Contacts of the strand formed by residues 130 - 140 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110L LEU* 4.4 18.6 - - + -
111L VAL 3.7 5.2 - - - +
112L LEU* 4.7 4.0 - - + +
113L ASN* 3.2 6.9 + - - +
126L LEU* 3.5 18.4 - - + +
127L TYR* 3.3 19.9 + - + +
128L ASN 4.7 1.0 - - - +
129L ALA* 1.3 77.4 - - - +
131L GLU* 1.3 61.4 + - - +
132L TRP 3.6 25.1 - - - +
133L VAL* 4.1 5.2 - - + -
173L PRO* 3.5 35.9 - - + +
178L LEU* 5.1 2.7 - - + -
205L LEU* 3.5 40.6 - - + -
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Residues in contact with GLU 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128K ASN* 2.9 33.2 + - - +
111L VAL* 2.7 27.2 + - - +
112L LEU 3.9 11.4 - - - +
113L ASN* 3.2 24.6 + - - +
129L ALA 3.5 0.4 + - - -
130L ILE* 1.3 74.5 - - - +
132L TRP* 1.3 71.3 + - + +
172L ARG* 3.2 39.8 + - - +
173L PRO* 3.8 6.2 - - - +
225L GLY* 5.3 2.4 - - - -
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Residues in contact with TRP 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124K ASP 5.4 2.0 - - - -
127K TYR* 4.5 17.5 - + + -
128K ASN* 2.8 38.7 - - + +
173K PRO* 4.8 9.4 - - + -
174K ALA* 3.6 37.9 - - + -
109L ALA 3.9 0.2 - - - +
110L LEU* 3.5 4.3 - - - -
111L VAL* 2.9 43.6 + - + -
130L ILE* 3.6 5.6 - - - +
131L GLU* 1.3 98.1 - - + +
133L VAL* 1.3 63.8 + - - +
134L LEU* 4.2 15.9 - - + +
170L ALA* 3.7 26.2 - - + -
171L GLN 3.4 21.1 - - - -
172L ARG* 3.3 39.3 - - + -
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Residues in contact with VAL 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L ILE* 4.2 10.8 - - + -
109L ALA 3.3 2.9 - - - -
110L LEU* 3.8 15.0 - - + -
130L ILE* 4.1 9.2 - - + -
132L TRP* 1.3 76.2 - - - +
134L LEU* 1.3 62.9 + - - +
171L GLN* 2.8 38.2 + - - +
173L PRO* 4.0 17.7 - - + -
176L LEU* 3.6 34.1 - - + -
178L LEU* 4.0 22.0 - - + -
252L ILE* 4.3 13.2 - - + +
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Residues in contact with LEU 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124K ASP* 4.9 6.5 - - + +
127K TYR* 3.7 34.5 - - + -
108L ILE* 3.8 2.9 - - - +
109L ALA* 2.8 56.1 + - + +
111L VAL* 3.9 26.9 - - + -
132L TRP* 4.2 8.3 - - + -
133L VAL* 1.3 79.1 - - - +
135L PRO* 1.3 75.2 - - + +
166L ILE* 4.0 20.6 - - + -
167L GLY 4.5 2.0 - - - +
169L PRO 4.3 4.7 - - - +
170L ALA* 3.8 15.5 - - + -
227L ILE* 5.1 3.4 - - + -
252L ILE* 4.1 5.4 - - - -
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Residues in contact with PRO 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107L GLU 3.9 4.9 - - - +
108L ILE* 5.0 0.4 - - - -
134L LEU* 1.3 91.1 - - + +
136L ALA* 1.3 59.7 + - - +
166L ILE* 3.8 2.1 - - - +
167L GLY* 2.9 26.9 + - - -
168L GLY 3.6 26.0 - - - +
169L PRO 3.9 9.6 - - - +
249L ILE* 3.8 20.0 - - + -
252L ILE* 3.8 15.5 - - + -
253L GLY 3.9 5.4 - - - -
254L SER 3.6 25.1 - - - +
255L VAL* 3.8 9.2 - - + -
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Residues in contact with ALA 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106L ALA* 3.6 4.7 - - - +
107L GLU* 2.8 39.7 + - + +
109L ALA* 4.1 10.3 - - + -
135L PRO* 1.3 75.8 - - - +
137L LEU* 1.3 63.0 + - - +
164L TYR* 5.6 0.7 - - + -
165L VAL 3.2 11.9 - - - +
166L ILE* 4.4 4.9 - - + -
229L LEU* 3.9 28.0 - - + -
249L ILE* 4.6 0.3 - - - +
255L VAL* 3.7 12.1 - - - +
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Residues in contact with LEU 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104L ILE* 4.2 13.2 - - + -
105L GLU 3.4 7.9 - - - +
106L ALA* 4.2 1.1 - - - -
107L GLU* 5.3 0.4 - - - -
136L ALA* 1.3 77.7 - - - +
138L GLU* 1.3 61.6 + - - +
164L TYR* 3.3 6.8 - - - +
165L VAL* 2.9 42.6 + - + +
185L MET* 3.8 20.2 - - - -
229L LEU* 5.7 0.2 - - - -
245L PHE* 4.2 11.0 - - + +
246L GLU 5.1 0.2 - - - -
247L ALA* 3.6 28.5 - - + +
255L VAL* 3.7 24.7 - - + +
256L ALA* 4.0 2.0 - - - -
257L ALA* 4.0 35.4 - - + +
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Residues in contact with GLU 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60L LYS* 3.1 49.5 + - - +
82L LEU* 5.0 1.7 - - + +
86L MET* 5.7 0.3 - - - +
104L ILE* 3.2 3.3 - - - -
105L GLU* 2.8 41.7 + - + +
107L GLU* 3.1 33.6 - - - +
136L ALA 4.2 0.4 - - - -
137L LEU* 1.3 73.3 - - - +
139L VAL* 1.3 64.0 + - - +
140L VAL* 3.5 15.5 + - - +
161L CYS* 3.7 15.9 - - - +
162L GLY 4.6 1.2 + - - -
163L VAL 3.7 10.1 - - - +
164L TYR* 4.2 1.1 - - + -
229L LEU* 3.9 17.4 - - + +
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Residues in contact with VAL 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L ILE* 4.3 7.9 - - + -
99L VAL* 4.1 15.0 - - + -
102L PRO* 4.0 23.1 - - + -
103L ARG 3.2 11.0 - - - +
104L ILE* 3.5 19.3 - - + -
138L GLU* 1.3 69.6 - - - +
140L VAL* 1.3 59.8 + - - +
162L GLY* 3.2 9.0 + - - -
163L VAL* 2.9 52.3 + - + +
165L VAL* 4.7 8.3 - - + -
239L VAL* 4.9 0.2 - - + -
257L ALA* 5.8 0.2 - - + -
259L PHE* 3.8 26.0 - - + -
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Residues in contact with VAL 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60L LYS* 4.1 2.9 - - - +
99L VAL* 3.7 1.9 - - - +
101L GLN 4.0 0.2 - - - +
102L PRO* 3.3 5.7 - - - +
103L ARG* 2.7 54.2 + - + +
105L GLU* 3.8 14.8 - - - +
138L GLU* 3.5 21.5 + - - +
139L VAL* 1.3 74.6 - - - +
141L GLY* 1.3 59.0 + - - +
147L TRP* 3.6 22.2 - - + -
160L SER* 3.2 16.8 - - - +
162L GLY 4.2 0.4 - - - +
236L MET* 3.9 13.2 - - + -
1262L PO4 3.3 22.0 - - - +
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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