Contacts of the helix formed by residues 166 - 175 (chain B) in PDB entry 1SIW
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 LYS 166 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B PHE* 3.4 17.1 - - + -
153B ASP 5.8 0.2 + - - -
156B ALA* 2.9 45.7 + - + +
157B LYS* 4.4 4.8 - - - +
161B PHE* 3.9 41.2 - - + +
164B ILE* 2.9 11.6 + - - +
165B GLN* 1.3 70.1 - - - +
167B ALA* 1.3 68.0 + - - +
168B MET 3.3 2.7 - - - -
169B TYR* 3.0 22.2 + - - +
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Residues in contact with ALA 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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152B PHE* 5.0 3.4 - - - -
165B GLN* 3.4 5.4 - - + +
166B LYS* 1.3 79.2 - - - +
168B MET* 1.3 61.1 + - - +
169B TYR 3.0 1.2 + - - -
170B SER* 2.8 28.9 + - - -
171B GLN* 4.4 3.1 + - - +
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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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165B GLN* 4.0 10.6 + - - +
167B ALA* 1.3 78.3 - - - +
169B TYR* 1.3 105.4 + - + +
170B SER 3.2 1.7 + - - -
171B GLN* 3.3 23.2 + - - +
174B ASN* 2.8 43.5 + - + +
363B GLN* 5.5 7.2 - - - +
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Residues in contact with TYR 169 (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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1152A GLN* 2.8 18.7 + - - -
152B PHE* 3.4 21.6 - - + -
161B PHE* 4.1 10.5 - + + -
164B ILE* 4.4 9.8 - - + +
165B GLN 4.1 8.3 - - - -
166B LYS* 3.0 22.1 + - - +
168B MET* 1.3 111.4 - - + +
170B SER* 1.3 55.4 + - - +
171B GLN 3.1 6.4 - - - +
174B ASN* 3.7 19.6 - - + +
175B THR* 4.6 1.4 - - - -
176B PHE* 3.7 26.9 + + + -
384B ARG 4.1 7.6 + - - -
386B PRO* 3.3 43.9 - - + +
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Residues in contact with SER 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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1121A GLU* 5.4 1.0 - - - +
1152A GLN* 3.2 24.1 - - - +
152B PHE* 3.4 30.2 - - - -
153B ASP* 5.7 0.7 - - - -
167B ALA* 2.8 20.3 + - - -
169B TYR* 1.3 77.2 - - - +
171B GLN* 1.3 63.0 + - - +
172B PHE 3.6 1.6 + - - -
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Residues in contact with GLN 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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1152A GLN* 3.7 2.6 + - - -
167B ALA 4.8 1.6 + - - -
168B MET* 3.4 29.4 - - - +
169B TYR 3.1 0.6 - - - -
170B SER* 1.3 84.7 - - - +
172B PHE* 1.3 57.1 + - - +
173B GLU* 3.2 10.2 - - - +
174B ASN* 2.7 42.3 + - - +
175B THR 3.3 7.1 + - - -
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Residues in contact with PHE 172 (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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282A PRO 3.3 26.7 - - - -
283A ASP* 4.3 0.7 - - - -
284A TYR* 4.7 1.3 - - + -
294A TRP* 3.8 31.5 - + - -
296A ALA* 4.6 7.9 - - + -
1152A GLN* 3.5 22.6 - - + +
1153A ARG* 3.9 22.0 - - - -
1154A VAL 4.9 0.2 - - - -
1155A PRO* 3.9 25.8 - - + -
170B SER 3.6 4.4 + - - -
171B GLN* 1.3 69.5 - - - +
173B GLU* 1.3 82.9 + - + +
175B THR* 2.6 29.5 + - - -
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Residues in contact with GLU 173 (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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294A TRP* 4.1 8.8 - - - -
171B GLN* 3.0 9.4 + - + +
172B PHE* 1.3 96.6 + - + +
174B ASN* 1.3 61.8 + - - +
175B THR 3.4 0.9 - - - -
364B SER* 2.8 33.7 + - - +
384B ARG* 2.7 17.9 + - - -
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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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168B MET* 2.8 49.4 + - + +
169B TYR* 3.7 28.7 - - + -
171B GLN* 2.7 33.5 + - - +
173B GLU* 1.3 79.0 - - - +
175B THR* 1.3 65.9 + - - +
176B PHE* 3.4 5.0 + - - +
363B GLN* 6.0 1.0 - - - +
364B SER* 4.3 13.5 + - - +
384B ARG* 3.5 7.6 + - - +
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Residues in contact with THR 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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284A TYR* 3.4 36.0 - - + -
1152A GLN* 3.1 28.9 + - - +
1153A ARG* 4.5 5.4 - - + -
148B LEU* 3.7 27.8 - - + -
169B TYR 4.6 2.0 - - - -
171B GLN 3.3 1.6 + - - -
172B PHE* 2.6 29.0 + - - -
173B GLU 3.4 0.8 - - - -
174B ASN* 1.3 77.0 - - - +
176B PHE* 1.3 62.2 + - - +
384B ARG* 2.8 27.9 + - - +
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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