Contacts of the helix formed by residues 191 - 201 (chain B) in PDB entry 1XUQ
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 ASP 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B THR 5.0 0.9 - - - +
89B ILE* 2.8 26.9 + - - +
90B LEU 4.0 2.4 - - - +
91B SER* 3.6 29.4 + - - -
93B ASN 5.3 2.3 - - - +
94B GLY* 4.1 7.0 - - - -
189B VAL 3.4 0.2 + - - -
190B VAL* 1.3 72.8 - - - +
192B TRP* 1.3 57.4 + - - +
193B ASN* 3.0 23.0 + - - +
194B ALA* 3.0 21.7 + - + +
195B ALA* 2.9 26.3 + - - +
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Residues in contact with TRP 192 (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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94B GLY* 5.2 0.6 - - - -
95B GLY 3.6 17.6 + - - +
96B GLY 3.1 26.6 + - - -
97B GLN 3.7 13.9 - - - +
98B PRO* 3.8 20.2 - - + -
99B VAL* 3.8 11.5 + - + +
102B LEU* 4.2 13.8 - - + +
106B ILE* 4.0 20.6 - - + -
113B PHE* 3.4 28.2 - + - -
116B PHE* 3.9 22.7 - + - -
135B LEU* 5.0 2.0 - - + -
162B ILE* 4.2 20.0 - - + -
187B TRP* 4.1 10.1 + + - -
190B VAL* 3.4 32.9 + - + +
191B ASP* 1.3 70.0 + - - +
193B ASN* 1.3 62.1 + - - +
195B ALA* 3.5 12.3 - - + +
196B GLU* 2.9 30.1 + - - +
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Residues in contact with ASN 193 (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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93B ASN* 5.0 10.3 + - - -
99B VAL* 3.5 25.6 - - - +
191B ASP* 3.0 9.7 + - - +
192B TRP* 1.3 77.5 - - - +
194B ALA* 1.3 61.6 + - - +
196B GLU* 3.3 6.5 + - - +
197B LYS* 3.2 22.7 + - - +
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Residues in contact with ALA 194 (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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88B THR 3.6 22.4 - - - +
89B ILE* 4.6 5.2 - - + -
191B ASP* 3.0 29.6 + - + +
193B ASN* 1.3 75.3 - - - +
195B ALA* 1.3 63.4 + - - +
197B LYS* 3.2 10.8 + - - +
198B ARG* 3.0 31.3 + - - +
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Residues in contact with ALA 195 (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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89B ILE* 4.9 2.2 - - + +
102B LEU* 3.7 15.7 - - + -
161B VAL* 3.7 14.1 - - - +
162B ILE* 3.6 28.0 - - + -
191B ASP 2.9 17.8 + - - +
192B TRP* 3.5 13.2 - - + +
193B ASN 3.2 0.2 - - - -
194B ALA* 1.3 77.2 - - - +
196B GLU* 1.3 56.7 + - - +
198B ARG* 3.2 5.1 + - - +
199B TYR* 2.8 29.6 + - - +
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Residues in contact with GLU 196 (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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99B VAL* 3.6 15.3 - - + +
100B GLY* 3.5 11.5 - - - -
101B GLU* 2.9 18.6 + - - +
102B LEU* 2.9 32.0 + - + +
192B TRP 2.9 17.8 + - - +
193B ASN* 3.4 7.0 - - - +
195B ALA* 1.3 75.2 - - - +
197B LYS* 1.3 53.5 + - + +
199B TYR* 3.0 6.8 + - - +
200B GLN* 2.7 70.3 + - + +
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Residues in contact with LYS 197 (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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193B ASN 3.2 11.2 + - - +
194B ALA* 3.4 12.1 - - - +
196B GLU* 1.3 80.8 - - + +
198B ARG* 1.3 54.2 + - + +
200B GLN* 3.7 6.2 - - - +
201B GLU* 2.6 66.0 + - + +
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Residues in contact with ARG 198 (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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85B PHE* 3.1 44.7 - - - +
88B THR* 2.9 45.9 + - - +
89B ILE* 3.7 16.3 - - - +
159B THR* 5.0 1.6 - - - +
160B PRO 4.2 12.8 - - - +
161B VAL* 3.9 11.8 - - - +
194B ALA* 3.0 13.8 + - - +
195B ALA 3.6 7.2 - - - +
197B LYS* 1.3 77.8 - - + +
199B TYR* 1.3 62.3 + - - +
201B GLU* 3.6 10.6 + - - +
202B ALA* 3.5 20.1 + - - +
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Residues in contact with TYR 199 (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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101B GLU* 3.9 16.8 - - + -
102B LEU* 3.5 50.9 - - + -
105B ALA* 3.6 19.8 - - + +
137B VAL* 3.9 20.9 - - + -
140B GLY 4.7 12.4 + - - -
142B LEU* 3.9 20.5 - - + +
161B VAL* 4.2 9.5 - - + +
195B ALA 2.8 13.4 + - - +
196B GLU* 3.3 10.1 - - - +
198B ARG* 1.3 74.4 - - - +
200B GLN* 1.3 72.1 + - - +
202B ALA* 3.4 20.4 + - - +
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Residues in contact with GLN 200 (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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101B GLU* 3.1 43.0 + - - +
196B GLU* 2.7 53.1 + - + +
197B LYS* 3.7 6.1 - - - +
199B TYR* 1.3 79.0 - - - +
201B GLU* 1.3 58.3 + - + +
202B ALA* 2.9 10.2 + - - -
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Residues in contact with GLU 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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197B LYS* 2.6 57.2 + - + +
198B ARG* 3.8 7.9 - - - +
199B TYR 3.3 0.8 - - - -
200B GLN* 1.3 71.6 - - + +
202B ALA* 1.3 57.6 + - - +
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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