Contacts of the strand formed by residues 366 - 370 (chain A) in PDB entry 1F7U
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 LYS 366 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LYS 3.3 2.4 + - - -
145A VAL* 3.1 22.3 - - + -
146A ILE 3.0 21.8 + - - -
176A TYR* 3.5 31.4 + - + +
181A TRP* 3.8 23.6 - - + -
364A PHE* 3.3 10.9 - - - +
365A ASP* 1.3 82.8 - - - +
367A MET* 1.3 65.1 + - - +
368A ILE* 3.9 8.5 - - + +
396A ASP* 3.5 14.5 + - + +
398A GLN* 2.8 34.3 + - + +
545A HIS* 4.5 0.8 - - - -
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Residues in contact with MET 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 3.3 23.6 - - + +
148A GLU* 5.8 0.7 - - + +
355A ALA* 4.1 10.5 - - + -
358A ARG* 3.5 37.2 - - - +
364A PHE* 3.8 39.3 - - + -
366A LYS* 1.3 76.2 - - - +
368A ILE* 1.3 66.0 + - - +
369A TYR* 3.0 39.4 + - + +
396A ASP 3.0 7.9 + - - +
397A LEU* 3.4 13.0 - - + -
398A GLN* 2.9 27.4 + - - +
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Residues in contact with ILE 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL* 4.2 7.2 - - + -
146A ILE 2.7 12.1 + - - +
147A ILE* 3.4 14.0 - - + +
148A GLU* 2.8 28.9 + - - +
172A LEU* 4.4 7.6 - - + -
176A TYR* 3.6 39.5 - - + +
366A LYS* 3.9 17.3 - - + +
367A MET* 1.3 76.5 - - - +
369A TYR* 1.3 64.7 + - - +
370A VAL* 3.9 13.0 + - + -
398A GLN* 3.5 12.8 - - + +
400A VAL* 3.5 29.8 - - + -
545A HIS* 4.2 9.9 - - + +
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Residues in contact with TYR 369 (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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148A GLU* 3.3 32.1 - - + -
351A ASP* 4.1 3.3 + - - -
355A ALA* 3.7 17.5 + - - +
358A ARG* 3.5 10.2 + - - -
367A MET* 3.0 42.9 - - + +
368A ILE* 1.3 76.4 - - - +
370A VAL* 1.3 60.3 + - - +
371A ILE* 3.4 19.5 + - + -
379A ALA* 6.3 0.4 - - + -
382A PHE* 3.6 26.9 - + - -
383A PHE* 4.0 22.2 - + + -
397A LEU* 4.0 7.6 - - + +
398A GLN 2.9 17.6 + - - +
399A HIS* 3.6 6.6 - - + -
400A VAL 2.9 25.9 + - - +
800A ARG* 3.6 15.0 - - - -
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Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ILE* 4.2 5.4 - - + -
148A GLU* 2.9 24.2 + - - +
149A PHE* 3.9 7.3 - - + -
150A SER 4.6 0.2 + - - -
151A SER* 6.2 0.2 - - - -
165A SER* 2.9 44.8 + - - +
168A ILE* 3.8 19.7 - - + -
169A GLY* 4.0 19.5 - - - -
172A LEU* 4.2 9.4 - - + -
368A ILE* 4.2 16.8 - - + -
369A TYR* 1.3 70.6 - - - +
371A ILE* 1.3 64.7 + - - +
400A VAL* 3.3 11.2 - - + +
402A PHE* 4.1 6.7 - - + -
800A ARG* 5.3 1.0 - - - -
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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