 14.5 - - + +
253I GLY 3.9 4.0 - - - -
254I SER 3.6 25.1 - - - +
255I VAL* 3.8 9.9 - - + -
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Residues in contact with ALA 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106I ALA* 3.6 5.0 - - - +
107I GLU* 2.9 37.5 + - + +
109I ALA* 4.1 10.3 - - + -
135I PRO* 1.3 76.2 - - - +
137I LEU* 1.3 62.6 + - - +
164I TYR* 5.6 0.4 - - + -
165I VAL 3.1 13.2 - - - +
166I ILE* 4.4 5.4 - - + -
229I LEU* 3.9 28.3 - - + -
249I ILE* 4.7 0.3 - - - +
255I VAL* 3.7 11.8 - - - +
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Residues in contact with LEU 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I ILE* 4.2 13.5 - - + -
105I GLU 3.4 9.4 - - - +
106I ALA* 4.2 0.9 - - - -
136I ALA* 1.3 79.1 - - - +
138I GLU* 1.3 60.0 + - - +
139I VAL 4.1 0.4 - - - -
164I TYR* 3.3 6.2 - - - +
165I VAL* 2.8 42.9 + - + +
185I MET* 3.9 19.5 - - - -
245I PHE* 4.5 11.4 - - + +
246I GLU 5.3 0.2 - - - -
247I ALA* 3.8 29.2 - - + +
255I VAL* 3.8 23.8 - - + +
256I ALA* 4.0 1.6 - - - -
257I ALA* 3.9 35.4 - - + +
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Residues in contact with GLU 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60I LYS* 3.0 49.6 + - - +
82I LEU* 5.1 1.2 - - + +
86I MET* 5.7 0.5 - - - +
104I ILE* 3.2 3.4 - - - -
105I GLU* 2.8 42.2 + - + +
107I GLU* 3.1 33.3 - - - +
137I LEU* 1.3 73.6 - - - +
139I VAL* 1.3 64.0 + - - +
140I VAL* 3.5 15.8 + - - +
161I CYS* 3.7 15.6 - - - -
162I GLY 4.7 1.4 + - - -
163I VAL 3.8 10.1 - - - +
164I TYR* 4.2 1.8 - - + -
229I LEU* 3.8 17.5 - - + -
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Residues in contact with VAL 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I ILE* 4.3 8.3 - - + -
99I VAL* 4.1 14.8 - - + -
102I PRO* 4.0 23.3 - - + -
103I ARG 3.3 11.4 - - - +
104I ILE* 3.5 18.4 - - + -
138I GLU* 1.3 70.7 - - - +
140I VAL* 1.3 60.2 + - - +
162I GLY* 3.2 8.1 + - - -
163I VAL* 2.9 52.9 + - + +
165I VAL* 4.7 8.3 - - + -
239I VAL* 4.9 0.2 - - + -
259I PHE* 3.9 25.4 - - + -
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Residues in contact with VAL 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I LYS* 4.0 1.3 - - - +
99I VAL* 3.7 2.2 - - - +
102I PRO* 3.4 5.2 - - - +
103I ARG* 2.7 56.2 + - + +
105I GLU* 3.7 15.5 - - - +
138I GLU* 3.5 20.1 + - + +
139I VAL* 1.3 75.5 - - - +
141I GLY* 1.3 58.3 + - - +
147I TRP* 3.7 21.8 - - + -
160I SER* 3.2 17.7 - - - +
162I GLY 4.2 0.4 - - - +
236I MET* 3.9 13.2 - - + -
1262I PO4 3.3 24.9 - - - +
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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