Contacts of the strand formed by residues 145 - 160 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60D LYS* 5.9 1.0 - - - -
122D HIS* 2.8 31.1 + - - +
123D VAL 3.2 13.0 - - - +
124D ARG* 3.9 11.0 - - + +
125D MSE 4.6 3.1 - - - -
143D GLN* 3.2 26.8 + - - +
144D PRO* 1.3 79.8 - - - +
146D GLU* 1.3 62.1 + - - +
147D LYS* 5.5 1.2 - - + -
188D LEU* 3.6 11.9 - - + +
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Residues in contact with GLU 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LYS* 3.7 36.9 - - - +
123D VAL* 2.9 27.8 + - + +
125D MSE 4.5 10.5 - - + +
145D GLU* 1.3 75.5 - - - +
147D LYS* 1.3 72.9 + - - +
148D ARG* 2.7 33.0 + - - -
183D TYR* 2.9 40.7 + - + -
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Residues in contact with LYS 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D MSE 3.2 6.1 - - - +
122D HIS* 3.7 46.7 + - + +
145D GLU* 5.8 0.7 - - + -
146D GLU* 1.3 82.9 - - - +
148D ARG* 1.3 70.5 + - - +
149D GLN* 5.9 0.9 - - + -
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Residues in contact with ARG 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D HIS* 3.6 3.8 + - - +
121D MSE 2.9 31.8 + - + +
146D GLU* 2.7 28.0 + - - -
147D LYS* 1.3 78.9 - - - +
149D GLN* 1.3 69.0 + - - +
151D ILE* 4.2 23.2 - - + +
178D ASP* 4.5 3.4 + - - -
180D GLU* 5.5 5.7 + - - -
182D ALA 4.8 3.4 + - - -
183D TYR* 3.4 64.5 - - + +
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Residues in contact with GLN 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D PHE 4.1 0.2 - - - -
119D LYS 3.2 8.5 - - - +
120D HIS* 3.4 32.6 - - + +
147D LYS* 5.9 1.3 - - + -
148D ARG* 1.3 78.1 - - - +
150D ASP* 1.3 81.6 + - - +
151D ILE* 3.3 5.6 + - - +
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Residues in contact with ASP 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D THR* 6.0 2.7 - - - -
118D PHE 3.0 9.5 + - - +
119D LYS* 2.9 27.4 + - - +
149D GLN* 1.3 80.3 - - - +
151D ILE* 1.3 58.2 + - - +
193D ASP* 4.5 10.3 - - - +
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Residues in contact with ILE 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D THR* 3.5 2.7 - - - -
118D PHE* 2.7 44.3 + - + +
121D MSE 3.9 30.5 - - + +
148D ARG* 4.2 21.8 - - + +
149D GLN 4.2 7.0 - - - +
150D ASP* 1.3 76.3 - - - +
152D ARG* 1.3 69.1 + - - +
176D PHE* 4.1 5.6 - - + -
178D ASP* 3.8 19.5 - - + +
183D TYR* 3.5 33.9 - - + -
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Residues in contact with ARG 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D TYR* 3.2 28.5 + - + +
116D GLY* 3.3 17.4 - - - +
117D THR* 3.6 27.7 - - + +
151D ILE* 1.3 78.4 - - - +
153D GLY* 1.3 60.8 + - - +
176D PHE* 4.4 0.9 - - - -
178D ASP* 3.4 10.8 - - - +
179D ASP* 2.9 47.8 + - + +
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Residues in contact with GLY 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D TYR* 3.0 18.8 - - - -
116D GLY 3.0 20.6 + - - +
118D PHE* 3.6 2.6 - - - -
151D ILE 4.2 0.2 + - - -
152D ARG* 1.3 77.4 - - - +
154D ALA* 1.3 60.3 + - - -
176D PHE* 3.7 12.7 - - - -
177D ALA 3.5 10.3 - - - -
179D ASP* 3.3 15.9 - - - -
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Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ILE* 5.5 0.5 - - - +
