Contacts of the helix formed by residues 434 - 442 (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 ASN 434 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A GLN 5.8 0.2 + - - -
335A GLU* 5.1 3.6 - - - +
336A ALA* 3.3 25.9 - - - +
339A ASP* 3.2 24.5 + - - +
430A SER* 2.7 26.9 + - - +
431A ARG* 3.0 23.4 + - - +
433A SER* 1.3 98.8 + - - +
435A TRP* 1.3 59.7 + - - +
436A VAL 3.4 2.5 - - - -
437A GLY 3.2 4.5 + - - -
438A ILE* 2.9 33.2 + - + +
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Residues in contact with TRP 435 (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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245A ILE* 4.0 22.4 - - + -
428A HIS* 3.9 17.9 - + - -
429A GLY 4.4 0.2 - - - -
430A SER* 3.5 32.9 + - - -
431A ARG 3.5 11.4 + - - -
432A MET* 3.6 29.4 + - + -
433A SER 3.6 1.6 - - - -
434A ASN* 1.3 74.3 - - - +
436A VAL* 1.3 60.0 + - - +
438A ILE* 3.7 30.2 - - + -
439A LEU* 2.8 43.7 + - + +
484A LEU* 3.2 56.1 + - + +
485A LEU 4.7 0.2 - - - -
486A LEU* 4.0 23.8 - - + -
572A LEU* 4.4 10.8 - - + -
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Residues in contact with VAL 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE* 3.6 45.0 + - + +
246A CYS* 3.9 14.8 - - - -
251A MET* 4.8 1.3 - - + -
339A ASP 5.3 0.2 - - - +
342A ILE* 4.6 0.4 - - + -
343A ALA* 3.8 34.1 - - + +
346A LEU* 3.7 32.5 - - + -
365A LEU* 4.0 9.2 - - + +
433A SER 4.9 1.7 + - - +
434A ASN 3.4 0.6 - - - -
435A TRP* 1.3 74.9 - - - +
437A GLY* 1.3 53.1 + - - +
440A SER* 2.6 40.2 + - - +
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Residues in contact with GLY 437 (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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339A ASP* 3.7 21.6 + - - -
342A ILE* 3.9 15.9 - - - +
433A SER 5.3 0.2 + - - -
434A ASN 3.2 7.1 + - - -
436A VAL* 1.3 79.1 - - - +
438A ILE* 1.3 56.8 + - - +
440A SER* 3.6 5.2 - - - -
441A HIS* 2.8 36.4 + - - +
444A ARG* 3.4 7.2 + - - -
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Residues in contact with ILE 438 (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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339A ASP* 4.3 2.0 - - - +
428A HIS* 4.7 2.5 - - - +
430A SER* 3.7 33.7 - - - +
434A ASN* 2.9 25.8 + - + +
435A TRP* 3.8 30.5 - - + +
437A GLY* 1.3 76.8 - - - +
439A LEU* 1.3 57.6 + - + +
442A GLY* 2.7 34.9 + - - +
443A LEU* 3.7 33.4 - - + +
444A ARG* 3.7 15.7 - - - +
486A LEU* 4.3 1.8 - - + -
569A MET* 3.8 16.7 - - - +
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Residues in contact with LEU 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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245A ILE* 3.9 24.2 - - + -
365A LEU* 3.5 15.7 - - + +
367A CYS* 3.5 22.9 - - - +
369A LEU* 4.3 19.7 - - + -
407A VAL* 4.4 14.4 - - + -
409A LYS* 3.0 30.1 + - - +
435A TRP* 2.8 30.8 + - + +
436A VAL 4.3 1.8 - - - +
438A ILE* 1.3 77.2 - - + +
440A SER* 1.3 58.0 + - - +
486A LEU* 4.9 5.6 - - + -
569A MET* 4.4 13.9 - - + -
572A LEU* 4.1 26.0 - - + -
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Residues in contact with SER 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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342A ILE* 3.5 10.2 - - - +
346A LEU* 3.8 22.1 - - - +
364A ASN 4.2 2.9 - - - -
365A LEU* 3.3 18.4 - - - +
366A HIS* 5.1 1.2 + - - +
409A LYS* 2.7 18.9 + - - -
436A VAL 2.6 25.3 + - - -
437A GLY 3.4 1.4 + - - -
439A LEU* 1.3 76.9 - - - +
441A HIS* 1.3 82.8 + - - +
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Residues in contact with HIS 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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342A ILE* 3.7 36.3 - - + +
346A LEU* 6.3 0.4 - - + -
409A LYS* 4.5 4.0 - - - -
437A GLY 2.8 14.6 + - - +
440A SER* 1.3 104.3 + - - +
442A GLY* 1.3 62.1 + - - +
443A LEU 4.7 0.7 - - - +
444A ARG* 3.7 28.5 - - - +
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Residues in contact with GLY 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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409A LYS* 4.3 4.3 - - - +
412A GLU* 4.4 8.1 - - - -
438A ILE 2.7 26.4 + - - +
439A LEU 4.2 2.4 + - - -
440A SER 3.7 1.4 - - - -
441A HIS* 1.3 73.6 - - - +
443A LEU* 1.3 65.2 + - - -
444A ARG* 2.9 27.0 + - - -
569A MET* 4.1 13.9 - - - -
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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