Contacts of the strand formed by residues 162 - 168 (chain B) in PDB entry 1R88
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 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B TYR* 3.8 34.3 - + - -
120B LEU 3.5 24.9 - - - -
121B SER* 4.4 4.5 - - - -
125B PRO* 5.6 1.8 - - + -
139B HIS* 3.2 16.6 - + + +
140B ALA 3.9 22.4 - - - -
141B ALA* 4.0 10.1 - - + +
154B LEU* 3.9 37.2 - - + -
155B ALA* 3.9 26.0 - - + +
158B HIS* 3.2 9.3 + - + -
159B PRO* 3.3 21.8 + - - +
161B ARG* 1.3 97.7 - - + +
163B GLY* 1.3 60.6 + - - +
164B PHE 3.4 6.7 + - - +
224B THR* 4.4 2.6 + - - +
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Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B GLY* 4.3 8.2 - - - -
139B HIS 2.9 13.0 + - - +
159B PRO 4.3 3.8 + - - -
162B PHE* 1.3 71.6 - - - +
164B PHE* 1.3 59.2 + - - +
223B ASN 4.9 0.3 - - - +
224B THR* 3.8 11.7 - - - +
225B ARG* 3.1 24.3 + - - +
297B ALA* 5.1 2.5 - - - +
298B ILE* 5.3 2.9 - - - -
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Residues in contact with PHE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B HIS 3.4 1.6 + - - +
140B ALA* 3.4 26.9 - - + -
141B ALA* 2.9 27.2 + - - +
142B VAL* 3.8 8.7 - - + -
155B ALA* 4.7 1.1 - - - -
162B PHE* 3.4 6.0 - - - +
163B GLY* 1.3 81.3 - - - +
165B ALA* 1.3 66.2 + - - +
166B GLY* 3.8 19.1 - - - -
224B THR* 4.2 2.0 - - - +
225B ARG* 3.3 29.2 - - + -
227B TRP* 3.8 21.8 - + + -
290B MET* 4.3 5.4 - - - -
293B ASP* 3.4 32.5 - - - -
294B ILE* 3.6 26.5 - - + -
297B ALA* 3.8 12.6 - - + -
298B ILE* 4.1 9.2 - - + -
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ALA 3.3 4.3 - - - -
151B ALA 3.6 22.9 - - - +
152B MET* 3.7 28.9 - - - +
155B ALA* 3.7 11.9 - - + -
164B PHE* 1.3 78.1 - - - +
166B GLY* 1.3 58.7 + - - +
224B THR* 4.3 3.6 - - + +
225B ARG 2.9 9.6 + - - +
226B VAL* 3.4 3.7 - - + -
227B TRP* 2.9 26.0 + - - +
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Residues in contact with GLY 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ALA 2.8 13.8 + - - -
142B VAL* 3.3 12.1 - - - -
143B GLY 3.1 25.3 + - - +
151B ALA* 3.5 8.9 - - - +
152B MET* 4.9 0.4 - - - -
164B PHE* 3.8 12.6 - - - -
165B ALA* 1.3 73.7 - - - +
167B SER* 1.3 60.7 + - - -
227B TRP* 3.3 9.6 - - - -
290B MET* 4.6 4.0 - - - -
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Residues in contact with SER 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B GLY 3.6 3.1 - - - -
148B GLY* 3.5 18.8 - - - -
152B MET* 4.1 11.4 - - - -
166B GLY* 1.3 74.6 - - - -
168B MET* 1.3 64.2 + - - +
170B GLY* 3.3 26.0 + - - -
172B LEU* 3.5 21.8 - - - +
227B TRP* 2.8 11.1 + - - +
228B VAL* 3.5 3.2 - - - +
229B TRP* 2.8 28.7 + - - +
253B SER* 4.9 0.7 + - - -
290B MET* 5.0 0.8 - - - +
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Residues in contact with MET 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B TRP* 3.7 20.9 - - + -
142B VAL* 4.3 7.0 - - + -
143B GLY 3.0 12.1 + - - +
144B ALA* 3.2 3.9 - - - +
145B ALA 3.0 19.2 + - - -
167B SER* 1.3 76.5 + - - +
169B SER* 1.3 72.5 + - - +
170B GLY* 3.2 0.7 + - - -
229B TRP* 3.4 9.4 - - + -
283B TRP* 3.6 58.1 - - + +
286B GLN* 3.8 16.4 - - + -
287B LEU* 3.7 18.6 - - + +
290B MET* 3.7 27.6 - - + -
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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