Contacts of the strand formed by residues 194 - 199 (chain B) in PDB entry 2QNU
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 GLY 194 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ARG* 4.1 13.2 - - - +
160A SER 3.8 7.4 - - - -
162A ALA 3.5 17.9 - - - -
163A VAL* 4.2 1.9 - - - +
58B TRP* 4.6 6.3 - - - -
183B TRP 4.1 0.2 - - - +
184B TRP* 3.3 24.5 - - - +
185B GLY 3.4 8.0 + - - -
192B SER 3.5 2.2 + - - -
193B ALA* 1.3 76.2 - - - +
195B LEU* 1.3 61.5 + - - -
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Residues in contact with LEU 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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158A LEU 3.8 0.3 - - - +
159A ARG* 3.4 5.6 - - - +
160A SER* 2.9 43.1 + - - +
162A ALA* 4.2 9.6 - - + +
168A ARG* 3.9 27.8 - - + +
171A ALA* 4.4 9.0 - - + -
172A LEU* 3.7 19.5 - - + -
105B VAL* 4.3 5.4 - - + -
182B HIS* 4.0 24.0 - - + -
183B TRP 3.5 9.2 - - - +
184B TRP* 3.8 13.0 - - + -
194B GLY* 1.3 75.5 - - - -
196B MSE 1.3 69.1 + - - +
227B ACT 3.5 22.9 - - - +
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Residues in contact with MSE 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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157A LEU* 3.3 43.7 - - + -
158A LEU 3.5 4.9 - - - -
159A ARG* 5.0 15.0 - - + +
58B TRP* 3.6 36.6 - - + -
182B HIS* 3.3 7.3 - - - +
183B TRP* 2.7 46.6 + - + +
195B LEU* 1.3 81.4 - - - +
197B ARG* 1.3 60.6 + - - +
198B TYR* 3.8 16.4 - - + +
209B ARG* 4.3 17.5 - - + +
210B PHE* 3.9 23.6 - - + -
213B GLY* 6.4 0.4 - - - -
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Residues in contact with ARG 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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156A ASN 4.1 1.0 - - - +
157A LEU* 3.7 6.8 - - - +
158A LEU* 3.0 40.6 + - + +
175A HIS* 3.4 34.2 + - - -
175B HIS 5.1 0.6 + - - -
176B ALA* 3.0 31.1 + - - +
178B ASP 3.9 9.1 + - - -
180B ALA* 3.5 14.2 - - - +
181B SER 3.4 4.0 - - - +
182B HIS* 3.7 11.2 - - + +
196B MSE 1.3 73.8 - - - +
198B TYR* 1.3 68.1 + - - +
199B GLN* 2.9 41.9 + - - +
227B ACT 3.3 34.5 + - - +
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Residues in contact with TYR 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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156A ASN* 3.3 24.5 - - + -
157A LEU* 3.5 30.1 - - + +
180B ALA* 3.3 7.1 - - - +
181B SER* 2.9 35.5 + - - +
183B TRP* 4.0 10.5 - + - -
196B MSE 3.8 14.0 - - + +
197B ARG* 1.3 79.5 - - - +
199B GLN* 1.3 63.3 + - - +
200B GLY 3.1 13.9 + - - +
201B LEU 4.3 0.4 - - - +
202B PRO* 3.7 29.8 - - + -
203B PRO* 3.9 16.2 - - + -
206B ALA* 3.7 24.4 + - + +
209B ARG* 3.5 36.2 + - - +
210B PHE* 4.3 7.7 - + - -
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Residues in contact with GLN 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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156A ASN 4.9 3.2 + - - +
175A HIS* 5.2 0.7 + - - -
178B ASP 4.5 5.5 + - - -
179B GLY* 4.0 15.2 + - - -
197B ARG* 2.9 39.6 + - - +
198B TYR* 1.3 70.3 - - - +
200B GLY* 1.3 61.6 + - - +
201B LEU 4.2 5.5 - - - +
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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