Contacts of the strand formed by residues 110 - 124 (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 SER 110 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ILE* 5.7 0.9 - - - +
103D MSE 4.4 12.4 - - - +
105D SER 5.7 1.3 - - - -
108D LEU* 4.8 1.3 - - - -
109D PHE* 1.3 77.0 - - - +
111D ALA* 1.3 58.3 + - - +
112D VAL* 4.9 4.0 - - - +
158D PHE* 3.2 6.8 - - - +
159D PHE* 2.8 52.6 + - - +
172D PHE* 5.4 0.3 - - - -
199D ILE* 4.3 9.7 - - - +
200D GLN 3.1 14.8 - - - -
201D ASN* 4.1 14.6 - - - -
202D PHE* 3.5 8.2 - - - -
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Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D LEU* 4.4 2.0 - - + -
77D THR* 4.1 0.9 - - + -
79D PHE* 3.9 12.3 - - + -
110D SER* 1.3 72.6 - - - +
112D VAL* 1.3 69.0 + - - +
157D GLY 3.4 5.8 - - - +
158D PHE* 3.6 16.2 - - + -
198D GLU 3.8 0.2 - - - +
199D ILE* 3.4 3.5 - - - +
200D GLN* 2.8 42.4 + - - +
202D PHE* 3.4 24.0 - - + -
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Residues in contact with VAL 112 (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* 4.3 3.6 - - - +
79D PHE* 4.5 3.8 - - - -
99D ILE* 3.9 39.0 - - + -
110D SER* 4.9 5.8 - - - +
111D ALA* 1.3 81.7 - - - +
113D LYS* 1.3 63.8 + - - +
114D ILE* 5.0 7.6 - - + -
155D ILE* 5.3 0.7 - - + -
156D VAL* 3.3 6.3 - - - +
157D GLY 2.9 33.7 + - - +
158D PHE 4.7 0.4 - - - +
159D PHE 5.7 0.7 - - - +
172D PHE* 4.3 15.3 - - + -
174D ILE* 4.0 23.8 - - + -
197D VAL* 5.3 1.1 - - + -
198D GLU 3.4 5.8 - - - +
199D ILE* 4.3 11.0 - - + -
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Residues in contact with LYS 113 (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* 4.1 12.8 - - + -
49D LEU* 4.0 17.3 - - - -
50D ASP* 2.8 31.4 + - - -
79D PHE* 4.0 22.8 - - + -
112D VAL* 1.3 75.3 - - - +
114D ILE* 1.3 67.5 + - - +
115D TYR* 4.0 12.3 - - + +
154D ALA* 4.6 9.2 - - + -
155D ILE 3.3 8.5 - - - +
156D VAL* 4.1 7.2 - - + +
196D VAL 3.6 2.1 - - - +
197D VAL* 3.4 3.8 - - - +
198D GLU* 3.0 52.7 + - + +
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Residues in contact with ILE 114 (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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95D VAL* 4.1 14.6 - - + -
96D PHE* 5.4 2.9 - - + -
99D ILE* 3.9 24.7 - - + -
112D VAL* 5.0 5.6 - - + -
113D LYS* 1.3 78.4 - - - +
115D TYR* 1.3 58.5 + - - +
118D PHE* 3.6 19.6 - - + -
154D ALA* 3.3 2.4 - - - -
155D ILE* 2.8 57.8 + - + -
174D ILE* 5.9 0.7 - - + -
190D PHE* 4.3 11.2 - - + -
192D VAL* 4.3 4.3 - - + -
195D VAL* 3.7 31.0 - - + -
196D VAL 3.6 3.1 - - - -
197D VAL* 4.2 16.6 - - + -
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Residues in contact with TYR 115 (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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113D LYS* 4.0 15.6 - - + -
114D ILE* 1.3 74.5 - - - +
116D GLY* 1.3 59.7 + - - +
152D ARG* 3.2 26.1 + - + -
153D GLY* 3.0 25.4 - - - -
154D ALA* 3.9 14.1 - - + +
179D ASP* 2.8 39.4 + - - -
195D VAL* 3.3 4.8 - - - -
196D VAL* 3.0 40.7 + - + +
198D GLU* 5.9 1.3 - - - +
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Residues in contact with GLY 116 (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* 1.3 82.5 - - - +
117D THR* 1.3 64.7 + - - -
118D PHE* 3.5 5.1 - - - -
152D ARG* 3.3 17.4 - - - +
153D GLY 3.0 33.9 + - - +
194D ASP 3.5 9.0 - - - -
195D VAL* 3.9 3.5 - - - +
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Residues in contact with THR 117 (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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116D GLY* 1.3 74.3 - - - -
