Contacts of the helix formed by residues 200 - 209 (chain B) in PDB entry 1QXP
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 THR 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B TRP* 3.1 36.0 + - + +
109B ALA* 3.8 18.7 - - + +
110B ALA* 4.6 3.1 + - - +
199B CYS* 1.3 78.7 - - - +
201B SER* 1.3 67.7 + - - +
203B ALA* 3.5 7.6 + - - +
204B PHE* 3.2 30.7 + - + -
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Residues in contact with SER 201 (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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199B CYS* 3.9 16.8 - - - -
200B THR* 1.3 84.9 - - - +
202B GLU* 1.2 67.1 + - - +
204B PHE* 2.8 23.6 + - - +
205B GLU* 3.3 13.7 + - - +
212B THR* 3.6 33.0 + - - +
340B ILE* 4.6 0.7 - - - +
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Residues in contact with GLU 202 (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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185B TYR* 3.3 9.9 + - - +
198B GLY* 5.8 0.9 - - - -
199B CYS* 3.9 24.4 + - + +
201B SER* 1.2 82.1 + - - +
203B ALA* 1.3 63.2 + - - +
205B GLU* 4.1 4.9 - - - +
206B ASP* 3.3 12.1 - - - +
470B ARG* 2.6 54.0 + - + +
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Residues in contact with ALA 203 (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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106B TRP* 3.9 10.1 - - + -
107B LEU* 3.6 31.4 - - + -
110B ALA* 3.8 17.5 - - + -
185B TYR* 3.7 11.4 + - + +
199B CYS 3.7 3.6 + - - +
200B THR* 3.5 7.9 + - - +
201B SER 3.0 1.2 - - - -
202B GLU* 1.3 80.5 - - - +
204B PHE* 1.3 55.7 + - - +
206B ASP* 3.5 0.7 + - - -
207B PHE* 2.7 44.9 + - + -
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Residues in contact with PHE 204 (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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109B ALA* 3.8 13.2 - - + -
110B ALA* 3.5 20.0 - - + -
113B SER* 2.8 42.4 - - - -
114B LEU* 5.0 4.9 - - + -
200B THR* 3.2 28.0 + - - -
201B SER* 2.8 17.6 + - - +
203B ALA* 1.3 68.2 - - - +
205B GLU* 1.3 64.2 + - - +
207B PHE* 2.9 3.0 + - + -
208B THR* 2.7 36.2 + - - -
237B LEU* 4.9 12.8 - - + -
239B GLY* 5.7 11.0 - - - -
338B LEU* 5.8 7.4 - - + -
340B ILE* 3.3 31.6 - - + -
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Residues in contact with GLU 205 (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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144B TRP* 3.5 14.8 - - + +
201B SER* 3.3 13.6 + - - +
202B GLU* 4.1 3.7 - - - +
203B ALA 3.3 0.4 - - - -
204B PHE* 1.3 77.0 - - - +
206B ASP* 1.4 69.3 + - - +
209B GLY* 2.7 33.2 + - - +
210B GLY 3.3 24.5 - - - +
212B THR* 3.8 15.5 - - - +
340B ILE* 4.5 4.9 - - + +
414B MET* 4.3 3.7 - - - +
470B ARG* 3.6 27.2 + - - -
471B GLU* 2.6 39.5 - - - +
501B ARG* 3.8 8.7 + - - +
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Residues in contact with ASP 206 (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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142B GLN 4.9 0.2 - - - +
143B LEU* 3.9 8.9 - - + -
144B TRP* 3.1 39.3 + - - +
145B GLN* 3.0 23.2 + - - +
149B TRP* 4.8 0.3 - - - -
185B TYR* 3.8 23.1 + - + +
202B GLU 3.3 14.7 + - - +
203B ALA 3.5 3.7 + - - +
204B PHE 3.2 0.2 - - - -
205B GLU* 1.4 80.2 - - - +
207B PHE* 1.3 65.9 + - + +
470B ARG* 2.7 35.8 + - - -
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Residues in contact with PHE 207 (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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107B LEU* 4.3 9.9 - - + -
110B ALA* 3.6 31.2 - - + -
111B ILE* 4.3 8.5 - - + -
114B LEU* 3.8 36.2 - - + +
120B ILE 4.6 3.6 - - - +
123B ARG* 5.5 1.4 - - - +
124B VAL* 3.2 27.4 - - + +
143B LEU* 3.6 25.6 - - + -
149B TRP* 4.3 6.8 - - - -
181B LEU* 3.9 25.6 - - + -
182B GLU* 6.4 0.2 - - - -
185B TYR* 4.1 31.9 - + + -
203B ALA* 2.7 26.0 + - + +
204B PHE* 2.9 7.2 + + - +
206B ASP* 1.3 80.6 - - - +
208B THR* 1.3 58.8 + - - +
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Residues in contact with THR 208 (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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114B LEU* 4.3 4.7 - - - +
120B ILE* 4.1 9.9 - - + +
123B ARG* 3.3 0.9 + - - -
149B TRP* 3.3 15.0 - - - -
204B PHE* 2.7 18.2 + - - -
205B GLU 3.1 0.4 + - - -
207B PHE* 1.3 78.4 + - - +
209B GLY* 1.3 62.4 + - - +
210B GLY 3.8 8.1 - - - +
237B LEU* 4.0 18.9 - - + +
340B ILE* 4.0 8.8 - - + +
342B ASN* 3.3 15.5 - - - +
343B LEU* 3.9 0.9 - - - +
346B ASP* 2.3 59.3 - - - +
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Residues in contact with GLY 209 (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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144B TRP* 3.6 24.9 + - - -
149B TRP* 3.7 5.3 - - - -
205B GLU 2.7 17.1 + - - -
208B THR* 1.3 81.3 - - - +
210B GLY* 1.3 60.2 + - - +
343B LEU* 3.5 19.5 - - - +
501B ARG* 2.7 20.3 + - - -
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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