Contacts of the strand formed by residues 167 - 176 (chain A) in PDB entry 2XN9
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 PHE 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ASN* 5.4 17.5 - - + -
137A ASP* 4.6 7.4 - - - -
161A ASP* 3.6 4.7 + - - +
162A MET* 2.7 49.2 + - + +
165A MET* 3.1 22.4 - - + +
166A ASP* 1.3 78.9 - - - +
168A LYS* 1.3 70.1 + - - +
169A SER* 3.5 27.1 - - - -
138B THR* 6.5 0.2 - - - -
140B LYS* 3.5 37.5 - - + +
195B ARG* 3.6 15.9 - - - -
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Residues in contact with LYS 168 (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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15A GLU* 5.1 3.0 + - - -
81A PRO* 4.0 27.1 - - - +
110A PRO* 4.1 18.3 - - + +
111A ASN 4.9 6.7 - - - +
112A ILE* 4.2 21.4 - - + +
113A GLN 5.9 0.2 + - - -
159A VAL* 4.2 13.5 - - + -
160A LEU 3.4 7.9 - - - +
161A ASP* 4.0 27.1 + - + +
166A ASP 5.9 0.4 - - - -
167A PHE* 1.3 88.6 - - - +
169A SER* 1.3 65.9 + - - +
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Residues in contact with SER 169 (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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112A ILE* 4.4 6.3 - - - -
136A THR* 4.8 0.3 + - - -
137A ASP* 3.5 27.4 - - - +
158A CYS 3.6 0.7 - - - +
159A VAL* 3.3 6.7 - - - -
160A LEU* 3.0 53.1 + - - +
167A PHE* 3.5 7.2 - - - -
168A LYS* 1.3 78.4 - - - +
170A ASN* 1.3 63.6 + - - +
195B ARG* 3.0 18.8 + - - -
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Residues in contact with ASN 170 (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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112A ILE* 3.7 8.5 - - - +
136A THR* 3.1 19.1 + - - -
137A ASP* 3.1 10.2 + - - +
138A PHE* 3.0 51.4 + - + +
139A ASP 3.7 2.6 + - - -
140A SER* 3.3 32.3 + - - +
157A LYS* 4.6 12.1 - - + +
158A CYS 3.4 5.0 - - - +
159A VAL* 2.9 28.6 - - - +
160A LEU* 6.2 0.2 - - - -
169A SER* 1.3 75.6 - - - +
171A SER* 1.3 59.9 + - - +
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Residues in contact with SER 171 (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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134A LEU* 3.9 13.9 - - - -
135A PHE 3.1 13.9 - - - -
136A THR* 3.8 9.9 - - - -
138A PHE* 3.8 4.7 - - - -
157A LYS* 3.2 4.9 - - - -
158A CYS 3.0 30.1 + - - +
160A LEU* 5.0 5.4 - - - +
170A ASN* 1.3 77.6 - - - +
172A ALA* 1.3 62.0 + - - +
142B THR* 6.1 0.4 - - - -
193B ARG* 2.7 40.8 + - - +
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Residues in contact with ALA 172 (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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134A LEU* 3.6 4.3 - - - +
135A PHE* 2.8 34.2 + - + +
144A VAL* 3.8 30.7 - - + -
155A THR 3.7 17.0 - - - +
156A ASP 4.0 8.3 - - - +
157A LYS* 4.3 0.2 - - - -
171A SER* 1.3 76.6 - - - +
173A VAL* 1.3 65.2 + - - +
187A PHE* 3.6 10.9 - - + -
193B ARG* 4.0 2.5 - - - +
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Residues in contact with VAL 173 (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 VAL* 4.0 19.3 - - + -
133A CYS 3.5 9.0 - - - +
134A LEU* 4.2 15.0 - - + -
153A TYR 3.8 0.7 - - - +
154A ILE* 3.3 3.8 - - - +
155A THR* 3.0 38.4 + - + +
172A ALA* 1.3 78.8 - - - +
174A ALA* 1.3 63.9 + - - +
175A TRP* 3.9 17.7 - - + -
187A PHE* 4.2 1.1 - - - -
144B VAL* 4.2 22.0 - - + -
146B LEU* 4.3 2.9 - - + -
191B SER* 4.0 21.3 - - - +
193B ARG* 4.1 15.3 - - - +
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Residues in contact with ALA 174 (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 VAL* 3.6 1.4 - - - +
133A CYS* 2.8 34.2 + - + +
153A TYR 3.0 9.4 - - - +
154A ILE* 4.0 12.3 - - + -
173A VAL* 1.3 76.2 - - - +
175A TRP* 1.3 63.4 + - - +
181A PHE* 4.0 5.8 - - + -
186A ALA* 3.9 21.3 - - + -
187A PHE* 3.5 25.5 - - + -
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Residues in contact with TRP 175 (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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131A SER 3.9 15.5 - - - +
132A VAL* 4.1 7.9 - - + -
152A VAL* 3.6 1.0 - - - +
153A TYR* 2.7 82.5 + + + -
155A THR* 3.5 33.0 - - + -
173A VAL* 3.9 8.1 - - + -
174A ALA* 1.3 79.3 - - - +
176A SER* 1.3 68.2 + - - +
181A PHE* 4.0 10.0 - - - -
146B LEU* 3.6 41.7 - - + +
148B THR* 4.2 15.6 - - + +
177B LEU* 4.1 6.3 - - + -
179B GLU* 5.7 0.4 + - - -
189B SER* 3.7 27.8 - - - -
190B LEU 5.0 3.1 - - - -
191B SER* 4.9 1.8 - - - -
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Residues in contact with SER 176 (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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131A SER 4.5 9.3 + - - +
151A ASP 2.5 25.6 + - - -
152A VAL* 3.8 3.8 - - - +
153A TYR* 5.1 2.5 - - - -
175A TRP* 1.3 85.2 - - - +
177A ASN* 1.3 67.3 + - - +
178A LYS* 3.2 18.7 + - - +
181A PHE* 3.5 38.2 - - - -
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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