Contacts of the strand formed by residues 145 - 160 (chain B) in PDB entry 1XV2
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 GLU 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B LYS* 5.6 2.7 - - - -
122B HIS* 2.8 32.6 + - - +
123B VAL 3.3 6.1 - - - +
124B ARG* 3.7 15.7 - - + +
125B MSE 4.6 2.0 - - - -
143B GLN* 3.6 23.7 + - - +
144B PRO* 1.3 84.5 - - - +
146B GLU* 1.3 61.0 + - - +
147B LYS* 4.4 1.8 + - - +
188B LEU* 3.6 14.3 - - + +
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LYS* 3.5 47.1 - - - +
122B HIS* 4.7 0.2 - - - -
123B VAL* 3.1 22.8 + - + +
125B MSE 4.4 13.4 - - + +
145B GLU* 1.3 74.2 - - - +
147B LYS* 1.3 69.4 + - - +
148B ARG* 2.7 41.0 + - - -
183B TYR* 2.9 34.7 + - + -
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Residues in contact with LYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B MSE 3.1 6.7 - - - +
122B HIS* 3.5 47.4 + - + -
145B GLU* 5.5 1.8 - - - +
146B GLU* 1.3 80.4 - - - +
148B ARG* 1.3 81.5 + - - +
149B GLN* 6.3 0.7 - - + -
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Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B HIS* 3.5 4.3 - - - +
121B MSE 2.9 28.0 + - + +
146B GLU* 2.7 28.4 + - - -
147B LYS* 1.3 82.7 + - - +
149B GLN* 1.3 72.0 + - - +
151B ILE* 4.2 22.9 - - + +
178B ASP* 4.4 2.4 + - - -
182B ALA 4.9 4.0 + - - -
183B TYR* 3.5 55.7 - - + +
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Residues in contact with GLN 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LYS 3.1 11.7 - - - +
120B HIS* 3.7 26.0 + - + +
147B LYS* 6.3 0.9 - - + -
148B ARG* 1.3 83.8 - - - +
150B ASP* 1.3 84.4 + - - +
151B ILE* 3.3 5.5 + - - +
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Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B THR* 5.8 4.5 - - - -
118B PHE 3.0 9.5 + - - +
119B LYS* 2.9 29.3 + - - +
149B GLN* 1.3 81.8 - - - +
151B ILE* 1.3 58.8 + - - +
152B ARG 4.4 0.2 + - - -
193B ASP* 4.4 10.6 - - - +
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B THR* 4.4 2.2 - - - -
118B PHE* 3.0 40.1 + - + +
121B MSE 4.0 24.7 - - + -
148B ARG* 4.2 19.7 - - + +
149B GLN 4.2 6.7 - - - +
150B ASP* 1.3 76.3 - - - +
152B ARG* 1.3 69.1 + - - +
176B PHE* 3.9 9.6 - - + -
178B ASP* 3.4 23.3 - - + +
183B TYR* 3.4 32.8 - - + -
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B TYR* 3.5 25.5 + - + +
116B GLY* 3.3 30.0 - - - +
117B THR* 3.3 28.2 - - + +
151B ILE* 1.3 75.8 - - - +
153B GLY* 1.3 61.2 + - - +
176B PHE* 4.4 0.2 - - - -
178B ASP* 3.5 9.9 - - - +
179B ASP* 3.1 37.3 + - + +
194B ASP 5.4 0.2 + - - -
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Residues in contact with GLY 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B TYR* 2.9 19.9 - - - -
116B GLY 3.0 17.9 + - - +
118B PHE* 3.5 3.5 - - - -
151B ILE 3.9 1.2 + - - -
152B ARG* 1.3 77.2 - - - +
154B ALA* 1.3 60.6 + - - -
176B PHE* 3.6 14.4 - - - -
177B ALA 3.6 10.8 - - - -
178B ASP* 3.8 0.9 - - - -
179B ASP* 3.0 13.5 - - - -
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Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 5.6 0.3 - - - +
