Contacts of the strand formed by residues 169 - 179 (chain B) in PDB entry 3C0M
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 ALA 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B VAL* 4.9 3.6 - - + -
151B ILE 3.5 5.6 - - - +
152B ARG* 3.1 36.8 - - + +
167B LYS 3.5 0.8 + - - -
168B THR* 1.3 76.4 - - - +
170B ILE* 1.3 61.9 + - - +
171B LYS* 3.8 23.6 - - + -
317B THR 3.6 4.3 - - - +
318B LEU* 3.8 0.9 - - - -
319B SER* 2.9 35.6 + - - +
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Residues in contact with ILE 170 (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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112B PHE* 5.1 0.2 - - + -
116B THR* 4.0 25.8 - - - +
117B SER* 4.6 10.5 - - - +
120B ALA* 3.9 19.1 - - + -
128B VAL* 4.9 2.5 - - + -
140B MET* 4.9 6.5 - - + -
150B VAL* 3.3 0.7 - - - -
151B ILE* 2.5 71.0 + - + +
168B THR* 4.7 4.9 - - + +
169B ALA* 1.3 74.6 - - - +
171B LYS* 1.3 59.3 + - - +
172B VAL* 4.7 0.9 - - + -
316B LEU* 3.9 25.8 - - + -
317B THR 3.7 2.7 - - - -
318B LEU* 3.3 26.7 - - + -
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Residues in contact with LYS 171 (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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145B ASP* 4.4 17.6 + - - +
149B TRP 3.3 6.3 - - - +
150B VAL* 4.0 17.0 - - + -
152B ARG* 5.0 5.9 - - - +
169B ALA* 3.9 23.3 - - + -
170B ILE* 1.3 75.0 - - - +
172B VAL* 1.3 63.0 + - - +
173B SER* 4.0 5.4 + - - +
315B ASP 3.7 3.5 - - - +
316B LEU* 3.7 2.4 - - - +
317B THR* 3.0 49.0 + - + +
319B SER* 4.3 11.7 - - - +
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 6.1 0.4 - - + -
106B VAL* 4.2 11.9 - - + -
112B PHE* 3.3 34.8 - - + -
148B GLY* 2.9 4.2 - - - -
149B TRP* 2.7 40.9 + - + +
151B ILE* 3.7 15.7 - - + -
170B ILE 4.7 0.2 - - - +
171B LYS* 1.3 74.7 - - - +
173B SER* 1.3 63.0 + - - +
175B PHE* 3.4 31.6 - - + -
314B TYR* 4.0 20.2 - - + -
315B ASP 3.7 3.1 - - - -
316B LEU* 4.1 9.4 - - + -
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Residues in contact with SER 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ASP* 4.7 5.6 - - - -
148B GLY* 4.0 16.6 - - - -
171B LYS* 4.6 7.1 + - - +
172B VAL* 1.3 77.8 - - - +
174B ASN* 1.3 70.1 + - - +
175B PHE* 3.5 7.6 - - - -
314B TYR* 3.6 2.6 - - - +
315B ASP* 2.8 40.4 + - - +
317B THR* 5.3 3.5 + - - -
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Residues in contact with ASN 174 (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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147B ASP* 4.0 14.7 + - - -
173B SER* 1.3 81.5 - - - +
175B PHE* 1.3 65.5 + - - +
176B ALA* 3.8 3.5 + - - +
313B SER 4.5 0.3 - - - -
314B TYR* 3.7 9.9 - - - -
315B ASP* 2.6 33.1 + - - +
349B LYS* 5.8 3.0 - - - +
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Residues in contact with PHE 175 (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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98B GLU* 5.0 0.9 - - - +
102B GLN* 3.6 46.9 - - + +
105B LEU* 4.3 10.3 - - + -
106B VAL* 4.6 5.8 - - + -
147B ASP* 4.7 5.8 + - - -
149B TRP* 4.3 7.2 - + - -
172B VAL* 3.4 42.0 - - + -
173B SER* 4.2 8.7 - - - -
174B ASN* 1.3 77.8 - - - +
176B ALA* 1.3 60.0 + - - +
177B TYR* 3.3 27.7 - + + +
312B VAL* 3.8 23.1 - - + -
313B SER 3.3 8.5 - - - -
314B TYR* 4.0 16.4 - + + -
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Residues in contact with ALA 176 (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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174B ASN* 4.8 2.9 - - - +
175B PHE* 1.3 75.2 - - - +
177B TYR* 1.3 74.8 + - - +
178B ASN* 4.2 8.3 - - - +
238B LYS 5.8 0.2 - - - -
311B ASP 3.4 1.5 - - - +
313B SER* 3.0 44.9 + - - +
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Residues in contact with TYR 177 (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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98B GLU* 2.7 31.7 + - - +
101B VAL* 5.2 6.1 - - + -
102B GLN* 3.1 21.5 + - + +
175B PHE* 3.3 34.2 - + + +
176B ALA* 1.3 87.1 - - - +
178B ASN* 1.3 65.2 + - - +
179B LEU 3.9 0.2 - - - -
235B LEU* 3.7 33.2 - - + -
238B LYS* 3.7 31.0 + - + +
239B VAL* 3.3 15.8 - - + +
240B THR* 3.1 24.1 + - - -
310B ALA* 4.1 11.4 - - + -
311B ASP 3.4 4.9 - - - -
312B VAL* 4.2 20.0 - - + -
398B ALA* 5.4 0.2 - - + -
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Residues in contact with ASN 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ALA* 5.3 7.7 - - - +
177B TYR* 1.3 76.6 + - - +
179B LEU* 1.3 67.3 + - - +
180B ASP 3.5 1.2 + - - -
240B THR* 3.2 28.2 + - - +
242B LYS* 3.6 39.7 - - + +
310B ALA* 3.4 0.6 - - - -
311B ASP* 2.9 44.4 + - + +
347B PRO* 5.5 4.3 - - - +
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Residues in contact with LEU 179 (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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177B TYR 3.8 2.2 + - - -
178B ASN* 1.3 73.1 - - - +
180B ASP* 1.3 61.5 + - - +
181B PRO* 3.4 18.7 - - - +
239B VAL* 3.9 15.0 - - + -
240B THR 2.7 18.5 + - - +
241B THR* 3.4 16.1 - - + +
242B LYS 5.2 0.3 + - - -
245B PHE* 4.0 14.6 - - + -
265B TRP* 3.6 45.5 - - + -
308B PHE* 3.8 42.2 - - + -
309B LYS 3.3 7.2 - - - +
310B ALA* 3.9 5.3 - - + +
400B ILE* 4.5 10.3 - - + -
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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