Contacts of the strand formed by residues 190 - 194 (chain C) in PDB entry 4XQ2
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 VAL 190 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LEU* 4.0 11.2 - - + -
168C ARG* 4.2 12.8 - - - -
169C VAL 3.1 4.3 + - - +
170C VAL* 3.3 18.6 - - + -
171C VAL* 2.9 26.3 + - - +
184C LEU* 3.6 3.7 - - - +
188C ALA* 4.3 5.1 - - - +
189C ASP* 1.3 92.0 - - + +
191C SER* 1.3 76.3 + - - +
210C LEU* 4.0 22.9 - - + -
211C VAL 3.4 9.4 - - - +
212C TYR* 4.2 4.3 - - + -
217C LEU* 3.8 25.4 - - + -
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Residues in contact with SER 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLU* 3.0 26.9 + - - -
171C VAL 3.5 5.4 - - - -
183C PRO* 3.2 29.2 - - - +
184C LEU* 3.9 3.5 - - - +
190C VAL* 1.3 74.7 - - - +
192C LEU* 1.3 59.8 + - - +
193C TYR* 3.6 23.4 + - - -
209C ALA 3.8 0.5 - - - +
210C LEU* 3.4 5.7 - - - -
211C VAL* 2.8 33.8 + - - -
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Residues in contact with LEU 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C GLY 4.0 9.4 - - - +
79C ALA* 3.6 30.1 - - + -
80C ALA* 4.0 12.8 - - + +
83C LEU* 5.9 0.2 - - + -
103C THR* 5.4 0.4 - - - +
141C TRP* 3.4 34.5 - - + -
170C VAL* 3.9 15.7 - - + -
171C VAL 2.9 9.0 + - - +
172C ASP* 3.5 29.8 - - + +
173C ASN 2.8 26.0 + - - -
174C THR 3.7 0.2 + - - -
190C VAL 4.1 0.6 - - - -
191C SER* 1.3 73.9 - - - +
193C TYR* 1.3 79.7 + - - +
194C SER 5.1 0.2 - - - +
197C LLP 5.5 3.8 - - + +
209C ALA 3.5 3.1 - - - +
210C LEU* 4.2 9.2 - - + -
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Residues in contact with TYR 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C LEU* 5.9 1.8 - - + -
65C GLU* 2.5 34.4 + - - -
76C GLY* 4.0 0.5 - - - -
173C ASN* 3.0 53.1 + - + -
174C THR* 3.5 7.4 - - - -
177C SER* 4.7 1.3 - - - -
178C PRO* 3.4 28.4 - - + +
183C PRO* 4.3 0.5 - - - +
191C SER* 3.6 18.8 + - - -
192C LEU* 1.3 86.0 - - - +
194C SER* 1.3 61.8 + - - +
195C THR* 4.3 6.3 - - + +
199C ILE* 3.9 27.8 - - + -
208C GLY* 3.1 4.9 - - - -
209C ALA* 2.8 41.8 + - + +
211C VAL* 4.0 13.7 - - + -
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Residues in contact with SER 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLY* 3.8 4.2 - - - -
174C THR* 2.8 23.2 + - - +
192C LEU* 4.7 0.6 - - - +
193C TYR* 1.3 73.8 - - - +
195C THR* 1.3 60.7 + - - +
196C THR* 3.0 14.8 + - - -
197C LLP 2.8 75.5 + - - +
198C SER 4.9 0.3 + - - -
199C ILE* 5.0 2.8 + - - +
207C GLY 3.6 4.5 - - - -
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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
------------------------------------------------------------
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