Contacts of the helix formed by residues 434 - 445 (chain K) in PDB entry 5ANC
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 434 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430K PRO* 2.8 25.2 + - - +
431K ARG 2.9 19.1 - - - +
432K PRO 3.8 1.1 - - - +
433K LEU* 1.3 69.5 - - - +
435K GLN* 1.3 64.1 + - - +
436K GLU* 3.3 8.0 + - + +
437K GLU* 3.6 45.1 + - + +
438K ILE* 3.7 1.9 + - - +
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Residues in contact with GLN 435 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K ILE* 4.0 6.9 - - - +
432K PRO 4.3 2.9 - - - -
433K LEU 3.2 4.4 + - - +
434K THR* 1.3 72.0 - - - +
436K GLU* 1.3 62.0 + - + +
438K ILE* 3.2 23.1 - - - +
439K ALA 3.6 0.9 + - - -
518K ARG* 3.7 39.9 + - - +
572K GLU 4.1 4.3 - - - +
573K TYR* 3.0 63.6 + - + +
575K GLU* 3.9 14.0 + - - +
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Residues in contact with GLU 436 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ASP* 3.4 24.2 - - - +
434K THR* 3.2 8.0 - - + -
435K GLN* 1.3 81.0 - - + +
437K GLU* 1.3 62.0 + - + +
438K ILE 3.2 0.2 - - - -
439K ALA* 3.2 9.6 + - - +
440K GLN* 2.9 56.2 + - - +
573K TYR* 3.6 28.8 + - + -
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Residues in contact with GLU 437 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430K PRO 5.0 0.7 - - - +
431K ARG* 3.9 23.2 - - - +
434K THR* 3.6 32.1 + - + +
436K GLU* 1.3 80.6 - - + +
438K ILE* 1.3 59.2 + - - +
440K GLN* 3.2 18.5 + - - +
441K ARG* 2.9 35.3 + - - +
444K ARG* 5.0 1.6 + - - -
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Residues in contact with ILE 438 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431K ARG 3.7 11.4 + - - +
432K PRO* 4.5 3.6 - - + +
434K THR 3.7 6.0 + - - +
435K GLN* 3.2 22.0 - - - +
437K GLU* 1.3 79.3 - - - +
439K ALA* 1.3 59.0 + - - +
441K ARG* 3.2 14.4 + - - +
442K ARG* 2.9 49.3 + - - +
496K LEU* 3.6 17.4 - - + +
570K GLU* 3.2 46.0 - - + +
571K LEU 3.6 22.9 - - - +
573K TYR 4.5 3.8 - - - +
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Residues in contact with ALA 439 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K LEU* 4.3 16.2 - - + +
7K ASP* 6.5 0.7 - - - -
435K GLN 3.6 2.2 - - - +
436K GLU* 3.2 15.7 + - - +
438K ILE* 1.3 81.6 - - - +
440K GLN* 1.3 62.0 + - - +
442K ARG* 3.2 16.0 + - - +
443K GLU* 3.1 25.4 + - - +
573K TYR* 3.6 37.7 - - + -
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Residues in contact with GLN 440 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ASP* 5.6 1.5 + - - +
436K GLU* 2.9 41.6 + - - +
437K GLU* 3.2 24.6 + - - +
439K ALA* 1.3 76.9 - - - +
441K ARG* 1.3 62.2 + - - +
443K GLU* 3.1 23.1 - - - +
444K ARG* 3.0 44.1 + - - +
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Residues in contact with ARG 441 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431K ARG* 3.4 39.0 - - - +
437K GLU* 2.9 13.9 + - - +
438K ILE* 3.4 23.5 - - - +
440K GLN* 1.3 76.4 - - - +
442K ARG* 1.3 54.7 + - - +
444K ARG* 3.0 17.9 + - - +
445K ALA* 2.6 44.8 + - + +
449K HIS* 6.0 5.6 - - + -
493K LYS* 4.5 17.6 - - + +
496K LEU* 3.8 36.6 - - + +
499K GLU* 5.6 5.1 + - - -
570K GLU* 3.4 23.8 + - - -
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Residues in contact with ARG 442 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K LEU* 4.1 25.3 - - + +
45K ILE* 4.2 5.3 - - + +
55K ARG* 3.8 26.0 - - - +
76K SER* 5.1 6.1 - - - -
438K ILE* 2.9 41.7 + - - +
439K ALA* 3.2 18.3 + - - +
441K ARG* 1.3 77.4 - - - +
443K GLU* 1.3 60.2 + - - +
444K ARG 3.5 0.2 + - - -
446K ARG* 2.8 41.0 + - - +
496K LEU* 4.1 9.9 - - + +
568K GLY* 2.9 40.4 + - - +
569K ARG 3.1 15.2 + - - -
572K GLU* 4.0 14.4 + - - +
573K TYR 4.7 4.9 - - - +
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Residues in contact with GLU 443 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K ASN 4.7 7.1 - - - +
5K SER* 2.7 33.6 + - - -
6K LEU* 4.4 17.0 - - + +
7K ASP* 4.1 14.3 - - - +
45K ILE* 4.5 10.5 - - + +
47K SER* 5.2 2.9 + - - -
439K ALA 3.1 15.0 + - - +
440K GLN* 3.1 33.7 - - - +
442K ARG* 1.3 78.5 - - - +
444K ARG* 1.3 62.6 + - + +
446K ARG* 4.2 9.7 - - - +
448K ARG* 4.1 22.0 + - - +
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Residues in contact with ARG 444 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437K GLU 5.0 1.2 + - - -
440K GLN* 3.0 30.4 + - - +
441K ARG* 3.4 25.8 - - - +
443K GLU* 1.3 84.8 - - + +
445K ALA* 1.3 55.2 + - - +
446K ARG 3.4 6.0 + - - -
448K ARG* 3.3 33.1 - - + +
449K HIS* 3.0 41.0 + - - +
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Residues in contact with ALA 445 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54K LEU* 4.9 0.2 - - - +
441K ARG* 2.6 27.3 + - + +
442K ARG 3.6 1.4 + - - -
444K ARG* 1.3 71.7 - - - +
446K ARG* 1.3 82.9 + - - +
448K ARG 5.2 0.2 - - - -
449K HIS* 4.1 12.8 - - + -
450K ALA 5.7 0.2 - - - -
492K PRO* 3.0 29.7 - - - +
493K LYS* 3.5 15.4 - - + +
496K LEU* 4.2 8.3 - - + -
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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