Contacts of the strand formed by residues 438 - 446 (chain A) in PDB entry 3CB4
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 GLN 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A VAL* 5.5 4.9 + - - +
146A GLU* 5.2 9.9 + - - -
150A ILE* 4.4 14.8 - - - +
409A LEU* 3.5 33.9 - - + +
410A LEU 3.7 17.0 + - - +
411A PRO* 4.3 10.6 - - + +
412A GLN* 3.8 0.9 - - - +
434A TYR* 3.6 2.9 - - - -
435A HIS* 2.7 46.6 + - + +
436A GLY 3.1 2.5 + - - +
437A ASN* 1.3 81.5 - - - +
439A VAL* 1.3 65.9 + - - +
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Residues in contact with VAL 439 (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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409A LEU* 3.5 5.5 - - - +
410A LEU* 2.7 48.9 + - + +
412A GLN* 3.6 27.8 - - + -
415A LEU* 3.6 21.5 - - + -
432A MET* 3.6 42.4 - - + -
433A VAL 3.7 6.1 - - - +
434A TYR* 3.9 11.9 - - + -
435A HIS* 5.3 0.2 - - - -
438A GLN* 1.3 78.0 - - - +
440A ALA* 1.3 65.4 - - - +
441A LEU* 3.7 6.1 - - + +
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Residues in contact with ALA 440 (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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408A MET 3.3 5.8 - - - -
409A LEU* 3.8 14.8 - - + -
431A ASN 4.0 0.3 - - - +
432A MET* 3.5 4.3 - - - -
433A VAL* 2.8 41.1 + - + +
435A HIS* 3.8 25.8 + - + +
439A VAL* 1.3 73.1 - - - +
441A LEU* 1.3 62.3 + - - +
442A THR* 3.8 5.8 + - - +
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Residues in contact with LEU 441 (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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406A CYS 3.6 1.1 - - - +
407A HIS* 3.5 2.1 - - - -
408A MET* 2.7 65.5 + - + +
410A LEU* 3.8 22.2 - - + -
415A LEU* 4.9 0.9 - - + -
418A VAL* 3.8 13.0 - - + -
419A ILE* 3.7 21.5 - - + -
429A GLN* 3.5 15.7 - - - +
431A ASN 3.9 1.6 - - - +
432A MET* 3.9 28.9 - - + -
439A VAL* 3.7 2.7 - - + -
440A ALA* 1.3 73.1 - - - +
442A THR* 1.3 60.4 + - - +
443A TYR* 3.5 26.2 - - + -
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Residues in contact with THR 442 (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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405A GLU* 4.1 15.1 + - - +
406A CYS 3.2 7.0 - - - -
407A HIS* 4.1 19.2 + - + -
429A GLN 4.0 0.2 - - - -
430A THR* 2.9 41.0 + - + +
431A ASN* 3.1 51.4 + - + +
433A VAL* 6.2 0.2 - - + -
440A ALA 4.3 4.3 - - - +
441A LEU* 1.3 76.8 - - - +
443A TYR* 1.3 63.1 + - - +
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Residues in contact with TYR 443 (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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404A ALA 3.7 0.3 - - - +
405A GLU* 3.4 5.4 - - - +
406A CYS* 2.8 39.9 + - + +
408A MET* 4.4 5.2 - - + -
419A ILE* 3.2 32.4 - - + +
422A CYS* 3.6 30.7 - - + -
423A VAL* 4.0 12.3 - - + +
427A GLY* 3.9 12.1 - - - -
428A VAL 3.3 25.4 - - - -
429A GLN* 3.3 46.8 + - + +
430A THR* 4.9 0.9 - - - -
441A LEU* 3.5 23.1 - - + -
442A THR* 1.3 74.9 - - - +
444A GLU* 1.3 62.0 + - - +
445A ILE* 3.8 17.0 - - + -
415F LEU* 5.4 0.7 - - - +
432F MET* 5.0 5.4 - - - +
434F TYR* 5.2 0.5 + - - -
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Residues in contact with GLU 444 (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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403A ILE* 3.9 17.1 - - + +
404A ALA 3.5 6.3 - - - +
405A GLU* 4.7 9.8 - - + +
426A ARG 4.3 0.7 - - - +
427A GLY* 3.5 2.3 - - - -
428A VAL* 2.7 42.2 + - + +
430A THR* 4.2 22.7 + - - +
443A TYR* 1.3 75.0 - - - +
445A ILE* 1.3 62.0 + - - +
446A PRO* 4.0 3.3 - - - +
473A LYS* 3.5 29.8 - - - +
474A ARG* 2.8 32.3 + - - -
476A GLN* 5.4 0.2 - - - +
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Residues in contact with ILE 445 (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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403A ILE* 4.2 1.3 - - - -
404A ALA* 2.9 34.3 + - - +
406A CYS* 3.8 18.8 - - + -
422A CYS* 3.9 20.9 - - + +
425A LYS* 3.9 23.3 - - + +
427A GLY* 4.0 12.1 - - - -
443A TYR* 3.8 15.9 - - + -
444A GLU* 1.3 75.4 - - - +
446A PRO* 1.3 78.2 - - + +
449A GLU* 4.5 2.9 - - + -
450A VAL* 3.7 19.5 - - + +
454A PHE* 3.7 32.1 - - + -
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Residues in contact with PRO 446 (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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401A GLU* 3.0 28.5 - - - +
402A PRO 3.6 7.9 - - - +
403A ILE* 4.0 11.4 - - + -
425A LYS 3.9 4.0 - - - +
426A ARG* 3.3 51.4 - - - +
444A GLU 4.0 3.4 - - - +
445A ILE* 1.3 88.4 - - + +
447A MET* 1.3 55.3 + - - +
448A ALA 3.2 0.9 - - - +
449A GLU* 2.7 31.3 + - + +
450A VAL* 3.2 8.9 + - - +
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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