Contacts of the helix formed by residues 428 - 439 (chain B) in PDB entry 4H1S
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 GLY 428 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426B LEU 3.7 0.6 + - - -
427B LYS* 1.3 71.4 - - - +
429B SER* 1.3 62.7 + - - +
431B LEU* 3.0 5.8 + - - +
432B LYS* 2.9 22.7 + - - +
487B LEU* 3.8 9.2 - - - +
488B LYS 3.3 21.5 - - - -
489B MET* 3.4 5.9 + - - -
491B GLU 2.8 14.1 + - - -
493B TYR* 3.7 14.3 - - - -
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Residues in contact with SER 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LYS* 3.7 20.1 - - - +
428B GLY* 1.3 76.2 - - - +
430B THR* 1.3 59.9 + - - +
432B LYS* 3.5 2.4 + - - +
433B LYS* 3.0 38.0 + - - +
489B MET* 3.1 43.5 + - - +
514B GLU* 4.7 2.4 + - - -
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Residues in contact with THR 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B LEU* 4.3 19.3 - - + -
427B LYS* 3.3 26.6 + - - +
429B SER* 1.3 80.2 + - - +
431B LEU* 1.3 57.9 + - - +
433B LYS* 3.1 7.6 + - - +
434B ALA* 2.8 26.7 + - - +
510B MET* 3.6 31.9 - - + +
511B ILE* 4.2 9.6 - - + -
514B GLU* 2.6 34.4 + - + +
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Residues in contact with LEU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B MET* 3.5 31.4 - - + -
388B ILE* 4.6 19.1 - - + -
426B LEU* 4.1 23.1 - - + -
427B LYS 3.3 5.8 + - - +
428B GLY 3.0 8.6 + - - +
430B THR* 1.3 79.2 - - - +
432B LYS* 1.3 58.0 + - - +
434B ALA* 3.0 7.5 + - + +
435B PHE* 2.9 60.8 + - + -
455B ILE* 5.3 0.2 - - + -
472B LEU* 4.7 0.2 - - - -
474B VAL* 5.3 0.2 - - + -
487B LEU* 3.8 20.9 - - + -
493B TYR* 4.2 13.2 - - + -
495B VAL* 4.1 13.0 - - + -
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Residues in contact with LYS 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B GLY 2.9 15.3 + - - +
429B SER 3.8 4.0 - - - +
431B LEU* 1.3 74.1 - - - +
433B LYS* 1.3 64.1 + - + +
435B PHE* 3.3 2.0 + - - +
436B GLU* 2.9 54.2 + - + +
466B GLY 4.2 5.5 + - - -
467B ASP* 5.0 6.5 + - - -
469B VAL* 3.9 32.6 + - + -
472B LEU* 4.0 18.7 - - + +
487B LEU* 4.5 2.9 - - + -
489B MET* 4.0 27.8 - - + +
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Residues in contact with LYS 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B SER* 3.0 22.7 + - - +
430B THR* 3.3 7.2 - - - +
432B LYS* 1.3 77.5 - - + +
434B ALA* 1.3 63.4 + - - +
436B GLU* 3.2 8.1 + - - +
437B HIS* 2.9 24.1 + - - +
489B MET* 6.4 0.2 - - + -
510B MET* 3.9 22.8 - - + +
514B GLU* 2.5 38.8 + - - +
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Residues in contact with ALA 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B ILE* 5.0 0.9 - - + -
430B THR 2.8 13.1 + - - +
431B LEU* 3.0 18.6 + - + +
433B LYS* 1.3 76.5 - - - +
435B PHE* 1.3 58.5 + - + +
437B HIS* 3.2 3.8 + - - +
438B SER* 2.9 25.6 + - - -
450B LEU* 4.3 8.1 - - + -
508B PHE* 3.4 26.8 - - + -
510B MET* 4.0 13.9 - - - -
511B ILE* 4.5 12.6 - - + -
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Residues in contact with PHE 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B ILE* 3.7 21.8 - - + -
431B LEU* 2.9 51.1 + - + +
432B LYS 3.9 2.5 - - - +
433B LYS 3.3 0.2 - - - -
434B ALA* 1.3 73.9 - - + +
436B GLU* 1.3 63.9 + - - +
438B SER* 3.2 15.8 - - - -
439B VAL* 3.8 1.4 + - - +
450B LEU* 4.0 16.4 - - + -
452B VAL* 3.7 25.6 - - + -
455B ILE* 3.9 14.4 - - + -
457B VAL* 4.1 17.0 - - + -
459B TYR* 3.3 35.7 - - + -
469B VAL* 3.7 17.7 - - + -
472B LEU* 4.0 26.5 - - + -
474B VAL* 6.4 0.2 - - + -
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Residues in contact with GLU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B LYS* 2.9 44.7 + - + +
433B LYS* 3.2 10.3 + - - +
435B PHE* 1.3 74.1 - - - +
437B HIS* 1.3 66.9 + - - +
439B VAL* 3.3 6.5 + - - +
440B HIS* 3.0 23.9 + - - +
466B GLY* 3.1 39.7 + - - +
467B ASP* 3.1 1.7 + - - -
468B ARG* 2.8 26.9 + - - +
469B VAL* 2.8 28.4 + - + +
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Residues in contact with HIS 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B LYS 2.9 13.6 + - - +
434B ALA 3.2 8.3 + - - +
436B GLU* 1.3 75.5 - - - +
438B SER* 1.3 62.1 + - - +
439B VAL 3.1 0.7 + - - -
440B HIS* 2.7 59.4 + + - -
441B ARG* 5.9 1.1 - - - -
448B GLU* 3.5 9.2 - - + +
506B ASP 2.8 27.7 + - - -
507B GLY* 3.3 20.6 + - - -
508B PHE* 3.7 28.5 - + - -
510B MET* 3.8 16.3 - - + +
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Residues in contact with SER 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ALA 2.9 12.2 + - - -
435B PHE* 3.2 15.9 - - - -
437B HIS* 1.3 76.5 - - - +
439B VAL* 1.3 60.7 + - - +
442B TYR* 5.4 0.9 - - - -
448B GLU* 3.7 18.1 - - - +
449B PHE* 3.4 22.9 + - - +
450B LEU* 3.1 35.1 + - - -
459B TYR* 3.1 18.5 + - - -
508B PHE* 4.5 0.7 - - - -
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Residues in contact with VAL 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B PHE 3.9 2.2 - - - +
436B GLU* 3.7 9.9 - - - +
437B HIS 3.1 0.2 - - - -
438B SER* 1.3 80.3 - - - +
440B HIS* 1.3 61.2 + - - +
441B ARG 3.2 4.0 + - - -
442B TYR* 3.2 18.8 + - + +
449B PHE* 3.8 16.4 - - + -
459B TYR* 3.5 56.8 - - + -
461B LEU* 4.1 10.5 - - + -
468B ARG* 2.9 46.2 + - + -
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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