Contacts of the strand formed by residues 162 - 167 (chain S) in PDB entry 2X86
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 ILE 162 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101S LEU* 3.8 19.1 - - + -
105S LEU* 3.7 26.9 - - + -
111S PHE* 3.3 14.8 - - + -
113S TYR* 4.2 12.1 - - + -
151S VAL* 3.7 26.7 - - + -
154S ILE* 3.9 13.0 - - + -
155S LEU* 4.0 14.2 - - + +
158S ALA* 3.7 18.8 - - + -
160S SER 3.3 6.0 + - - +
161S GLN* 1.3 79.4 - - - +
163S VAL* 1.3 64.8 + - - +
230S SER* 3.0 10.7 + - - -
231S GLY* 2.9 24.6 + - - +
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Residues in contact with VAL 163 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111S PHE 2.9 7.5 + - - -
112S LEU* 3.3 12.9 - - + -
113S TYR* 2.7 39.8 + - - +
161S GLN* 3.5 17.7 - - + +
162S ILE* 1.3 79.5 - - - +
164S GLY* 1.3 58.1 + - - +
165S PHE* 3.5 34.5 - - + -
224S PHE* 4.1 6.5 - - + -
229S VAL 3.0 28.7 - - - +
230S SER* 4.1 1.8 - - - -
231S GLY 3.2 9.9 - - - +
233S PHE* 4.0 11.7 - - + -
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Residues in contact with GLY 164 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113S TYR* 3.4 33.8 - - - -
115S SER* 4.8 1.6 - - - -
162S ILE* 5.3 0.2 - - - +
163S VAL* 1.3 77.4 - - - +
165S PHE* 1.3 64.1 + - - -
166S ARG 3.7 0.3 + - - -
231S GLY 2.9 10.3 + - - +
232S ILE* 3.4 7.9 - - - +
233S PHE 2.9 27.9 + - - +
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Residues in contact with PHE 165 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112S LEU* 4.2 13.0 - - + -
113S TYR 2.9 18.3 + - - +
114S ALA* 3.8 1.9 - - - -
115S SER* 2.8 25.3 + - - +
163S VAL* 3.5 24.9 - - + -
164S GLY* 1.3 72.9 - - - -
166S ARG* 1.3 59.6 + - - +
167S TYR* 3.1 35.2 + + + -
220S VAL* 3.6 18.4 - - + -
221S ASN* 3.3 37.7 - - - -
224S PHE* 3.4 46.4 - + + -
233S PHE* 3.5 11.7 - + + -
235S LEU* 4.1 8.3 - - + -
283S LEU* 5.8 0.2 - - + -
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Residues in contact with ARG 166 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115S SER* 3.3 14.7 + - - +
116S SER 3.3 21.5 - - - +
117S ALA* 3.6 3.1 - - - +
119S THR* 3.2 18.1 + - - -
120S TYR* 3.1 44.8 + - + -
129S GLU* 3.8 7.6 - - - +
134S GLU* 2.8 37.6 + - - -
145S PHE* 5.6 0.4 - - - -
148S ASP* 2.8 29.7 + - - +
152S ARG* 3.9 2.4 - - - +
164S GLY 3.7 1.0 + - - -
165S PHE* 1.3 70.9 - - - +
167S TYR* 1.3 63.3 + - - +
168S PHE* 3.2 8.7 - - - -
232S ILE* 4.1 18.3 - - + +
233S PHE 2.7 19.4 + - - +
234S ASN* 3.7 7.9 - - - +
235S LEU 2.9 19.3 + - - -
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Residues in contact with TYR 167 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S ILE* 3.5 24.6 - - + +
75S GLU* 2.8 31.6 + - - -
114S ALA* 3.5 17.4 - - + +
115S SER 4.1 3.0 + - - -
117S ALA* 3.0 22.7 + - - +
165S PHE* 3.1 31.0 + - + -
166S ARG* 1.3 72.7 - - - +
168S PHE* 1.3 64.2 + - - +
170S VAL* 3.7 12.3 - - + -
217S VAL* 3.6 20.6 - - + -
221S ASN* 3.1 21.0 + - - -
235S LEU* 3.5 29.6 - - + -
400S NAP 3.5 32.7 - + + -
402S BMA 4.6 0.2 + - - -
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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