49D LEU* 4.1 32.1 - - + +
113D LYS* 4.6 6.7 - - - -
114D ILE 3.3 7.4 - - - +
115D TYR* 3.9 18.8 - - + -
153D GLY* 1.3 75.2 - - - +
155D ILE* 1.3 62.5 + - - +
156D VAL* 4.1 1.8 + - - +
175D HIS 4.1 0.2 - - - +
176D PHE* 3.4 7.7 - - - -
177D ALA* 3.0 33.0 + - - +
179D ASP* 4.5 0.2 + - - -
181D ARG* 5.0 1.7 - - - +
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Residues in contact with ILE 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D VAL* 5.3 1.1 - - + -
113D LYS* 3.3 1.7 - - - +
114D ILE* 2.8 50.2 + - + +
118D PHE* 3.4 28.7 - - + -
121D MSE 4.8 3.6 - - - -
154D ALA* 1.3 72.7 - - - +
156D VAL* 1.3 67.8 + - - +
174D ILE* 3.5 34.3 - - + -
175D HIS 3.3 8.5 - - - +
176D PHE* 3.8 22.0 - - + -
187D VAL* 5.0 3.6 - - + -
190D PHE* 3.8 37.2 - - + -
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Residues in contact with VAL 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 3.6 32.8 - - + -
35D GLY 3.8 16.6 - - - +
36D ILE* 4.0 3.7 - - + +
47D ILE* 3.7 29.6 - - + -
48D PHE 3.9 5.2 - - - +
49D LEU* 3.9 24.7 - - + -
112D VAL 3.3 5.6 - - - -
113D LYS* 4.1 6.1 - - + -
154D ALA 4.8 1.8 - - - +
155D ILE* 1.3 82.4 - - - +
157D GLY* 1.3 58.3 + - - +
174D ILE* 3.3 5.0 - - - -
175D HIS 2.8 32.3 + - - +
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Residues in contact with GLY 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 4.4 2.8 - - - +
36D ILE* 4.6 5.6 - - - -
111D ALA* 3.4 5.7 - - - +
112D VAL* 2.9 34.4 + - - +
156D VAL* 1.3 76.6 - - - +
158D PHE* 1.3 76.7 + - - -
173D HIS 3.2 12.8 - - - -
174D ILE* 3.5 5.9 - - - +
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Residues in contact with PHE 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LEU* 3.3 37.7 - - + -
34D LEU* 3.6 25.1 - - + -
35D GLY* 3.7 10.5 - - - -
36D ILE* 4.1 13.7 - - + -
75D SER* 3.4 39.5 - - - -
76D ILE* 3.9 1.6 - - - -
77D THR* 3.8 9.0 - - + -
110D SER 3.2 8.1 - - - +
111D ALA* 3.6 26.5 - - + +
112D VAL* 4.8 1.6 - - - +
157D GLY* 1.3 82.6 - - - -
159D PHE* 1.3 63.8 + - - +
160D THR* 4.0 6.3 + - - +
171D GLY 3.5 2.1 - - - +
172D PHE* 3.6 6.1 - - - -
173D HIS* 3.0 34.7 + - + +
174D ILE* 4.4 0.4 - - - +
202D PHE* 4.1 1.8 - + - -
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Residues in contact with PHE 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LYS* 4.3 13.9 - - + -
103D MSE 4.0 21.1 - - + -
106D GLU* 3.3 37.7 - - + -
108D LEU 3.6 12.8 - - - -
109D PHE* 3.4 11.8 - - - -
110D SER* 2.8 41.1 + - - +
112D VAL* 5.7 0.8 - - + +
158D PHE* 1.3 73.8 - - - +
160D THR* 1.3 72.5 + - - +
161D PRO* 4.9 0.7 - - + -
162D GLU 5.7 0.7 - - - -
171D GLY* 3.3 31.9 - - - -
172D PHE* 3.8 37.9 - + + -
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Residues in contact with THR 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D PHE* 3.5 16.2 - - + -
158D PHE* 5.0 5.9 + - - +
159D PHE* 1.3 81.1 - - - +
161D PRO* 1.3 80.2 - - + +
162D GLU 3.7 0.5 + - - -
164D PHE* 3.6 31.4 - - + +
168D GLY* 4.4 6.7 - - - -
169D SER 3.3 27.5 + - - +
170D ALA* 3.5 4.1 - - - -
171D GLY 2.9 29.0 + - - -
173D HIS* 6.0 1.4 - - - +
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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