49B LEU* 4.2 30.3 - - + +
113B LYS* 4.9 5.8 - - - -
114B ILE 3.2 7.9 - - - +
115B TYR* 3.9 17.5 - - + -
153B GLY* 1.3 75.1 - - - +
155B ILE* 1.3 63.4 + - - +
156B VAL* 4.0 6.4 + - + +
176B PHE* 3.2 8.6 - - - -
177B ALA* 3.0 32.5 + - - +
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Residues in contact with ILE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B VAL* 4.3 1.1 - - + -
113B LYS* 3.2 5.7 - - - +
114B ILE* 2.7 50.3 + - + +
118B PHE* 3.5 26.5 - - + -
121B MSE 3.7 13.2 - - + -
154B ALA* 1.3 73.0 - - - +
156B VAL* 1.3 65.0 + - - +
174B ILE* 3.6 36.6 - - + -
175B HIS 3.3 6.1 - - - +
176B PHE* 3.6 23.1 - - + -
187B VAL* 4.5 2.0 - - + -
190B PHE* 4.0 28.7 - - + -
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 3.9 29.2 - - + -
35B GLY 3.8 15.9 - - - +
36B ILE* 3.7 5.2 - - + +
47B ILE* 3.8 27.6 - - + -
48B PHE 4.1 3.8 - - - +
49B LEU* 3.9 26.7 - - + -
112B VAL 3.4 4.5 - - - -
113B LYS* 4.2 7.0 - - + -
154B ALA 4.6 4.3 - - - +
155B ILE* 1.3 82.7 - - - +
157B GLY* 1.3 58.9 + - - +
174B ILE* 4.3 2.9 - - - -
175B HIS 2.9 33.2 + - - +
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Residues in contact with GLY 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 4.6 2.7 - - - +
35B GLY 5.9 0.2 - - - -
36B ILE* 4.5 3.8 - - - -
111B ALA* 3.3 3.8 - - - +
112B VAL* 3.0 35.6 + - - +
156B VAL* 1.3 75.6 - - - +
158B PHE* 1.3 78.5 + - - -
173B HIS 3.1 13.7 - - - -
174B ILE* 3.7 6.3 - - - -
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Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 3.4 36.3 - - + -
34B LEU* 3.6 24.2 - - + -
35B GLY* 3.7 10.5 - - - -
36B ILE* 4.1 13.7 - - + -
75B SER* 3.3 42.6 - - - -
76B ILE* 3.9 2.0 - - - -
77B THR* 3.7 8.7 - - + -
109B PHE* 5.8 0.2 - - + -
110B SER 3.2 9.0 - - - +
111B ALA* 3.5 27.8 - - + +
112B VAL* 4.8 1.1 - - - +
157B GLY* 1.3 79.1 - - - -
159B PHE* 1.3 64.1 + - - +
160B THR* 4.2 4.2 + - - +
171B GLY 3.5 1.4 - - - +
172B PHE* 3.4 7.5 - - - -
173B HIS* 2.9 36.6 + - + +
174B ILE* 4.6 0.8 - - - +
202B PHE* 3.9 2.0 - + - -
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Residues in contact with PHE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LYS* 4.8 10.3 - - + -
103B MSE 3.8 12.3 - - + -
106B GLU* 3.4 42.8 - - + -
108B LEU 3.6 16.4 - - - -
109B PHE* 3.3 13.0 - - - -
110B SER* 2.7 43.4 + - - +
112B VAL* 5.8 0.4 - - + +
158B PHE* 1.3 74.8 - - - +
160B THR* 1.3 75.5 + - - +
161B PRO* 4.7 0.9 - - + -
162B GLU 5.6 0.7 - - - -
165B HIS* 6.0 0.2 - - - -
171B GLY* 3.2 28.0 - - - -
172B PHE* 3.7 37.7 - + + -
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Residues in contact with THR 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B PHE* 3.5 25.5 - - + -
158B PHE* 5.1 4.5 + - - +
159B PHE* 1.3 86.6 - - - +
161B PRO* 1.3 79.1 - - - +
164B PHE* 3.5 21.3 - - + +
165B HIS* 3.4 11.8 + - - -
168B GLY* 4.0 5.8 - - - -
169B SER* 2.9 38.1 + - - +
171B GLY* 2.8 17.0 + - - -
173B HIS* 6.0 0.9 - - - +
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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