Contacts of the strand formed by residues 173 - 178 (chain F) in PDB entry 6XAV
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 ARG 173 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F GLY 3.8 2.6 + - - +
172F GLN* 1.3 80.9 - - - +
174F GLY* 1.3 57.8 + - - +
301F PHE* 3.4 53.4 - - + +
302F GLY* 4.2 9.9 + - - -
304F ALA* 3.2 29.0 + - + +
305F ARG* 5.4 0.4 - - - +
315F ILE 3.6 4.0 - - - -
338F THR* 3.2 29.5 + - - +
339F GLY* 3.4 10.1 - - - +
340F ASN* 2.9 51.4 + - - +
341F MET 3.7 1.0 + - - -
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Residues in contact with GLY 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F GLN* 3.9 1.4 - - - +
173F ARG* 1.3 75.3 - - - +
175F LEU* 1.3 63.7 + - - -
176F ILE* 5.7 0.7 - - - -
301F PHE* 3.2 17.9 - - - -
315F ILE 3.5 6.3 + - - -
316F ILE* 4.0 11.8 - - - +
317F ALA 3.3 17.5 + - - -
341F MET* 3.3 27.4 - - - -
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Residues in contact with LEU 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F GLY* 1.3 75.2 - - - +
176F ILE* 1.3 64.1 + - - +
177F VAL* 3.2 14.3 + - + +
267F ILE* 3.7 18.4 - - + -
301F PHE* 3.5 28.3 - - + -
317F ALA* 3.3 16.8 - - + +
319F ALA* 4.8 8.7 - - + -
332F TYR* 5.4 5.6 - - + +
335F PHE* 3.5 35.4 - - + +
336F LYS* 4.0 10.1 - - + +
339F GLY* 5.3 3.1 - - - +
341F MET* 2.7 13.8 + - - +
342F GLU* 3.4 13.4 - - + +
343F LEU 3.0 24.1 + - - -
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Residues in contact with ILE 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F LEU* 4.5 10.8 - - + -
168F ILE* 5.5 3.1 - - + -
174F GLY* 5.7 0.4 - - - -
175F LEU* 1.3 71.0 - - - +
177F VAL* 1.3 59.4 + - - +
178F ALA* 3.6 4.0 + - + +
184F LYS* 5.8 4.1 - - + +
187F LEU* 3.7 31.9 - - + -
191F ILE* 4.9 2.9 - - + -
316F ILE* 4.1 20.4 - - + -
317F ALA 2.6 21.7 + - - +
318F THR* 3.3 20.4 - - + +
319F ALA 2.7 27.3 + - - +
341F MET* 6.2 3.8 - - + -
343F LEU* 3.8 37.9 - - + +
345F LEU* 4.9 7.2 - - + -
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Residues in contact with VAL 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F LEU* 3.7 18.2 - - + +
176F ILE* 1.3 68.3 - - - +
178F ALA* 1.3 66.8 + - - +
319F ALA* 3.9 11.9 - - + -
321F ILE* 3.7 33.9 - - + -
332F TYR* 3.6 31.9 - - + -
342F GLU* 4.5 4.3 - - + -
343F LEU 2.9 20.7 + - - +
344F HIS* 3.9 32.3 - - + +
345F LEU* 3.1 16.6 + - - +
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Residues in contact with ALA 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F ILE* 4.6 4.5 - - + +
177F VAL* 1.3 80.6 - - - +
179F PRO* 1.3 76.3 - - + +
182F ALA* 4.2 2.2 - - + -
184F LYS* 3.7 30.7 - - + +
319F ALA 3.6 16.0 + - - +
320F LEU* 4.1 2.8 - - - +
321F ILE* 3.8 14.0 + - - -
345F LEU* 3.7 23.1 - - + -
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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