118D PHE* 1.3 60.7 + - - +
150D ASP* 6.0 2.2 - - - -
151D ILE 3.5 7.0 - - - +
152D ARG* 3.6 37.2 - - + +
193D ASP* 2.8 35.1 + - - +
194D ASP* 3.0 32.5 + - + +
195D VAL* 3.4 7.3 - - - +
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Residues in contact with PHE 118 (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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114D ILE* 3.6 26.0 - - + -
116D GLY 3.5 22.9 - - - -
117D THR* 1.3 73.8 - - - +
119D LYS* 1.3 65.2 + - - +
120D HIS 3.4 10.9 + - - +
121D MSE 4.6 4.7 - - + -
150D ASP* 3.0 4.7 + - - -
151D ILE* 2.7 48.9 + - + +
153D GLY 3.6 14.1 - - - -
155D ILE* 3.4 32.1 - - + -
176D PHE* 3.8 18.8 - + - -
190D PHE* 3.9 19.1 - + + -
191D GLU 3.5 6.3 - - - +
192D VAL* 3.9 24.0 - - + -
193D ASP* 4.3 2.0 - - - -
195D VAL* 4.2 2.9 - - + -
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Residues in contact with LYS 119 (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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89D GLN* 3.6 41.2 + - - +
118D PHE* 1.3 71.9 - - - +
120D HIS* 1.3 71.9 + - + +
149D GLN* 3.2 8.0 - - - +
150D ASP* 2.9 32.5 + - - +
191D GLU* 2.7 41.6 + - - +
192D VAL 4.1 3.8 - - - +
193D ASP* 3.8 30.9 - - + +
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Residues in contact with HIS 120 (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* 3.8 8.0 - - - +
119D LYS* 1.3 91.6 + - + +
121D MSE 1.3 62.4 + - - +
148D ARG 3.6 4.6 + - - -
149D GLN* 3.4 34.7 - - + +
151D ILE* 5.3 0.2 - - - -
190D PHE* 3.2 10.8 - - - +
191D GLU* 3.1 59.2 + - + +
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Residues in contact with MSE 121 (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* 4.6 6.1 - - + -
120D HIS* 1.3 76.4 - - - +
122D HIS* 1.3 71.2 + - - +
123D VAL* 3.7 30.1 - - + -
147D LYS* 3.2 6.8 - - - +
148D ARG* 2.9 33.5 + - + +
151D ILE* 3.9 21.1 - - + -
155D ILE* 4.8 4.5 - - - -
176D PHE* 3.5 60.6 - - + -
183D TYR* 3.7 14.4 + - + +
187D VAL* 3.9 21.1 - - + -
189D ASP 4.0 1.1 - - - -
190D PHE* 4.1 9.9 - - - -
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Residues in contact with HIS 122 (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 1.3 75.9 - - - +
123D VAL* 1.3 72.4 + - - +
145D GLU* 2.8 34.6 + - + +
146D GLU 3.8 2.9 - - - -
147D LYS* 3.7 42.4 + - + -
187D VAL* 3.5 3.6 - - - +
188D LEU* 2.8 46.9 + - + +
189D ASP* 2.9 36.1 + - + +
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Residues in contact with VAL 123 (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 3.7 12.1 - - + -
122D HIS* 1.3 78.7 - - - +
124D ARG* 1.3 66.7 + - - +
125D MSE 4.4 8.0 - - - +
145D GLU* 3.2 6.8 - - - +
146D GLU 2.9 32.8 + - - +
183D TYR* 3.3 34.3 - - + +
184D GLY 3.9 9.6 - - - +
185D GLY* 2.9 36.8 - - - +
186D HIS 2.8 23.1 - - - +
187D VAL* 4.1 0.4 - - - +
188D LEU* 4.4 1.3 - - - +
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Residues in contact with ARG 124 (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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45D GLU* 2.9 22.0 + - - +
123D VAL* 1.3 80.7 - - - +
125D MSE 1.3 66.9 + - - +
126D MSE 3.5 35.5 - - - +
143D GLN* 2.8 55.8 + - - +
144D PRO 3.3 10.3 - - - +
145D GLU* 3.9 0.9 - - + -
186D HIS* 2.9 61.3 + - + +
188D LEU* 3.7 10.0 - - + +
233D ALA 3.0 20.6 + - - -
234D GLU* 3.4 17.6 + - - -
804D ZN 4.1 5.7 - - - -
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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