Contacts of the strand formed by residues 162 - 167 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101P LEU* 3.8 18.8 - - + -
105P LEU* 3.7 26.5 - - + -
111P PHE* 3.3 15.3 - - + -
113P TYR* 4.2 12.3 - - + -
151P VAL* 3.7 27.4 - - + -
154P ILE* 3.9 13.2 - - + -
155P LEU* 4.0 14.5 - - + +
158P ALA* 3.7 18.4 - - + -
160P SER 3.3 5.6 + - - +
161P GLN* 1.3 79.4 - - - +
163P VAL* 1.3 63.0 + - - +
230P SER* 3.0 11.0 + - - -
231P GLY 2.9 24.7 + - - +
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Residues in contact with VAL 163 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111P PHE 2.9 7.9 + - - -
112P LEU* 3.3 12.9 - - + +
113P TYR* 2.7 40.4 + - - +
161P GLN* 3.5 18.2 - - + +
162P ILE* 1.3 79.4 - - - +
164P GLY* 1.3 58.2 + - - +
165P PHE* 3.5 34.1 - - + -
224P PHE* 4.1 6.5 - - + -
229P VAL 3.0 29.4 - - - +
230P SER* 4.1 1.8 - - - -
231P GLY 3.2 9.4 - - - +
233P PHE* 4.0 11.9 - - + -
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Residues in contact with GLY 164 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113P TYR* 3.4 33.5 - - - -
115P SER* 4.8 1.3 - - - -
151P VAL* 6.0 0.2 - - - +
163P VAL* 1.3 76.9 - - - +
165P PHE* 1.3 63.4 + - - -
166P ARG 3.7 0.4 + - - -
231P GLY 2.9 9.3 + - - +
232P ILE* 3.4 8.5 - - - +
233P PHE* 2.9 28.9 + - - +
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Residues in contact with PHE 165 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112P LEU* 4.2 12.6 - - + -
113P TYR 2.9 18.5 + - - +
114P ALA* 3.8 2.1 - - - -
115P SER* 2.8 24.3 + - - +
163P VAL* 3.5 25.4 - - + -
164P GLY* 1.3 72.3 - - - -
166P ARG* 1.3 60.7 + - - +
167P TYR* 3.1 34.4 + + + -
220P VAL* 3.6 18.6 - - + -
221P ASN* 3.3 36.6 - - - -
224P PHE* 3.5 46.2 - + + -
233P PHE* 3.5 11.0 - + + -
234P ASN 5.6 0.2 - - - -
235P LEU* 4.1 8.1 - - + -
283P LEU* 5.8 0.4 - - + -
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Residues in contact with ARG 166 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115P SER* 3.3 15.1 + - - +
116P SER 3.3 20.6 - - - +
117P ALA* 3.6 3.6 - - - +
119P THR* 3.2 17.6 + - - -
120P TYR* 3.1 45.9 + - + -
129P GLU* 3.8 7.6 - - - +
134P GLU* 2.8 38.4 + - - -
145P PHE* 5.6 0.2 - - - -
148P ASP* 2.8 29.1 + - - +
152P ARG* 4.0 2.2 - - - +
164P GLY 3.7 1.4 + - - -
165P PHE* 1.3 70.6 - - - +
167P TYR* 1.3 63.2 + - - +
168P PHE* 3.2 8.1 - - - -
232P ILE* 4.1 17.6 - - + +
233P PHE 2.7 18.4 + - - +
234P ASN* 3.7 7.4 - - - +
235P LEU* 2.9 19.9 + - - +
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Residues in contact with TYR 167 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11P ILE* 3.5 24.7 - - + +
75P GLU* 2.8 31.0 + - - -
114P ALA* 3.5 17.6 - - + +
115P SER 4.1 3.2 + - - -
116P SER* 4.2 0.2 + - - -
117P ALA 3.0 22.2 + - - -
165P PHE* 3.1 32.5 + - + -
166P ARG* 1.3 71.4 - - - +
168P PHE* 1.3 63.4 - - - +
170P VAL* 3.7 9.0 - - + -
217P VAL* 3.6 20.9 - - + -
221P ASN* 3.1 21.3 + - - -
235P LEU* 3.5 28.9 - - + -
400P NAP 3.5 35.5 - + + -
402P BMA 4.8 0.3 + - - -
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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