Contacts of the strand formed by residues 162 - 167 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101L LEU* 3.8 18.2 - - + -
105L LEU* 3.7 26.5 - - + -
111L PHE* 3.3 15.5 - - + -
113L TYR* 4.2 12.1 - - + -
151L VAL* 3.7 26.7 - - + -
154L ILE* 3.9 13.2 - - + -
155L LEU* 4.0 14.5 - - + +
158L ALA* 3.7 18.6 - - + -
160L SER 3.3 5.8 + - - +
161L GLN* 1.3 79.6 - - - +
163L VAL* 1.3 63.5 + - - +
164L GLY 5.3 0.2 - - - +
230L SER* 3.0 10.3 + - - -
231L GLY* 2.9 24.1 + - - +
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Residues in contact with VAL 163 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111L PHE 2.9 7.5 + - - -
112L LEU* 3.3 13.8 - - + -
113L TYR* 2.7 40.4 + - - +
161L GLN* 3.5 18.4 - - + +
162L ILE* 1.3 78.5 - - - +
164L GLY* 1.3 58.1 - - - +
165L PHE* 3.5 34.5 - - + -
224L PHE* 4.1 6.5 - - + -
229L VAL 3.0 29.6 - - - +
230L SER* 4.1 1.1 - - - -
231L GLY 3.2 9.6 - - - +
233L PHE* 4.0 12.3 - - + -
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Residues in contact with GLY 164 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113L TYR* 3.4 33.2 - - - -
115L SER* 4.8 1.3 - - - -
162L ILE* 5.3 0.2 - - - +
163L VAL* 1.3 77.7 - - - +
165L PHE* 1.3 63.6 + - - -
166L ARG 3.7 0.4 + - - -
231L GLY 2.9 9.5 + - - +
232L ILE* 3.4 7.9 - - - +
233L PHE* 2.9 28.8 + - - +
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Residues in contact with PHE 165 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L LEU* 4.2 12.6 - - + -
113L TYR 2.9 17.2 + - - +
114L ALA* 3.8 2.1 - - - -
115L SER* 2.8 24.1 + - - +
163L VAL* 3.5 24.9 - - + -
164L GLY* 1.3 71.8 - - - -
166L ARG* 1.3 61.6 + - - +
167L TYR* 3.1 34.9 + + + -
220L VAL* 3.6 18.6 - - + -
221L ASN* 3.3 37.5 - - - -
224L PHE* 3.5 47.1 - + + -
233L PHE* 3.5 11.7 - + + -
235L LEU* 4.1 8.1 - - + -
283L LEU* 5.8 0.2 - - + -
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Residues in contact with ARG 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115L SER* 3.3 15.7 + - - +
116L SER 3.3 21.1 - - - +
117L ALA* 3.6 3.4 - - - +
119L THR* 3.2 17.1 + - - +
120L TYR* 3.1 44.6 + - - -
129L GLU* 3.8 8.0 - - - +
134L GLU* 2.8 36.4 + - - -
145L PHE* 5.6 0.4 - - - -
148L ASP* 2.8 29.7 + - - +
152L ARG* 3.9 2.8 - - - +
164L GLY 3.7 1.0 + - - -
165L PHE* 1.3 70.2 - - - +
167L TYR* 1.3 63.3 + - - +
168L PHE* 3.2 8.1 - - - -
232L ILE* 4.1 17.0 - - + +
233L PHE 2.7 19.2 + - - +
234L ASN* 3.7 8.1 - - - +
235L LEU* 2.9 20.6 + - - +
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Residues in contact with TYR 167 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L ILE* 3.5 24.1 - - + +
75L GLU* 2.8 30.9 + - - -
114L ALA* 3.5 17.6 - - + +
115L SER 4.1 3.4 + - - -
117L ALA* 3.0 21.8 + - - +
165L PHE* 3.1 29.8 + - + -
166L ARG* 1.3 71.2 - - - +
168L PHE* 1.3 63.6 + - - +
170L VAL* 3.7 9.0 - - + -
217L VAL* 3.6 21.1 - - + -
221L ASN* 3.1 21.8 + - - -
235L LEU* 3.5 28.9 - - + -
400L NAP 3.3 36.8 - + + -
402L BMA 4.7 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