Contacts of the strand formed by residues 184 - 195 (chain A) in PDB entry 2XVA
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 ARG 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A GLU* 3.0 52.8 + - + +
175A LEU 3.3 19.4 + - - +
176A HIS* 3.0 53.9 + - - +
177A ARG 3.7 5.8 - - - -
178A THR* 4.1 7.4 - - + -
179A ASP* 4.8 1.6 - - - +
182A GLY 3.9 1.6 + - - +
183A ASN* 1.3 77.8 + - - +
185A ILE* 1.3 63.7 + - - +
186A LYS* 3.4 12.1 + - - +
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Residues in contact with ILE 185 (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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144A THR* 3.4 26.7 - - - +
145A VAL* 4.1 18.2 - - + -
174A GLU* 3.2 3.9 - - - -
175A LEU* 2.8 48.7 + - + +
177A ARG* 3.2 37.6 + - + +
178A THR 4.2 17.3 - - - +
179A ASP* 4.2 13.2 - - + +
183A ASN 4.3 0.2 - - - -
184A ARG* 1.3 70.0 - - - +
186A LYS* 1.3 71.5 + - - +
187A LEU* 3.8 3.7 + - + -
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Residues in contact with LYS 186 (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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141A TYR* 4.3 30.5 - - + +
142A PRO 4.9 6.1 - - - +
144A THR* 5.1 0.9 + - - +
172A VAL* 4.4 8.2 - - + +
173A GLY 3.4 10.8 - - - +
174A GLU* 3.7 22.5 + - + +
184A ARG 3.4 8.9 + - - +
185A ILE* 1.3 80.3 - - - +
187A LEU* 1.3 64.7 + - - +
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Residues in contact with LEU 187 (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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135A ALA* 3.6 26.5 - - + -
136A MET 3.7 14.4 - - - +
141A TYR* 4.3 11.9 - - + +
142A PRO 5.6 2.9 - - - +
143A CYS* 5.2 7.2 - - - -
144A THR 6.0 0.2 - - - +
145A VAL* 4.9 3.6 - - + -
147A PHE* 3.7 17.9 - - + -
172A VAL* 4.2 4.4 - - - +
173A GLY* 2.6 39.5 + - - +
175A LEU* 4.4 14.8 - - + -
185A ILE* 3.8 6.7 + - + +
186A LYS* 1.3 76.5 - - - +
188A ARG* 1.3 89.1 + - - +
189A PHE* 3.4 26.5 - - + -
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Residues in contact with ARG 188 (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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136A MET* 2.9 33.3 + - + -
138A THR* 4.0 20.2 - - + -
140A ASP* 2.8 34.9 + - - -
141A TYR* 3.7 21.0 - - + +
153A GLU* 6.6 0.2 - - - -
170A GLU* 2.9 36.9 + - - +
171A ASP* 3.4 7.3 + - - +
172A VAL* 3.9 26.6 - - + +
187A LEU* 1.3 96.4 - - - +
189A PHE* 1.3 56.4 + - - +
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Residues in contact with PHE 189 (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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103A VAL* 4.1 18.2 - - + -
106A MET* 4.6 5.4 - - + -
133A VAL* 4.3 20.0 - - + -
134A ALA* 3.4 8.1 - - - +
135A ALA* 3.5 27.4 - - + -
136A MET* 3.7 3.6 - - - -
169A ASN* 3.5 1.9 - - - +
170A GLU* 3.2 20.6 - - - -
171A ASP 2.9 11.6 + - - +
173A GLY* 4.0 9.9 - - - -
174A GLU 4.1 26.2 - - - -
175A LEU* 4.2 20.4 - - + -
187A LEU* 3.4 32.5 - - + -
188A ARG* 1.3 72.5 - - - +
190A ALA* 1.3 61.5 + - - +
191A THR* 3.5 7.8 + - - +
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Residues in contact with ALA 190 (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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132A ILE 3.5 2.3 - - - +
133A VAL* 3.2 5.7 - - - +
134A ALA 2.8 37.1 + - - +
136A MET* 3.5 22.6 - - + -
151A PHE* 4.1 14.4 - - + -
156A LEU* 3.8 28.1 - - + +
168A TYR* 4.6 1.8 - - - +
169A ASN 3.6 5.6 - - - +
170A GLU* 4.4 5.2 - - + +
189A PHE* 1.3 71.6 - - - +
191A THR* 1.3 59.0 + - - +
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Residues in contact with THR 191 (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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21A GLU* 3.7 34.8 + - + +
131A LEU* 4.9 1.8 - - + -
132A ILE 3.5 2.5 - - - -
133A VAL* 3.8 26.4 - - + +
167A LYS* 3.8 9.3 - - + +
168A TYR* 3.1 6.0 - - - -
169A ASN* 2.8 57.3 + - - +
189A PHE* 3.5 6.8 + - - +
190A ALA* 1.3 75.1 + - - +
192A MET* 1.3 65.7 + - - +
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Residues in contact with MET 192 (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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130A ASN* 3.6 13.3 - - + +
131A LEU* 3.3 9.5 - - - +
132A ILE* 3.0 43.3 + - + +
156A LEU* 3.7 22.2 - - + +
160A TYR* 3.5 63.5 - - + -
165A ARG* 5.1 5.4 - - + -
167A LYS 3.1 10.3 - - - +
168A TYR* 3.6 19.5 - - + -
191A THR* 1.3 79.1 - - - +
193A LEU* 1.3 62.6 + - - +
194A ALA* 3.6 21.1 - - + -
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Residues in contact with LEU 193 (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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24A GLU 5.5 0.2 - - - +
25A ALA* 4.0 26.7 - - + -
28A VAL* 4.3 16.8 - - + -
29A VAL* 4.2 7.6 - - + -
98A PHE* 4.3 2.7 - - + -
129A TYR* 3.9 27.4 - - + -
130A ASN 3.5 12.3 - - - +
131A LEU* 4.1 22.4 - - + -
165A ARG 3.6 0.7 - - - -
166A VAL* 2.9 43.8 + - + +
167A LYS* 2.8 29.9 + - + +
192A MET* 1.3 72.8 - - - +
194A ALA* 1.3 59.9 + - - +
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Residues in contact with ALA 194 (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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129A TYR* 3.2 8.4 - - - +
130A ASN 2.9 33.2 + - - +
160A TYR* 4.0 4.5 - - + -
163A TRP* 3.6 24.5 - - + -
164A GLU 3.1 11.7 - - - +
165A ARG* 4.5 2.9 - - + -
166A VAL 4.4 0.2 - - - +
192A MET* 3.6 32.1 - - + -
193A LEU* 1.3 75.8 - - - +
195A ARG* 1.3 59.7 + - - +
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Residues in contact with ARG 195 (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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127A GLY* 2.9 32.0 + - - +
128A GLY 3.4 10.1 - - - +
129A TYR* 3.3 41.1 + - + -
163A TRP* 3.5 5.1 - - - -
164A GLU* 2.7 58.8 + - + +
166A VAL* 4.4 2.9 - - + +
194A ALA* 1.3 74.3 - - - +
196A LYS* 1.3 70.2 + - - +
197A LYS* 3.8 0.5 + - - +
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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