Contacts of the strand formed by residues 379 - 385 (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 GLY 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A PRO* 1.3 76.5 - - - +
380A ASP* 1.3 60.5 + - - -
381A ASN* 3.0 9.6 + - - -
393A PHE* 3.4 20.3 - - - -
394A GLN 2.7 37.7 + - - -
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Residues in contact with ASP 380 (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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346A ALA* 3.7 3.8 - - - +
347A HIS* 2.9 47.8 + - + +
379A GLY* 1.3 70.9 - - - -
381A ASN* 1.3 64.0 + - - +
391A GLN* 5.8 2.0 - - - +
392A TRP 3.7 4.8 - - - -
393A PHE* 3.6 25.8 - - - +
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Residues in contact with ASN 381 (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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345A VAL 3.2 11.2 - - - +
346A ALA* 3.9 7.3 - - - +
347A HIS 4.1 1.1 - - - +
354A VAL* 3.8 10.6 - - - +
376A LEU* 4.2 26.4 - - + +
377A PRO* 3.2 38.1 + - - +
378A PRO 5.2 0.7 - - - +
379A GLY 3.0 25.6 + - - -
380A ASP* 1.3 78.3 - - - +
382A ILE* 1.3 71.7 + - - +
383A ILE 4.3 0.4 - - - -
391A GLN* 3.7 4.2 - - - +
392A TRP* 2.8 36.7 + - + +
394A GLN* 3.8 6.7 - - - +
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Residues in contact with ILE 382 (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 ALA* 3.2 4.3 - - - +
345A VAL* 2.9 40.2 + - + +
347A HIS* 3.9 33.4 - - + +
381A ASN* 1.3 78.2 - - - +
383A ILE* 1.3 69.8 + - - +
384A TYR* 3.6 36.5 - - + +
389A SER* 4.1 9.9 - - - -
390A HIS 3.3 10.3 - - - +
391A GLN* 3.4 32.8 - - - +
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Residues in contact with ILE 383 (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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314A TRP* 4.0 20.6 - - + -
318A PRO* 3.9 25.8 - - + -
326A VAL* 4.4 2.0 - - + -
328A MET* 4.2 21.1 - - + -
343A ARG 3.8 8.5 - - - +
344A ALA* 4.2 5.4 - - + -
374A MET* 4.3 11.2 - - + -
376A LEU* 3.9 24.9 - - + -
382A ILE* 1.3 76.1 - - - +
384A TYR* 1.3 66.8 + - - +
385A VAL* 4.6 2.2 - - + -
388A LEU 3.7 0.4 - - - +
389A SER* 3.1 7.4 - - - -
390A HIS* 2.8 39.9 + - + +
392A TRP* 3.9 24.2 - - + -
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Residues in contact with TYR 384 (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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341A PRO 3.5 0.3 - - - +
342A VAL* 3.3 4.9 - - - +
343A ARG* 2.8 80.8 + - + +
345A VAL* 4.0 22.0 - - + +
382A ILE* 3.6 32.4 - - + +
383A ILE* 1.3 72.5 - - - +
385A VAL* 1.3 64.1 + - - +
386A GLY 3.6 16.8 - - - +
387A GLU* 4.7 4.5 - - - -
388A LEU 3.2 7.6 - - - -
389A SER* 3.7 24.9 - - - -
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Residues in contact with VAL 385 (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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312A PHE* 3.6 33.3 - - + +
314A TRP* 3.8 26.9 - - + -
328A MET* 5.1 0.9 - - - -
330A VAL* 4.1 13.5 - - + -
340A ILE* 3.6 28.0 - - + -
341A PRO 3.4 4.3 - - - -
342A VAL* 4.1 15.9 - - + -
372A ILE* 4.8 4.7 - - + -
383A ILE* 4.6 2.0 - - + -
384A TYR* 1.3 78.1 - - - +
386A GLY* 1.3 62.8 + - - +
387A GLU 3.2 0.5 + - - -
388A LEU* 2.8 34.0 + - + +
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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