Contacts of the helix formed by residues 190 - 199 (chain A) in PDB entry 2UVQ
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 PHE 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A GLY 3.9 4.3 - - - -
83A GLN* 3.7 39.7 - - - -
85A ASN* 3.6 39.1 + - + +
186A GLN* 3.2 35.4 + - + +
189A THR* 1.3 103.3 + - - +
191A VAL* 1.3 63.9 + - + +
193A PRO* 3.5 4.0 - - - +
194A ALA* 3.2 25.5 + - - +
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Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A THR* 5.6 0.9 - - - +
87A ASP* 3.3 31.4 - - + +
165A ARG* 6.3 1.1 - - - +
169A ARG* 3.2 36.6 - - - +
186A GLN* 3.5 28.9 - - - +
187A TYR* 2.9 28.9 + - + +
190A PHE* 1.3 72.0 - - - +
192A LYS* 1.3 62.5 + - - +
194A ALA* 3.3 1.0 + - - +
195A PHE* 2.9 35.0 + - + +
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Residues in contact with LYS 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A SER* 5.5 7.9 + - - -
187A TYR* 2.7 46.6 + - + +
188A THR* 4.1 14.8 - - + +
191A VAL* 1.3 72.0 - - - +
193A PRO* 1.3 68.0 - - + +
195A PHE* 3.6 7.2 - - + +
196A GLU* 3.0 52.3 + - - +
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Residues in contact with PRO 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A THR 3.6 11.4 - - - +
189A THR 3.2 20.9 - - - +
190A PHE 3.5 11.2 - - - +
191A VAL 3.4 3.8 - - - -
192A LYS* 1.3 93.4 - - + +
194A ALA* 1.3 54.7 + - - +
196A GLU* 3.1 8.9 + - + +
197A GLU* 2.8 42.5 + - - +
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Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASN* 3.7 14.1 - - - +
87A ASP* 3.5 34.8 - - + +
190A PHE 3.2 19.3 + - - +
191A VAL 3.3 1.4 + - - +
193A PRO* 1.3 78.5 - - - +
195A PHE* 1.3 63.6 - - - +
197A GLU* 5.5 0.2 - - - -
198A PHE* 3.0 44.6 + - + +
199A CYS* 3.7 1.2 + - - +
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Residues in contact with PHE 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLY* 3.8 17.5 - - - -
32A THR 5.3 0.9 - - - -
87A ASP* 5.0 3.0 - - + +
140A ILE* 6.4 0.2 - - + -
157A PHE* 5.4 2.9 - + - -
162A SER* 4.2 7.0 - - - -
165A ARG* 3.2 39.5 - - - +
187A TYR* 6.1 1.6 - - + +
191A VAL* 2.9 23.7 + - + +
192A LYS* 3.6 6.3 - - + +
194A ALA* 1.3 78.0 - - - +
196A GLU* 1.3 72.4 + - + +
199A CYS* 3.1 39.8 + - + -
200A LEU* 2.9 68.7 + - + -
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Residues in contact with GLU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A SER* 5.7 0.7 + - - -
192A LYS* 3.0 52.3 + - - +
193A PRO* 3.1 8.4 + - + +
195A PHE* 1.3 92.7 - - + +
197A GLU* 1.3 61.0 + - - +
200A LEU* 4.1 18.5 - - + +
201A PRO* 3.3 18.4 - - - +
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Residues in contact with GLU 197 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A TYR* 5.3 0.7 - - - -
193A PRO* 2.8 22.7 + - - +
196A GLU* 1.3 75.9 - - - +
198A PHE* 1.3 97.7 + - + +
201A PRO* 3.4 14.3 - - - +
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Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASN* 5.3 0.4 - - - -
87A ASP 4.0 5.2 - - - +
88A HIS* 3.4 40.4 - + - -
89A PRO* 3.6 21.8 - - + -
141A LEU* 3.5 22.2 - - + +
144A TYR* 3.6 31.8 - + + -
194A ALA* 3.0 34.5 + - + +
197A GLU* 1.3 116.8 - - - +
199A CYS* 1.3 60.4 + - - +
201A PRO* 3.7 5.1 - - - +
202A THR* 3.1 25.1 - - - +
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Residues in contact with CYS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A SER* 5.3 0.2 - - - -
30A GLY 4.1 18.2 - - - -
31A GLY* 4.5 0.9 - - - -
140A ILE* 3.4 29.4 - - + +
141A LEU* 3.9 11.4 - - + -
157A PHE* 4.3 8.8 - - - -
194A ALA 3.7 0.6 + - - +
195A PHE* 3.1 44.6 + - + +
198A PHE* 1.3 79.0 - - - +
200A LEU* 1.3 65.8 + - - +
201A PRO 3.3 0.2 - - - -
202A THR* 2.7 25.2 + - - -
203A LYS 3.9 1.4 + - - -
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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