Contacts of the strand formed by residues 130 - 140 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110F LEU* 4.4 20.4 - - + -
111F VAL 3.7 4.9 - - - +
112F LEU* 4.7 3.6 - - + +
113F ASN* 3.2 8.9 + - - +
126F LEU* 3.6 18.8 - - + +
127F TYR* 3.3 20.0 + - + +
128F ASN 4.8 0.9 - - - +
129F ALA* 1.3 74.7 - - - +
131F GLU* 1.3 61.7 + - - +
132F TRP 3.7 24.7 - - - +
133F VAL* 4.2 5.4 - - + -
173F PRO* 3.5 34.5 - - + +
178F LEU* 5.1 2.5 - - + -
205F LEU* 3.5 40.8 - - + -
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Residues in contact with GLU 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F VAL* 2.7 27.2 + - - +
112F LEU 3.9 11.3 - - - +
113F ASN* 3.2 25.1 + - - +
129F ALA 3.6 0.6 + - - -
130F ILE* 1.3 73.9 - - - +
132F TRP* 1.3 70.8 + - + +
172F ARG* 3.2 39.1 + - - +
173F PRO* 3.8 5.7 - - - +
225F GLY* 5.2 2.8 - - - -
128I ASN* 3.0 33.0 + - - +
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Residues in contact with TRP 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F LEU* 3.4 4.3 - - - -
111F VAL* 2.9 42.9 + - + +
130F ILE* 3.7 6.1 - - - +
131F GLU* 1.3 100.4 - - + +
133F VAL* 1.3 64.7 + - - +
134F LEU* 4.2 15.3 - - + -
170F ALA* 3.6 36.6 - - + -
171F GLN 3.4 19.5 - - - -
172F ARG* 3.3 44.0 - - + -
173F PRO* 5.0 0.2 - - - -
124I ASP 5.3 4.3 - - - -
127I TYR* 4.4 15.0 - + + -
128I ASN* 2.7 40.1 - - + +
173I PRO* 5.0 9.4 - - + -
174I ALA* 4.0 21.3 - - + -
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Residues in contact with VAL 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F ILE* 4.2 10.5 - - + -
109F ALA 3.3 2.9 - - - -
110F LEU* 3.8 14.8 - - + -
130F ILE* 4.2 9.2 - - + -
132F TRP* 1.3 75.9 - - - +
134F LEU* 1.3 65.1 + - - +
171F GLN* 2.8 36.7 + - - +
173F PRO* 4.0 17.7 - - + -
176F LEU* 3.6 34.3 - - + -
178F LEU* 4.0 22.4 - - + -
252F ILE* 4.4 11.8 - - + +
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Residues in contact with LEU 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F ILE* 3.7 2.3 - - - +
109F ALA* 2.8 58.1 + - + +
111F VAL* 3.9 26.9 - - + -
132F TRP* 4.2 7.9 - - + -
133F VAL* 1.3 78.5 - - - +
135F PRO* 1.4 73.8 - - + +
166F ILE* 4.0 22.7 - - + -
167F GLY 4.3 2.2 - - - +
169F PRO 4.3 4.5 - - - +
170F ALA* 3.8 25.6 - - + -
227F ILE* 5.0 0.9 - - + -
252F ILE* 4.2 5.6 - - - -
124I ASP* 4.6 9.9 - - + +
127I TYR* 3.9 21.1 - - + -
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Residues in contact with PRO 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F GLU 3.9 4.7 - - - +
108F ILE* 5.0 0.4 - - - -
134F LEU* 1.4 91.6 - - + +
136F ALA* 1.3 60.8 + - - +
166F ILE* 3.8 1.7 - - - +
167F GLY 2.9 26.7 + - - -
168F GLY 3.6 17.7 - - - +
169F PRO 3.8 12.8 - - - +
249F ILE* 3.8 20.4 - - + -
252F ILE* 3.8 18.1 - - + +
253F GLY 3.9 3.1 - - - -
254F SER 3.6 29.6 - - - +
255F VAL* 3.8 10.5 - - + +
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Residues in contact with ALA 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F ALA* 3.6 4.5 - - - +
107F GLU* 2.8 38.8 + - + +
109F ALA* 4.1 10.5 - - + -
135F PRO* 1.3 76.4 - - - +
137F LEU* 1.3 62.2 + - - +
164F TYR* 5.6 0.4 - - + -
165F VAL 3.2 12.6 - - - +
166F ILE* 4.4 5.4 - - + -
229F LEU* 3.9 28.3 - - + -
249F ILE* 4.5 0.5 - - - +
255F VAL* 3.7 12.0 - - - +
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Residues in contact with LEU 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F ILE* 4.2 13.7 - - + -
105F GLU 3.4 8.7 - - - +
106F ALA* 4.3 0.7 - - - -
107F GLU* 5.3 0.2 - - - -
136F ALA* 1.3 78.2 - - - +
138F GLU* 1.3 61.0 + - - +
164F TYR* 3.3 6.1 - - - +
165F VAL* 2.9 43.7 + - + +
185F MET* 3.9 20.9 - - - -
245F PHE* 4.1 14.1 - - + +
246F GLU 5.2 0.2 - - - -
247F ALA* 3.8 29.2 - - + +
255F VAL* 3.7 20.6 - - + +
256F ALA 4.0 2.0 - - - -
257F ALA* 3.9 35.4 - - + +
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Residues in contact with GLU 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F LYS* 3.1 49.9 + - - +
82F LEU* 5.0 1.2 - - + +
86F MET* 5.7 0.5 - - - +
104F ILE* 3.2 4.3 - - - -
105F GLU* 2.8 40.9 + - + +
107F GLU* 3.1 33.1 - - + +
136F ALA 4.2 0.2 - - - -
137F LEU* 1.3 72.4 - - - +
139F VAL* 1.3 63.7 + - - +
140F VAL* 3.5 16.4 + - - +
161F CYS* 3.7 15.6 - - - -
162F GLY 4.7 1.4 + - - -
163F VAL 3.8 10.1 - - - +
164F TYR* 4.2 1.3 - - + -
229F LEU* 3.8 18.4 - - + -
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Residues in contact with VAL 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F ILE* 4.3 7.4 - - + -
99F VAL* 4.1 15.5 - - + -
102F PRO* 4.0 23.3 - - + -
103F ARG 3.2 11.0 - - - +
104F ILE* 3.5 19.1 - - + -
138F GLU* 1.3 70.0 - - - +
140F VAL* 1.3 59.5 + - - +
162F GLY* 3.2 8.5 + - - -
163F VAL* 2.8 52.9 + - + +
165F VAL* 4.7 8.5 - - + -
257F ALA* 5.9 0.2 - - + -
259F PHE* 3.9 25.8 - - + -
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Residues in contact with VAL 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F LYS* 4.0 3.4 - - - +
99F VAL* 3.6 2.7 - - - +
102F PRO* 3.3 5.0 - - - +
103F ARG* 2.7 54.7 + - + +
105F GLU* 3.8 24.7 - - - +
138F GLU* 3.5 20.3 + - - +
139F VAL* 1.3 74.8 - - - +
141F GLY* 1.3 59.0 + - - +
147F TRP* 3.6 22.9 - - + -
160F SER* 3.2 17.3 - - - +
162F GLY 4.2 0.7 - - - +
236F MET* 3.9 12.1 - - - -
1264F PO4 3.8 12.6 - - - +
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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