Contacts of the strand formed by residues 367 - 373 (chain A) in PDB entry 3KQ4
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 GLY 367 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A MET* 3.4 17.0 - - - -
364A THR* 2.7 43.5 + - - -
366A TRP* 1.3 79.8 - - - +
368A LEU* 1.3 64.6 + - - -
369A VAL* 3.5 1.8 + - - -
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Residues in contact with LEU 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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344A LEU* 3.9 26.7 - - + -
361A THR* 3.5 32.5 - - + +
362A THR 3.8 0.4 - - - -
363A MET* 3.7 32.0 - - + +
367A GLY* 1.3 69.8 - - - -
369A VAL* 1.3 61.3 + - - +
370A VAL 4.1 0.9 + - - -
398A GLY* 5.2 4.2 - - - -
399A VAL* 4.7 18.2 + - + +
400A ALA* 4.7 19.5 - - + +
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Residues in contact with VAL 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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361A THR* 3.2 4.6 + - - -
362A THR* 2.9 42.0 + - + +
364A THR* 3.5 30.7 - - + +
366A TRP* 6.3 0.4 - - + -
367A GLY 5.0 0.4 - - - -
368A LEU* 1.3 76.7 - - - +
370A VAL* 1.3 76.8 + - - +
371A SER* 3.2 3.3 + - - -
378A GLU* 4.4 13.9 - - - +
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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
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344A LEU* 5.5 0.2 - - + -
347A LEU* 4.5 6.7 - - + -
359A PHE* 4.4 23.1 - - + -
360A GLU 4.0 3.1 - - - +
361A THR* 4.6 4.5 - - - +
368A LEU* 4.1 1.2 + - + -
369A VAL* 1.3 82.2 - - - +
371A SER* 1.3 59.1 + - - +
372A SER 4.3 7.6 - - - +
373A ILE* 3.9 28.7 - - + -
378A GLU* 4.5 2.6 - - - +
386A TRP* 4.1 18.6 + - + +
388A PHE* 3.9 34.1 - - + -
399A VAL* 4.3 22.6 - - + +
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Residues in contact with SER 371 (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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360A GLU* 3.2 15.4 + - - +
361A THR 4.5 0.9 + - - -
362A THR* 2.8 35.4 - - - +
369A VAL* 3.2 3.0 + - - -
370A VAL* 1.3 73.5 - - - +
372A SER* 1.3 67.7 + - - +
377A ALA* 3.4 2.4 - - - +
378A GLU* 2.8 50.3 + - - +
386A TRP* 4.1 4.3 - - - -
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Residues in contact with SER 372 (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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359A PHE* 3.1 4.9 - - - +
360A GLU* 2.6 61.8 + - - +
370A VAL* 3.6 1.9 - - - +
371A SER* 1.3 90.3 + - - +
373A ILE* 1.3 63.6 + - - +
375A ASN* 3.6 11.8 + - - -
376A ILE 3.2 13.5 + - - -
377A ALA* 3.7 13.2 - - - +
386A TRP* 3.9 1.6 - - - +
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Residues in contact with ILE 373 (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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316A TYR* 3.8 20.9 - - + +
318A ILE* 3.7 32.3 - - + -
328A LEU* 5.1 0.6 - - + +
347A LEU* 5.0 2.0 - - + -
357A PHE 5.0 2.0 - - - +
358A LYS 3.6 12.1 - - - +
359A PHE* 4.0 5.8 - - + +
370A VAL* 3.9 17.7 - - + -
372A SER* 1.3 75.9 + - - +
374A ASN* 1.3 75.2 + - + +
375A ASN 3.2 1.1 - - - -
376A ILE* 3.1 21.5 + - - +
386A TRP* 3.2 42.7 - - + +
388A PHE* 4.5 2.2 - - + -
412A ALA* 4.1 11.4 - - + -
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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