Contacts of the strand formed by residues 193 - 197 (chain C) in PDB entry 4QUG
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 193 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C THR* 3.7 19.7 - - - -
143C PHE* 3.4 31.0 - - + -
144C ARG* 3.8 4.3 - - + -
156C LYS* 3.3 21.5 - - + -
158C PHE* 3.6 33.9 - + - -
189C VAL 3.8 20.0 - - - -
190C GLU* 3.4 25.8 + - - +
191C ALA 3.3 5.1 - - - -
192C ASP* 1.3 79.4 - - - +
194C LEU* 1.3 59.7 + - - +
195C TYR* 3.3 37.9 - + + +
266C VAL 4.2 0.3 - - - +
268C MET* 2.9 31.9 + - + +
269C LEU* 3.5 3.1 + - - -
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Residues in contact with LEU 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C LYS 2.9 7.6 + - - +
157C LEU* 3.4 23.8 - - + -
158C PHE* 2.7 34.1 + - - +
159C ILE* 5.9 0.4 - - + -
193C PHE* 1.3 75.3 - - - +
195C TYR* 1.3 60.2 + - - +
196C ALA* 3.8 17.3 - - + +
232C PHE* 3.9 12.3 - - + -
233C MET* 3.5 29.6 - - + -
236C LEU* 3.8 20.4 - - + -
265C ILE* 3.9 7.9 - - + -
266C VAL 3.2 20.0 - - - +
267C SER* 3.5 16.8 - - - -
269C LEU* 3.9 8.9 - - + +
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Residues in contact with TYR 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LYS* 5.4 2.1 + - - -
140C THR* 3.7 31.5 + - + -
158C PHE* 3.3 20.9 - + + +
160C ILE* 4.7 5.6 - - + -
190C GLU* 4.2 11.6 + - - -
193C PHE* 3.3 45.8 - + + +
194C LEU* 1.3 73.3 - - - +
196C ALA* 1.3 60.6 + - - +
197C TYR* 3.4 37.1 + + + -
264C CYS 3.6 0.7 - - - +
266C VAL* 2.8 58.3 + - + +
268C MET* 3.8 24.0 - - + +
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Residues in contact with ALA 196 (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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158C PHE 2.7 13.0 + - - +
159C ILE* 3.6 14.6 - - + -
160C ILE* 3.0 24.2 + - - -
194C LEU* 3.8 18.4 - - + +
195C TYR* 1.3 70.9 - - - +
197C TYR* 1.3 62.3 + - - +
215C PHE* 3.6 19.7 - - + -
219C LEU* 5.8 0.4 - - + -
232C PHE* 5.4 0.7 - - + -
236C LEU* 4.2 19.1 - - + -
264C CYS 4.1 2.9 - - - -
265C ILE* 4.8 4.3 - - + +
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Residues in contact with TYR 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C GLY* 5.9 1.6 - - - -
136C LEU* 4.1 21.6 - - + +
160C ILE* 3.5 33.7 - - + -
164C ARG* 3.5 54.3 + - + +
195C TYR* 3.6 34.5 - + + +
196C ALA* 1.3 73.3 - - - +
198C SER* 1.3 59.3 + - - +
199C THR 3.7 6.5 - - - +
215C PHE* 3.8 3.6 - - - -
263C PRO* 3.3 6.6 - - - +
264C CYS 2.9 41.0 + - - +
266C VAL* 3.8 19.7 - - + -
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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