Contacts of the strand formed by residues 110 - 124 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A MSE 4.0 15.5 - - - +
105A SER 5.7 1.3 - - - -
108A LEU 4.8 1.6 - - - -
109A PHE* 1.3 77.6 - - - +
111A ALA* 1.3 61.5 + - - +
112A VAL* 5.0 3.6 - - - +
158A PHE* 3.2 7.4 - - - +
159A PHE* 2.8 52.2 + - - +
199A ILE* 4.5 9.1 - - - +
200A GLN 3.1 13.2 - - - -
201A ASN* 4.2 13.9 - - - -
202A PHE* 3.6 6.7 - - - -
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.7 2.0 - - + -
77A THR* 4.3 1.6 - - + -
79A PHE* 3.9 22.6 - - + -
110A SER* 1.3 73.9 - - - +
112A VAL* 1.3 66.4 + - - +
157A GLY 3.5 5.8 - - - +
158A PHE* 3.6 15.0 - - + -
199A ILE* 3.3 6.6 - - - +
200A GLN* 2.8 30.4 + - + +
202A PHE* 3.5 25.3 - - + -
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 4.5 4.3 - - - +
79A PHE* 4.6 3.1 - - - -
96A PHE* 6.4 0.4 - - + -
99A ILE* 3.8 39.0 - - + -
110A SER* 5.0 4.5 - - - +
111A ALA* 1.3 81.9 - - - +
113A LYS* 1.3 63.7 + - - +
114A ILE* 4.9 12.3 - - + -
155A ILE 5.3 0.4 - - - +
156A VAL* 3.5 6.4 - - - +
157A GLY 3.1 35.3 + - - +
158A PHE 4.7 0.7 - - - +
159A PHE* 5.8 0.9 - - + +
172A PHE* 4.3 13.2 - - + -
174A ILE* 4.1 17.7 - - + -
197A VAL* 5.3 0.9 - - + -
198A GLU 3.2 8.5 - - - +
199A ILE* 4.5 6.7 - - + -
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.0 19.7 - - + +
49A LEU* 4.1 21.1 - - - +
50A ASP* 3.6 23.4 + - - +
79A PHE* 3.9 24.4 - - + -
112A VAL* 1.3 75.9 - - - +
114A ILE* 1.3 65.6 + - - +
115A TYR* 4.0 10.8 - - + +
154A ALA* 5.0 8.1 - - + -
155A ILE 3.3 8.3 - - - +
156A VAL* 4.4 2.9 - - + +
196A VAL 3.5 1.4 - - - +
197A VAL* 3.4 4.2 - - - -
198A GLU* 2.8 56.4 + - + +
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Residues in contact with ILE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A VAL* 4.1 14.8 - - + -
96A PHE* 5.5 3.4 - - + -
99A ILE* 4.0 22.2 - - + -
112A VAL* 4.9 6.3 - - + -
113A LYS* 1.3 79.4 - - - +
115A TYR* 1.3 60.3 + - - +
118A PHE* 3.7 22.6 - - + -
154A ALA* 3.3 2.2 - - - -
155A ILE* 2.8 57.3 + - + +
174A ILE* 5.6 1.1 - - + -
190A PHE* 4.5 11.0 - - + -
192A VAL* 4.4 4.3 - - + -
195A VAL* 3.7 27.4 - - + -
196A VAL 3.4 3.8 - - - +
197A VAL* 4.2 16.6 - - + -
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Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS* 4.0 12.5 - - + -
114A ILE* 1.3 74.6 - - - +
116A GLY* 1.3 66.1 + - - +
152A ARG* 2.7 31.5 + - - -
153A GLY* 2.9 24.9 - - - -
154A ALA* 3.7 13.9 - - + -
179A ASP* 2.6 43.1 + - - -
195A VAL* 3.2 5.2 - - - -
196A VAL* 2.9 40.4 + - + +
198A GLU* 5.9 1.8 - - - +
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Residues in contact with GLY 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A TYR* 1.3 91.0 - - - +
117A THR* 1.3 65.0 + - - -
118A PHE* 3.7 2.9 - - - -
152A ARG* 3.3 8.1 - - - +
153A GLY 3.1 29.3 + - - +
194A ASP 3.4 9.4 - - - -
195A VAL* 3.7 3.9 - - - +
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Residues in contact with THR 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLY* 1.3 76.5 - - - +
118A PHE* 1.3 61.5 + - - +
150A ASP* 5.7 3.4 - - - -
151A ILE 3.5 6.7 - - - -
152A ARG* 4.3 22.0 - - + +
193A ASP* 2.9 34.9 + - - +
