Contacts of the helix formed by residues 421 - 434 (chain A) in PDB entry 3H13
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 SER 421 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A ASN* 4.5 1.0 - - - +
358A GLN* 2.6 29.3 + - - -
360A TYR* 3.4 19.3 + - - -
419A SER 3.6 3.0 + - - -
420A PRO* 1.3 77.2 - - - +
422A LEU* 1.3 63.4 + - - +
423A TYR 3.5 0.6 + - - -
424A LEU* 3.2 26.0 + - - +
425A GLN* 3.1 18.9 + - - +
463A TYR* 3.4 25.6 - - - -
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Residues in contact with LEU 422 (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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420A PRO 3.7 0.8 + - - -
421A SER* 1.3 72.1 - - - +
423A TYR* 1.3 56.8 + - - +
425A GLN* 3.7 25.1 - - + +
426A CYS* 2.7 37.3 + - - +
449A TYR* 3.7 37.0 - - + +
450A MET* 3.9 6.3 - - + -
453A TRP* 3.4 51.6 - - + -
463A TYR* 3.6 22.7 + - + +
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Residues in contact with TYR 423 (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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356A PHE* 3.7 13.3 - - - +
357A ILE 3.8 19.3 - - - -
358A GLN* 3.5 20.0 - - + +
404A SER* 2.7 42.9 + - - -
406A CYS* 3.5 33.9 - - + -
421A SER* 3.1 1.2 + - - -
422A LEU* 1.3 79.1 - - - +
424A LEU* 1.3 76.3 + - + +
426A CYS* 3.3 1.2 + - - +
427A LEU* 2.9 43.1 + - + +
443A HIS* 4.6 0.2 - - - -
446A LEU* 4.0 31.8 - - + +
450A MET* 3.9 15.2 - - - +
463A TYR* 4.8 1.6 - - + -
465A VAL* 4.2 8.5 - - + -
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Residues in contact with LEU 424 (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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262A ASN* 4.6 6.1 - - - +
263A GLU* 4.2 23.1 - - + +
266A LEU* 4.4 12.2 - - + +
267A LEU* 4.0 28.3 - - + +
311A VAL* 4.7 3.8 - - + -
313A VAL* 3.9 33.2 - - + -
356A PHE* 5.8 1.1 - - + +
358A GLN* 4.2 10.8 - - + +
420A PRO* 5.1 0.2 - - + -
421A SER* 3.2 26.5 + - - +
423A TYR* 1.3 99.7 - - + +
425A GLN* 1.3 62.1 + - - +
427A LEU* 3.8 4.4 - - + +
428A SER* 3.0 25.1 + - - -
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Residues in contact with GLN 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 3.8 26.9 - - + +
420A PRO* 2.9 35.8 + - + +
421A SER 3.1 13.5 + - - +
422A LEU* 3.2 26.2 + - + +
424A LEU* 1.3 76.9 - - - +
426A CYS* 1.3 57.2 + - - +
428A SER* 3.4 4.0 + - - -
429A GLN* 2.9 29.3 + - - +
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Residues in contact with CYS 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LEU* 2.7 21.2 + - - +
423A TYR 3.8 1.8 - - - +
425A GLN* 1.3 70.4 - - - +
427A LEU* 1.3 59.9 + - - +
429A GLN* 3.2 11.9 + - - +
430A LYS* 2.9 48.6 + - - +
446A LEU* 3.7 30.5 - - + -
449A TYR* 3.8 35.2 - - + -
450A MET* 3.8 12.1 - - + -
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Residues in contact with LEU 427 (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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267A LEU* 3.9 23.1 - - + -
271A PHE* 5.7 0.2 - - + -
356A PHE* 3.5 50.7 - - + -
423A TYR* 2.9 32.2 + - + +
424A LEU* 3.8 4.7 - - + +
426A CYS* 1.3 77.4 - - - +
428A SER* 1.3 63.3 + - - +
430A LYS* 3.9 4.1 - - + +
431A LEU* 3.1 46.4 + - + +
439A LEU* 5.4 3.1 - - + -
443A HIS* 5.1 7.4 - - + -
446A LEU* 3.9 19.0 - - + +
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Residues in contact with SER 428 (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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266A LEU* 3.3 22.7 + - - +
267A LEU* 3.8 10.0 - - - +
270A THR* 2.8 24.2 + - - -
424A LEU 3.0 18.4 + - - -
425A GLN 3.6 4.3 - - - -
427A LEU* 1.3 76.8 - - - +
429A GLN* 1.3 64.0 + - - +
432A ARG* 3.0 48.9 + - - +
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Residues in contact with GLN 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A GLN 2.9 18.8 + - - +
426A CYS* 3.5 10.8 - - - +
428A SER* 1.3 76.4 + - - +
430A LYS* 1.3 69.9 + - + +
432A ARG* 4.8 1.1 - - - -
433A GLN* 2.8 70.6 + - - +
449A TYR* 4.9 16.1 + - - -
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Residues in contact with LYS 430 (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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426A CYS* 2.9 40.0 + - - +
427A LEU* 3.9 6.1 - - + +
429A GLN* 1.3 88.8 - - + +
431A LEU* 1.3 59.0 + - + +
434A GLU* 2.8 56.2 + - - +
442A LEU* 4.0 27.9 - - + +
445A GLU* 3.3 42.1 + - + +
446A LEU* 4.5 4.7 - - + +
449A TYR* 5.4 7.7 - - - +
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Residues in contact with LEU 431 (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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267A LEU* 5.4 0.2 - - + -
270A THR* 3.6 15.7 - - + -
271A PHE* 3.6 36.3 - - + -
274A LEU* 3.7 9.1 - - + +
356A PHE* 4.5 7.2 - - + -
427A LEU* 3.1 37.7 + - + +
430A LYS* 1.3 80.1 - - + +
432A ARG* 1.3 63.2 + - - +
435A ARG* 3.3 30.3 + - - +
439A LEU* 3.8 18.2 - - + -
442A LEU* 3.5 24.2 - - + -
477A LEU* 4.1 16.2 - - + -
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Residues in contact with ARG 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 3.0 35.0 + - - +
269A ASP* 3.5 27.2 + - - +
270A THR* 3.0 28.1 + - + +
273A SER* 4.5 7.0 - - - +
274A LEU* 5.0 0.4 - - - -
428A SER* 3.0 32.2 + - - +
429A GLN* 4.1 2.0 - - - +
431A LEU* 1.3 79.4 - - - +
433A GLN* 1.3 64.6 + - + +
435A ARG* 3.1 37.6 + - - +
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Residues in contact with GLN 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A GLN* 2.8 58.2 + - - +
432A ARG* 1.3 77.9 - - + +
434A GLU* 1.3 71.8 + - + +
435A ARG* 3.8 1.1 - - - -
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Residues in contact with GLU 434 (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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430A LYS* 2.8 46.1 + - - +
433A GLN* 1.3 94.3 - - + +
435A ARG* 1.3 56.0 + - - +
436A LYS* 2.8 13.8 + - - -
437A ARG* 2.6 56.1 + - - +
442A LEU* 3.7 18.0 - - + +
445A GLU* 3.7 4.3 - - - +
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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