Contacts of the strand formed by residues 482 - 491 (chain A) in PDB entry 3KCZ
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 THR 482 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A LEU* 4.2 19.4 - - + +
402A LEU* 4.6 10.4 - - + +
432A MET* 3.8 17.3 - - - +
476A ALA* 5.0 2.5 - - - +
480A LYS* 3.3 8.5 - - - +
481A ASN* 1.3 86.9 + - - +
483A GLY* 1.3 62.0 + - - +
574A LYS* 4.0 35.3 - - + -
575A VAL 3.4 9.1 + - - +
576A GLN* 5.2 1.2 - - - +
577A PHE* 4.6 0.9 - - - -
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Residues in contact with GLY 483 (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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432A MET* 4.0 10.1 - - - -
474A CYS* 4.9 7.4 - - - -
476A ALA* 5.2 1.6 - - - -
482A THR* 1.3 75.8 - - - +
484A LEU* 1.3 66.8 + - - +
575A VAL* 2.8 37.8 + - - +
577A PHE* 3.8 19.9 - - - -
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Residues in contact with LEU 484 (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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241A LEU* 4.0 18.8 - - + -
244A LEU* 4.8 7.0 - - + -
245A ILE* 3.7 22.9 - - + -
429A GLY* 4.5 0.2 - - - -
430A SER 5.3 0.4 + - - -
432A MET* 3.9 11.9 - - + -
435A TRP* 3.2 51.5 - - + +
474A CYS* 3.2 21.6 - - - -
482A THR* 5.4 0.2 - - + -
483A GLY* 1.3 84.6 - - - +
485A LEU* 1.3 63.1 + - - +
572A LEU* 4.1 19.1 - - + -
573A LEU 3.2 13.2 - - - +
574A LYS* 3.6 23.1 - - + -
575A VAL* 5.2 0.7 - - - -
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Residues in contact with LEU 485 (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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386A LEU* 3.8 30.1 - - + -
399A MET* 4.3 11.0 - - - -
427A TRP* 3.9 21.8 - - + -
428A HIS 3.9 15.5 - - - +
429A GLY* 3.9 6.3 - - - -
435A TRP* 4.7 0.2 - - - -
467A SER 4.2 8.7 - - - +
470A SER* 3.9 11.0 - - - -
471A ALA* 3.8 29.4 - - + +
474A CYS* 4.6 2.0 - - - -
484A LEU* 1.3 77.2 - - - +
486A LEU* 1.3 59.9 + - - +
572A LEU* 3.6 4.0 - - - -
573A LEU* 2.7 48.8 + - + +
575A VAL* 4.3 9.4 - - + +
577A PHE* 5.7 0.9 - - + -
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Residues in contact with LEU 486 (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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407A VAL* 4.4 6.7 - - + -
426A LEU 3.6 0.5 - - - +
427A TRP* 3.4 6.5 - - - -
428A HIS* 2.9 45.1 + - + +
435A TRP* 4.0 13.4 - - + -
438A ILE* 4.3 6.5 - - + -
439A LEU* 4.9 4.0 - - + -
443A LEU* 3.9 24.9 - - + -
485A LEU* 1.3 74.4 - - - +
487A LEU* 1.3 64.8 + - - +
488A SER* 3.7 17.0 + - - +
569A MET* 3.7 38.1 - - + -
571A TYR 3.4 16.8 - - - +
572A LEU* 4.0 14.8 - - + -
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Residues in contact with LEU 487 (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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382A ILE* 3.9 34.3 - - + -
385A TYR* 3.6 22.0 - - + -
425A LEU* 4.2 24.0 - - + -
426A LEU 3.4 13.0 - - - +
427A TRP* 3.4 48.2 - - + -
485A LEU 4.2 0.2 + - - -
486A LEU* 1.3 72.2 - - - +
488A SER* 1.3 56.8 + - - +
569A MET* 4.0 0.3 - - - -
570A ARG* 2.8 28.6 + - - -
571A TYR* 2.7 31.0 + - + +
573A LEU* 3.9 6.7 - - + -
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Residues in contact with SER 488 (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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424A MET 3.4 0.3 - - - +
425A LEU* 3.3 7.3 - - - -
426A LEU 2.9 30.2 + - - -
428A HIS* 5.5 0.2 - - - +
443A LEU* 4.2 0.2 - - - +
463A PHE* 3.9 20.4 - - - -
486A LEU* 3.7 18.9 + - - +
487A LEU* 1.3 77.2 + - - +
489A GLU* 1.3 62.8 + - - +
490A VAL* 3.6 2.5 + - - +
567A VAL* 3.9 19.8 - - - +
568A ARG 3.4 11.4 - - - -
569A MET* 3.6 12.0 - - - +
570A ARG 4.1 0.4 - - - +
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Residues in contact with GLU 489 (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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416A PHE* 3.5 21.2 - - + -
423A ARG* 4.4 5.8 + - - -
424A MET 3.5 4.9 - - - -
425A LEU* 4.1 13.3 - - + +
488A SER* 1.3 73.5 - - - +
490A VAL* 1.3 60.0 + - - +
491A ALA 4.1 0.2 - - - -
531A LEU 4.6 3.3 - - - +
532A ASN* 4.1 16.8 - - - +
534A SER* 3.3 25.7 + - - +
567A VAL* 3.4 4.7 - - - -
568A ARG* 2.8 64.6 + - + +
570A ARG* 4.0 25.9 + - + +
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Residues in contact with VAL 490 (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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422A ASN 3.6 1.0 - - - +
423A ARG* 3.3 4.4 - - - -
424A MET 2.8 35.6 + - - +
426A LEU* 4.1 12.8 - - + -
463A PHE* 3.8 48.7 - - + -
488A SER* 3.6 12.3 - - - +
489A GLU* 1.3 78.9 - - - +
491A ALA* 1.3 60.2 + - - +
492A LEU* 3.2 30.5 + - + +
561A VAL* 3.7 18.8 - - + -
566A GLN 3.2 6.7 - - - +
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Residues in contact with ALA 491 (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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416A PHE* 3.9 16.6 - - + -
417A ARG* 3.5 29.6 - - + +
420A LEU* 3.6 18.1 - - + +
423A ARG* 4.6 7.6 - - + +
490A VAL* 1.3 69.8 - - - +
492A LEU* 1.3 61.0 - - - +
493A GLY 3.4 2.6 + - - -
561A VAL* 4.1 0.3 - - - +
566A GLN* 2.8 42.9 + - - +
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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