Contacts of the helix formed by residues 412 - 421 (chain A) in PDB entry 5ZCS
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 TYR 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A ARG* 5.3 2.8 + - - -
366A MET* 3.4 41.8 - - + +
367A GLU* 4.5 5.3 + - - +
370A PHE* 4.5 9.4 - - + -
396A LEU* 5.3 6.5 - - + +
399A LEU* 4.5 14.6 - - + -
400A ALA* 3.9 24.9 - - + +
403A ARG 3.8 21.3 + - - -
404A PRO* 3.9 20.4 - - + -
410A THR 3.3 4.1 - - - +
411A GLN* 1.3 84.5 - - + +
413A LEU* 1.3 61.1 + - - +
414A GLN 3.4 1.3 - - - -
415A ASP* 3.7 19.7 + - + +
416A THR* 3.0 26.6 + - - +
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Residues in contact with LEU 413 (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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400A ALA* 5.8 1.6 - - - -
410A THR* 3.8 17.2 + - - +
411A GLN 3.3 1.6 - - - -
412A TYR* 1.3 78.1 - - - +
414A GLN* 1.3 59.9 + - - +
416A THR* 3.2 2.8 + - - -
417A MET* 2.9 59.2 + - + +
440A LEU* 4.9 10.3 - - + -
447A GLU* 3.3 35.9 - - - +
450A VAL* 5.4 10.8 - - + -
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Residues in contact with GLN 414 (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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374A CYS* 5.4 1.4 - - - +
410A THR 5.0 0.8 + - - +
411A GLN* 3.7 16.1 + - - +
413A LEU* 1.3 77.4 - - - +
415A ASP* 1.3 95.0 + - - +
416A THR 3.6 0.2 + - - -
417A MET* 4.2 4.0 - - - +
418A ASN* 2.4 46.2 + - - +
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Residues in contact with ASP 415 (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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370A PHE* 3.4 31.0 - - + +
373A VAL 5.1 0.2 - - - -
374A CYS* 3.3 31.5 - - + +
396A LEU* 3.3 22.4 - - + +
411A GLN 4.0 7.8 - - - +
412A TYR* 3.7 17.1 + - + +
413A LEU 3.2 0.6 - - - -
414A GLN* 1.3 106.5 + - - +
416A THR* 1.3 60.7 + - - +
418A ASN* 4.4 2.1 + - - +
419A HIS* 4.4 9.0 + - - +
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Residues in contact with THR 416 (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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396A LEU* 3.3 37.6 + - + +
397A PRO* 4.4 9.9 - - + -
400A ALA* 4.7 2.3 - - - +
412A TYR 3.0 17.8 + - - -
413A LEU* 3.2 6.1 + - - -
415A ASP* 1.3 75.8 - - - +
417A MET* 1.3 78.7 + - + +
418A ASN 3.2 2.0 - - - -
419A HIS* 3.1 5.9 + - - +
420A VAL* 2.9 39.3 + - + +
436A ALA 5.8 0.4 - - - +
440A LEU* 4.2 14.6 - - + -
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Residues in contact with MET 417 (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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413A LEU* 2.9 39.5 + - + +
414A GLN* 5.0 2.9 - - - -
416A THR* 1.3 99.2 - - + +
418A ASN* 1.3 63.2 + - - +
419A HIS 3.2 0.2 - - - -
420A VAL* 4.1 13.2 - - + +
421A LEU* 3.3 51.9 + - + +
437A LEU* 4.8 17.0 - - + -
440A LEU* 3.9 19.1 - - + -
451A TYR* 6.0 6.1 - - - -
454A ARG* 6.4 2.0 - - - -
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Residues in contact with ASN 418 (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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374A CYS* 5.4 13.2 - - + +
377A VAL* 5.8 3.3 - - - +
414A GLN* 2.4 39.9 + - - +
415A ASP* 4.7 4.6 - - - +
416A THR 3.2 1.2 - - - -
417A MET* 1.3 79.6 - - - +
419A HIS* 1.3 57.4 + - - +
422A SER* 3.1 20.3 + - - -
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Residues in contact with HIS 419 (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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373A VAL 4.9 6.5 + - - +
374A CYS* 6.3 0.2 - - - -
377A VAL* 4.6 18.8 - - + +
389A GLN* 3.7 49.3 + - + +
392A ILE* 3.5 33.1 - - + +
393A LEU* 3.5 25.1 - - + +
396A LEU* 5.0 2.0 - - + -
415A ASP 4.4 8.5 + - - +
416A THR 3.1 7.5 + - - +
418A ASN* 1.3 79.3 - - - +
420A VAL* 1.3 63.4 + - + +
422A SER* 3.0 18.7 + - - -
423A CYS* 3.3 29.1 + - - -
426A LYS* 5.7 1.3 + - - -
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Residues in contact with VAL 420 (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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393A LEU* 3.8 22.9 - - + -
397A PRO* 5.9 0.2 - - + -
416A THR* 2.9 37.2 + - + +
417A MET* 4.5 10.3 - - + -
419A HIS* 1.3 78.5 - - + +
421A LEU* 1.3 66.5 + - + +
422A SER 3.3 0.7 + - - -
423A CYS* 3.4 11.4 + - - +
424A VAL* 3.4 13.9 + - + +
433A ALA* 3.9 26.8 - - + +
436A ALA* 4.3 10.8 - - + -
437A LEU* 4.5 22.4 - - + +
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Residues in contact with LEU 421 (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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417A MET* 3.3 43.9 + - + +
420A VAL* 1.3 80.8 - - + +
422A SER* 1.3 59.6 + - - +
424A VAL* 3.7 24.5 + - + +
425A LYS* 5.0 2.3 + - - +
437A LEU* 6.1 5.2 - - + -
454A ARG* 4.1 43.1 - - + +
458A ILE* 5.3 7.4 - - + -
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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