194A ASP* 2.8 32.5 + - + +
195A VAL* 3.4 7.4 - - - +
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Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ILE* 3.7 28.0 - - + -
116A GLY 3.7 9.2 - - - -
117A THR* 1.3 75.1 - - - +
119A LYS* 1.3 60.7 + - - +
120A HIS 3.4 9.6 + - - +
121A MSE 3.7 13.2 - - + -
149A GLN 3.9 0.3 - - - -
150A ASP* 2.9 22.4 + - - -
151A ILE* 2.8 36.6 + - + +
153A GLY 3.6 15.9 - - - -
155A ILE* 3.6 24.9 - - + -
176A PHE* 3.6 27.6 - + - -
190A PHE* 3.9 7.4 - + + -
191A GLU 3.4 6.5 - - - +
192A VAL* 3.6 32.1 - - + -
193A ASP* 4.4 1.1 - - - -
195A VAL* 3.9 4.9 - - + -
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Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLN* 2.7 38.8 + - - +
118A PHE* 1.3 72.7 - - - +
120A HIS* 1.3 60.7 + - - +
149A GLN* 3.2 13.2 - - - +
150A ASP* 3.0 31.8 + - - +
191A GLU* 2.7 39.1 + - + +
192A VAL 3.8 7.2 - - - +
193A ASP* 3.5 27.3 - - + +
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Residues in contact with HIS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A PHE* 3.9 6.3 - - - +
119A LYS* 1.3 81.9 - - - +
121A MSE 1.3 74.4 + - - +
122A HIS* 3.9 13.9 + - + +
147A LYS* 3.9 30.5 + - + +
148A ARG 3.6 9.4 + - - -
149A GLN* 4.8 7.6 - - + +
189A ASP* 4.0 17.1 + - - -
190A PHE* 3.2 13.7 - - - +
191A GLU* 2.8 42.4 + - + +
66C LYS* 3.8 47.9 + - + +
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Residues in contact with MSE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A PHE* 3.7 21.1 - - + -
120A HIS* 1.3 76.4 - - - +
122A HIS* 1.3 67.3 + - - +
123A VAL* 4.1 3.1 - - + -
147A LYS* 3.1 7.1 - - - +
148A ARG 2.9 34.8 + - - +
151A ILE* 4.1 17.7 - - + -
155A ILE* 3.7 19.7 - - + -
176A PHE* 3.4 45.1 - - + -
183A TYR* 3.6 27.9 + - + +
187A VAL* 3.9 19.7 - - - -
189A ASP 3.8 1.3 - - - +
190A PHE* 3.9 11.0 - - + -
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Residues in contact with HIS 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A HIS* 3.9 15.4 + - - +
121A MSE 1.3 75.4 - - - +
123A VAL* 1.3 77.4 + - - +
145A GLU* 2.6 33.6 + - + +
146A GLU 3.8 3.1 - - - -
147A LYS* 3.7 30.1 + - + -
187A VAL* 3.7 0.9 - - - +
188A LEU* 2.8 41.6 + - + +
189A ASP* 2.8 33.9 + - + +
64C GLU* 3.6 19.9 - - - -
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A MSE 4.1 16.4 - - + -
122A HIS* 1.3 82.6 - - - +
124A ARG* 1.3 61.8 + - - +
125A MSE 4.4 8.7 - - - -
145A GLU* 3.2 7.8 - - - +
146A GLU 3.0 30.4 + - - +
176A PHE* 4.3 4.0 - - + -
183A TYR* 3.4 28.3 - - + +
184A GLY 3.6 20.6 - - - +
185A GLY* 3.9 17.0 - - - +
186A HIS 3.1 15.3 - - - +
187A VAL* 4.0 11.4 - - + -
188A LEU* 4.3 1.8 - - - +
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Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLU* 2.9 22.9 + - - +
123A VAL* 1.3 75.7 - - - +
125A MSE 1.3 64.6 + - - +
126A MSE 3.3 34.8 - - - +
140A ALA* 4.4 0.2 - - - +
143A GLN* 2.7 55.0 + - - +
144A PRO 3.3 12.8 - - - +
145A GLU* 3.8 4.7 - - + +
185A GLY* 3.6 3.1 - - - -
186A HIS* 3.0 71.3 + - + +
188A LEU* 4.0 6.5 - - + +
233A ALA 2.9 20.4 + - - -
234A GLU* 3.6 14.5 - - - +
801A ZN 4.0 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