Contacts of the strand formed by residues 371 - 375 (chain A) in PDB entry 1K4R
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 PHE 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A SER* 3.9 24.0 - - - -
4A THR* 4.8 6.1 - - + -
146A HIS* 5.9 3.1 - - - -
148A GLY* 2.9 38.1 + - - +
149A ASP 4.4 12.8 - - - -
150A TYR* 3.8 42.2 - + + +
327A VAL* 3.8 37.7 - - + -
328A MET 3.4 16.6 - - - -
329A GLU* 4.1 10.6 - - + +
359A THR* 3.7 12.5 - - + +
362A PRO* 5.4 1.0 - - - +
369A GLY 4.0 0.4 + - - -
370A GLY* 1.3 75.9 + - - +
372A ILE* 1.3 64.8 + - - +
373A GLU* 4.2 15.3 - - + -
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Residues in contact with ILE 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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326A VAL 3.8 0.7 - - - +
327A VAL* 3.4 2.4 - - - -
328A MET* 3.0 47.9 + - + +
330A VAL* 4.9 4.5 - - + -
340A ILE* 4.4 15.7 - - + -
342A VAL* 3.9 30.5 - - + -
357A LEU* 3.9 27.6 - - + -
359A THR* 3.5 9.0 - - - +
362A PRO* 4.2 14.6 - - + -
370A GLY 4.1 10.5 - - - +
371A PHE* 1.3 84.3 - - - +
373A GLU* 1.3 68.5 + - - +
374A MET* 4.2 11.9 - - + -
385A VAL* 4.8 7.4 - - + -
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Residues in contact with GLU 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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1A SER* 4.9 1.6 - - - -
4A THR* 4.1 9.5 - - - +
9A ARG* 2.8 41.8 + - - -
146A HIS* 4.5 5.5 - - - +
321A SER* 4.3 0.3 + - - -
325A THR* 2.7 35.1 + - - +
326A VAL 3.2 7.2 - - - +
327A VAL* 3.8 16.1 - - + +
357A LEU* 3.9 0.9 - - - -
358A ILE* 2.9 42.1 + - + +
359A THR* 2.8 16.9 + - - +
371A PHE* 4.2 8.2 - - + -
372A ILE* 1.3 77.8 - - - +
374A MET* 1.3 64.2 + - - +
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Residues in contact with MET 374 (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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325A THR* 3.3 6.7 - - - -
326A VAL* 2.7 41.1 + - + +
328A MET* 3.9 31.4 - - + -
342A VAL* 3.6 30.5 - - + -
343A ARG 5.1 0.9 - - - +
344A ALA* 4.7 0.7 - - - -
355A ALA* 4.1 20.2 - - + -
356A MET 3.4 14.8 - - - +
357A LEU* 3.9 18.6 - - + -
358A ILE* 4.2 3.8 - - - +
372A ILE* 4.2 4.0 - - + -
373A GLU* 1.3 74.8 - - - +
375A GLN* 1.3 60.2 + - - +
376A LEU* 4.1 23.1 - - + -
383A ILE* 4.3 13.5 - - + -
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Residues in contact with GLN 375 (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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323A HIS 5.5 0.6 + - - -
324A ASP* 3.7 27.3 + - - +
325A THR* 4.6 13.3 - - + +
355A ALA* 3.9 0.5 - - - -
356A MET* 2.9 64.6 + - + +
358A ILE* 5.3 7.4 - - + +
374A MET* 1.3 74.6 - - - +
376A LEU* 1.3 74.2 + - - +
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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