Contacts of the strand formed by residues 130 - 140 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110T LEU* 4.4 19.5 - - + -
111T VAL 3.7 4.9 - - - +
112T LEU* 4.7 4.0 - - + +
113T ASN* 3.2 9.9 + - - +
126T LEU* 3.5 19.1 - - + +
127T TYR* 3.3 20.1 + - + +
128T ASN 4.8 0.7 - - - +
129T ALA* 1.3 74.0 - - - +
131T GLU* 1.3 60.8 + - - +
132T TRP 3.6 25.6 - - - +
133T VAL* 4.1 6.1 - - + -
173T PRO* 3.5 33.9 - - + +
178T LEU* 5.1 2.9 - - + -
205T LEU* 3.6 38.8 - - + -
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Residues in contact with GLU 131 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128Q ASN* 2.8 35.5 + - - +
111T VAL* 2.7 27.2 + - - +
112T LEU 3.9 11.3 - - - +
113T ASN* 3.2 24.7 + - - +
129T ALA 3.5 0.4 + - - -
130T ILE* 1.3 74.5 - - - +
132T TRP* 1.3 70.7 + - + +
172T ARG* 3.2 39.5 + - - +
173T PRO* 3.8 6.2 - - - +
225T GLY* 5.3 2.3 - - - -
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Residues in contact with TRP 132 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124Q ASP 5.4 2.0 - - - -
127Q TYR* 4.6 15.9 - + + -
128Q ASN* 2.8 39.2 - - + +
173Q PRO* 4.9 9.0 - - + -
174Q ALA* 3.7 32.5 - - + -
110T LEU* 3.5 4.7 - - - -
111T VAL* 3.0 45.6 + - + -
130T ILE* 3.6 5.6 - - - +
131T GLU* 1.3 99.1 - - + +
133T VAL* 1.3 63.6 + - - +
134T LEU* 4.2 11.7 - - + -
170T ALA* 3.7 29.6 - - + -
171T GLN 3.4 21.8 - - - -
172T ARG* 3.3 38.8 - - - -
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Residues in contact with VAL 133 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108T ILE* 4.2 10.1 - - + -
109T ALA 3.4 2.9 - - - -
110T LEU* 3.8 15.0 - - + -
130T ILE* 4.1 9.2 - - + -
132T TRP* 1.3 77.3 - - - +
134T LEU* 1.3 63.7 + - - +
171T GLN* 2.8 37.3 + - - +
173T PRO* 4.0 17.5 - - + -
176T LEU* 3.6 34.5 - - + -
178T LEU* 4.0 22.9 - - + -
252T ILE* 4.3 11.2 - - + +
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Residues in contact with LEU 134 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124Q ASP* 4.8 8.3 - - + +
127Q TYR* 3.8 32.5 - - + -
108T ILE* 3.8 2.9 - - - +
109T ALA* 2.8 57.3 + - + +
111T VAL* 3.9 26.9 - - + -
132T TRP* 4.2 8.1 - - + -
133T VAL* 1.3 78.9 - - - +
135T PRO* 1.4 75.3 - - + +
166T ILE* 4.0 22.9 - - + -
167T GLY 4.4 2.0 - - - +
169T PRO 4.3 4.0 - - - +
170T ALA* 3.8 14.6 - - + -
227T ILE* 5.0 1.3 - - + -
252T ILE* 4.2 5.4 - - - -
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Residues in contact with PRO 135 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107T GLU 3.9 5.2 - - - +
108T ILE* 5.0 0.4 - - - -
134T LEU* 1.4 92.7 - - + +
136T ALA* 1.3 60.4 + - - +
166T ILE* 3.8 1.7 - - - +
167T GLY 2.9 26.3 + - - -
168T GLY 3.5 26.0 - - - +
169T PRO 3.9 8.5 - - - +
249T ILE* 3.8 20.9 - - + -
252T ILE* 3.8 17.0 - - + -
253T GLY 3.9 2.0 - - - -
254T SER 3.6 24.0 - - - +
255T VAL* 3.7 9.9 - - + -
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Residues in contact with ALA 136 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106T ALA* 3.6 5.0 - - - +
107T GLU* 2.8 37.8 + - + +
109T ALA* 4.1 10.8 - - + -
135T PRO* 1.3 75.8 - - - +
137T LEU* 1.3 62.4 + - - +
164T TYR* 5.6 0.4 - - + -
165T VAL 3.1 12.8 - - - +
166T ILE* 4.5 5.2 - - + -
229T LEU* 3.9 28.3 - - + -
249T ILE* 4.7 0.5 - - - +
255T VAL* 3.7 11.2 - - - +
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Residues in contact with LEU 137 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104T ILE* 4.2 13.7 - - + -
105T GLU 3.4 8.5 - - - +
106T ALA* 4.3 1.3 - - - -
107T GLU* 5.3 0.4 - - - -
136T ALA* 1.3 79.0 - - - +
138T GLU* 1.3 60.1 + - - +
164T TYR* 3.3 5.9 - - - +
165T VAL* 2.8 44.2 + - + +
185T MET* 3.9 19.5 - - - -
245T PHE* 4.5 11.2 - - + +
246T GLU 5.3 0.2 - - - -
247T ALA* 3.8 28.5 - - + +
255T VAL* 3.8 23.3 - - + +
256T ALA* 4.1 2.2 - - - -
257T ALA* 3.9 35.7 - - + +
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Residues in contact with GLU 138 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60T LYS* 3.1 48.8 + - - +
82T LEU* 5.1 1.0 - - + +
86T MET* 5.7 0.7 - - - +
104T ILE* 3.2 4.0 - - - -
105T GLU* 2.8 41.6 + - + +
107T GLU* 3.1 33.5 - - + +
137T LEU* 1.3 71.9 - - - +
139T VAL* 1.3 64.0 + - - +
140T VAL* 3.4 16.0 + - - +
161T CYS* 3.6 17.0 - - - -
162T GLY 4.6 1.0 + - - -
163T VAL 3.8 10.5 - - - +
164T TYR* 4.2 1.1 - - + -
229T LEU* 3.8 18.4 - - + -
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Residues in contact with VAL 139 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94T ILE* 4.4 7.2 - - + -
99T VAL* 4.1 13.9 - - + -
102T PRO* 4.0 23.8 - - + -
103T ARG 3.2 10.3 - - - +
104T ILE* 3.5 18.8 - - + -
138T GLU* 1.3 69.4 - - - +
140T VAL* 1.3 60.3 + - - +
162T GLY* 3.2 8.3 + - - -
163T VAL* 2.9 51.9 + - + +
165T VAL* 4.7 8.5 - - + -
259T PHE* 3.9 25.8 - - + -
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Residues in contact with VAL 140 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60T LYS* 4.0 4.3 - - - +
99T VAL* 3.6 2.3 - - - +
101T GLN 4.0 0.2 - - - +
102T PRO* 3.3 5.2 - - - +
103T ARG* 2.7 54.6 + - + +
105T GLU* 3.8 14.8 - - - +
138T GLU* 3.4 21.9 + - + +
139T VAL* 1.3 74.5 - - - +
141T GLY* 1.3 58.8 + - - +
147T TRP* 3.6 22.4 - - + -
160T SER* 3.2 17.7 - - - +
162T GLY 4.1 0.9 - - - +
236T MET* 3.9 12.6 - - - -
1262T PO4 3.5 20.2 - - - +
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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