Contacts of the helix formed by residues 164 - 169 (chain B) in PDB entry 1SXQ
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 GLN 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B TYR* 5.5 0.4 + - - -
161B PRO* 3.2 25.3 + - - +
162B ILE 2.9 2.4 + - - -
163B GLU* 1.3 85.7 + - - +
165B TYR* 1.3 65.5 + - - +
166B LYS 2.9 4.0 + - - -
167B ILE* 2.9 16.3 + - + +
168B HIS* 3.0 36.7 + - + +
271B TRP* 3.6 27.4 - - + +
334B THR* 3.6 19.7 - - - +
341B TRP* 3.4 27.8 - - - +
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Residues in contact with TYR 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLU* 3.4 32.2 - - - +
25B TYR* 3.5 36.6 - + + -
26B LEU* 3.6 28.3 - - + -
29B VAL* 4.0 20.4 - - + -
99B THR* 6.0 2.2 - - + -
162B ILE* 3.0 31.7 + - + +
163B GLU* 3.0 4.9 - - - -
164B GLN* 1.3 78.2 - - - +
166B LYS* 1.3 81.3 + - + +
168B HIS 3.8 1.3 - - - +
169B MET* 2.9 33.2 + - - +
240B MET* 3.5 12.4 - - + +
268B LEU* 3.5 26.5 - - + +
341B TRP* 3.6 20.9 - - + -
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Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 5.2 12.8 + - + +
163B GLU 3.4 13.0 + - - +
164B GLN 2.9 0.2 - - - -
165B TYR* 1.3 90.5 - - + +
167B ILE* 1.3 60.8 + - + +
169B MET* 3.8 11.9 - - + +
172B PHE* 3.4 28.2 - - + +
240B MET* 5.0 14.9 + - + -
241B ASN* 5.8 2.8 - - - +
243B VAL* 5.8 0.4 - - - +
244B SER* 3.6 30.3 + - - +
268B LEU* 4.2 13.7 - - + -
271B TRP* 3.9 23.3 - - + -
272B GLU* 4.0 26.1 + - + +
275B ALA* 5.2 0.4 - - - -
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Residues in contact with ILE 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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164B GLN* 2.9 20.7 + - + +
166B LYS* 1.3 77.5 - - + +
168B HIS* 1.3 76.5 + - + +
169B MET 3.4 1.4 + - - +
172B PHE* 3.8 17.4 - - + +
271B TRP* 3.7 46.4 - - + -
331B LEU* 4.1 19.5 - - + +
334B THR* 3.6 33.9 - - + -
335B ARG* 3.2 42.6 + - + +
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Residues in contact with HIS 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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29B VAL* 4.7 4.6 - - + +
32B GLU* 4.2 1.9 - - - +
164B GLN* 3.0 48.1 + - + +
165B TYR* 3.3 2.9 + - - +
167B ILE* 1.3 87.5 + - + +
169B MET* 1.3 62.9 + - - +
170B ASN 3.4 0.2 + - - -
334B THR 3.6 23.8 - - - -
335B ARG* 3.9 6.5 - - - +
337B LYS 4.6 0.4 - - - -
338B LYS* 2.9 69.2 + - + +
341B TRP* 3.3 44.7 - + + -
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Residues in contact with MET 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 3.9 32.3 - - + +
28B LYS* 3.6 34.5 - - + -
29B VAL* 3.7 25.1 - - - +
32B GLU* 3.7 14.6 - - - +
165B TYR* 2.9 31.6 + - - +
166B LYS* 3.8 13.0 - - + +
167B ILE 3.4 1.7 - - - +
168B HIS* 1.3 78.8 - - - +
170B ASN* 1.3 63.7 + - - +
171B ASP* 3.2 20.2 - - - +
172B PHE* 3.1 20.6 + - + +
335B ARG* 4.9 4.2 + - - -
338B LYS* 4.8 0.2 + - - -
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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