Contacts of the strand formed by residues 198 - 203 (chain B) in PDB entry 1QA7
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 ILE 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142B THR 4.1 3.8 - - - +
143B TYR* 4.4 7.0 - - + -
144B VAL* 5.9 2.5 - - + -
162B ARG* 3.7 57.7 - - + +
163B GLY 3.4 5.2 - - - +
164B LYS* 4.8 8.1 - - + -
194B GLY* 3.2 5.9 - - - -
195B GLY 3.1 30.3 + - - +
196B ASN* 2.9 15.1 + - + +
197B SER* 1.3 85.1 - - - +
199B LEU* 1.3 66.7 + - - +
200B VAL* 4.1 13.0 - - + -
139C GLU* 5.5 0.3 - - - +
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Residues in contact with LEU 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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119B LEU* 5.1 0.4 - - + -
130B ILE* 4.1 11.0 - - + -
132B GLU* 3.3 47.7 - - + +
161B TRP 3.7 0.9 - - - +
162B ARG* 3.3 5.7 - - - -
163B GLY 2.6 37.7 + - - +
164B LYS 4.3 0.4 - - - -
165B GLY* 3.6 36.1 - - - +
167B GLY* 4.3 8.1 - - - +
171B MET* 3.9 26.9 - - + -
191B HIS* 3.8 10.3 - - + +
193B ALA 4.0 1.6 - - - -
194B GLY* 5.4 2.2 - - - -
195B GLY 5.9 0.4 - - - +
198B ILE* 1.3 80.5 - - - +
200B VAL* 1.3 62.8 + - - +
201B ALA* 4.2 0.4 + - - -
139C GLU* 5.1 2.9 - - - +
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Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ALA* 4.3 15.3 - - + -
142B THR 4.7 0.9 - - - +
143B TYR* 4.1 29.6 - - + -
157B VAL* 3.5 35.7 - - + -
160B ALA* 3.7 13.9 - - + -
161B TRP 3.4 3.6 - - - +
162B ARG* 4.7 1.3 - - + -
191B HIS* 3.6 4.4 + - - -
192B VAL* 2.9 26.6 + - + +
193B ALA* 2.8 26.4 + - + +
198B ILE* 4.1 10.1 - - + -
199B LEU* 1.3 79.5 - - - +
201B ALA* 1.3 62.1 + - - +
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Residues in contact with ALA 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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132B GLU* 5.8 2.7 - - - +
160B ALA* 3.3 4.4 - - - -
161B TRP* 2.7 39.2 + - + -
176B LEU* 4.0 31.4 - - + -
189B GLY 4.5 0.9 - - - -
190B ILE 3.2 26.0 - - - +
191B HIS* 3.9 6.3 - - + +
199B LEU 4.2 1.0 + - - -
200B VAL* 1.3 74.1 - - - +
202B LYS* 1.3 62.9 + - - +
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Residues in contact with LYS 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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78B LEU* 6.2 1.1 - - + -
84B ASP* 2.8 40.2 - - + +
85B VAL* 3.9 27.6 - - + +
157B VAL* 3.6 11.7 - - + -
158B ASP* 2.8 31.7 + - - +
159B GLN* 3.3 16.2 + - - +
160B ALA* 4.2 3.6 - - - -
189B GLY* 3.0 21.3 - - - -
190B ILE 2.9 11.6 + - - +
192B VAL* 3.9 11.3 - - + +
201B ALA* 1.3 68.6 - - - +
203B LEU* 1.3 77.3 + - - +
204B VAL* 3.6 2.8 - - + +
208B MET* 5.5 5.1 - - - +
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Residues in contact with LEU 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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78B LEU* 5.4 0.3 - - - +
104B ILE* 4.1 4.5 - - + -
106B LYS* 4.0 24.7 - - + +
109B VAL* 3.8 9.9 - - + -
137B MET* 4.2 16.2 - - + -
159B GLN* 3.2 25.8 + - + +
160B ALA* 4.1 0.2 - - - +
161B TRP* 3.5 37.5 - - + +
188B LEU 3.5 12.3 - - - +
201B ALA 3.4 3.4 + - - -
202B LYS* 1.3 82.4 + - - +
204B VAL* 1.3 62.7 + - - +
205B THR* 3.6 31.2 - - + -
208B MET* 3.7 22.1 - - + +
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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