Contacts of the strand formed by residues 174 - 178 (chain C) in PDB entry 6F0X
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 174 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C TYR* 3.9 4.9 + - - -
172C ASN* 2.9 25.2 - - + +
173C ARG* 1.3 81.4 - - - +
175C VAL* 1.3 67.8 + - - +
176C LEU* 4.8 2.5 - - + -
284C ILE* 4.0 29.4 - - + -
287C ILE* 6.1 0.2 - - + -
295C ILE* 3.0 18.0 - - + +
297C THR* 3.8 24.9 - - + +
309C PHE* 4.9 13.0 - - + +
312C ARG* 4.5 11.0 - - + +
314C ASP* 3.0 30.3 - - + +
315C ILE 4.6 0.3 + - - -
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Residues in contact with VAL 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LEU* 3.8 19.5 - - + -
152C TYR* 4.0 21.1 - - + -
153C VAL* 5.8 0.2 - - + -
174C VAL* 1.3 78.5 - - - +
176C LEU* 1.3 56.1 + - - +
177C LEU* 3.6 24.2 - - + -
192C LEU* 5.5 1.1 - - + -
294C VAL* 3.7 21.8 - - + -
295C ILE 2.3 24.4 + - - +
296C LEU* 3.5 15.0 - - + -
297C THR* 2.5 41.2 + - - +
314C ASP* 3.4 3.1 - - - -
315C ILE* 4.6 7.9 - - + +
317C GLN* 6.3 0.9 - - + -
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C VAL* 4.8 2.5 - - + -
175C VAL* 1.3 72.8 - - - +
177C LEU* 1.3 80.1 + - - +
178C HIS* 4.1 10.5 - - + +
254C VAL* 5.3 5.6 - - + -
297C THR* 3.1 27.6 - - - +
298C THR* 4.1 7.6 - - - +
299C SER* 5.6 0.2 - - - -
305C ILE* 4.9 21.3 - - + -
309C PHE* 5.7 6.7 - - + -
310C VAL* 4.8 23.1 - - + +
313C ALA* 6.6 0.2 - - - -
314C ASP* 3.3 21.2 - - + +
316C LYS* 3.6 19.0 - - + +
317C GLN* 3.0 26.1 + - - +
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Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LEU* 4.1 14.1 - - + -
175C VAL* 3.6 25.1 - - + +
176C LEU* 1.3 91.5 - - - +
178C HIS* 1.3 61.9 + - - +
185C LYS* 3.3 45.2 + - + +
188C LEU* 3.5 32.5 - - + -
189C CYS* 3.8 17.5 - - - -
296C LEU* 4.8 2.7 - - + -
297C THR 2.8 9.0 + - - +
298C THR* 3.5 14.4 - - + -
299C SER 4.3 0.2 + - - -
317C GLN* 3.7 12.8 - - + -
319C ILE* 5.3 5.4 - - + -
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Residues in contact with HIS 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B GLU 5.7 0.9 - - - -
427B LYS* 3.2 26.4 + - + -
428B LEU* 4.1 6.3 - - + -
176C LEU* 4.1 13.7 - - + +
177C LEU* 1.3 80.4 + - - +
179C GLY* 1.3 58.4 + - - +
185C LYS* 3.1 11.4 + - - +
299C SER* 4.8 0.6 + - - -
302C THR* 3.0 45.5 + - + +
305C ILE* 4.6 8.0 - - + +
316C LYS* 5.1 5.8 - - + -
317C GLN 2.9 17.0 + - - +
318C TYR* 3.2 35.7 - + + -
319C ILE* 2.4 40.5 + - - +
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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
------------------------------------------------------------
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