Contacts of the strand formed by residues 364 - 369 (chain A) in PDB entry 7ATU
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 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A LYS* 4.2 14.4 - - + -
356A VAL 3.2 11.9 - - - +
357A THR* 4.2 13.2 - - - +
362A GLY 3.0 10.9 + - - +
363A GLU* 1.3 71.3 - - - +
365A MET* 1.3 64.5 + - - +
414A GLU* 4.9 0.9 - - - -
415A TYR* 3.5 47.5 + - + +
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Residues in contact with MET 365 (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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334A PHE* 3.6 25.1 - - + -
355A LYS* 3.4 6.8 - - - +
356A VAL* 2.6 50.2 + - + +
358A HIS* 4.6 10.1 - - - -
361A THR* 5.8 0.7 - - - -
363A GLU* 3.1 30.7 - - + +
364A VAL* 1.3 76.3 - - - +
366A VAL* 1.3 64.5 + - - +
400A ILE* 3.4 39.5 - - + -
412A ILE* 3.2 27.4 - - + -
413A THR 3.5 9.4 - - - +
415A TYR* 4.1 2.0 - - - -
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Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 5.7 4.0 - - + -
353A ALA* 4.2 11.7 - - + -
354A ILE 3.3 13.5 - - - +
355A LYS* 4.5 6.1 - - + -
365A MET* 1.3 79.6 - - - +
367A MET* 1.3 59.0 - - - +
412A ILE* 3.9 2.2 - - - -
413A THR* 2.7 45.1 + - - +
414A GLU 4.4 1.8 - - - +
415A TYR* 3.6 35.9 - - + -
479A PHE* 6.1 0.4 - - + -
701A RXN 3.0 31.5 - - + -
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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
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353A ALA* 3.7 0.7 - - - -
354A ILE* 2.9 40.9 + - + +
356A VAL* 4.8 14.9 - - + +
365A MET 4.3 0.4 - - - -
366A VAL* 1.3 73.9 - - - +
368A LYS* 1.3 60.2 + - - +
403A LEU* 5.1 6.3 - - + -
410A ASN* 4.8 11.7 - - + +
411A PHE 3.1 13.0 - - - +
412A ILE* 3.7 17.9 - - + -
701A RXN 4.1 1.1 - - - -
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Residues in contact with LYS 368 (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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350A PHE* 2.5 30.6 + - - +
351A GLY* 4.8 0.2 - - - -
352A GLN 3.0 31.4 - - - +
353A ALA* 4.2 2.0 - - + +
354A ILE* 5.8 0.9 - - - -
367A MET* 1.3 73.9 - - - +
369A GLU* 1.3 77.6 + - + +
370A LEU* 3.6 9.7 + - + +
371A ILE* 5.5 2.6 - - - +
372A ARG* 6.1 2.6 - - - +
373A PHE* 6.3 1.0 - - - -
410A ASN* 3.3 5.7 - - - -
411A PHE* 3.0 30.9 + - + -
479A PHE 4.5 4.9 + - - -
480A GLY* 5.8 1.2 - - - -
701A RXN 3.3 51.8 - - + +
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Residues in contact with GLU 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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354A ILE* 6.1 2.9 - - + +
368A LYS* 1.3 94.2 - - - +
370A LEU* 1.3 58.3 + - - +
371A ILE* 3.0 23.8 + - + +
408A ARG* 5.8 5.6 - - + -
409A LEU 3.7 0.9 - - - +
410A ASN* 3.2 29.5 + - - +
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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
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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