Contacts of the strand formed by residues 420 - 427 (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 THR 420 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B GLY 5.2 1.1 - - - +
419B GLY* 1.3 79.3 - - - +
421B PHE* 1.3 65.6 + - - +
422B ASP* 2.7 23.8 + - - -
498B PRO* 3.4 5.0 - - - +
499B ASN* 2.8 46.4 + - - +
520B SER* 4.8 5.0 - - - -
521B GLY 3.6 15.2 + - - +
522B ASP 3.2 10.8 - - - +
523B GLN* 3.5 27.1 - - - +
524B ASP* 4.1 0.7 - - - +
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Residues in contact with PHE 421 (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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364B ILE* 3.7 21.8 - - + -
368B MET* 3.4 47.6 - - + -
389B LEU* 4.9 4.0 - - + -
415B LEU* 4.7 6.5 - - + -
420B THR* 1.3 76.0 - - - +
422B ASP* 1.3 63.4 + - - +
423B LEU* 5.1 1.4 - - - +
496B ILE* 4.2 16.3 - - + +
497B LEU 3.6 2.7 - - - -
498B PRO* 4.4 15.9 - - + -
521B GLY* 3.2 17.7 - - - -
522B ASP 2.9 12.9 + - - +
524B ASP* 3.3 44.0 - - + -
527B VAL* 3.7 32.3 - - + -
528B VAL* 4.2 6.5 - - + -
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Residues in contact with ASP 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B THR* 2.7 25.7 + - - -
421B PHE* 1.3 73.3 - - - +
423B LEU* 1.3 63.8 + - - +
495B VAL 3.9 0.3 - - - +
496B ILE* 3.2 5.5 - - - +
497B LEU* 2.7 46.3 + - + +
499B ASN* 3.1 23.2 - - - +
518B HIS* 2.5 34.3 + - + +
519B ASP 3.3 8.1 - - - +
520B SER* 3.3 12.3 - - - -
521B GLY 2.9 14.1 + - - +
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Residues in contact with LEU 423 (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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372B ASN* 3.3 32.8 - - - +
381B TRP* 3.3 45.8 - - + +
384B VAL* 4.1 17.9 - - + -
421B PHE 5.1 2.0 - - - +
422B ASP* 1.3 75.6 - - - +
424B VAL* 1.3 62.7 + - - +
495B VAL 3.6 2.0 - - - +
496B ILE* 3.7 35.0 - - + -
518B HIS* 3.4 3.8 - - - -
519B ASP* 2.9 40.1 + - + +
520B SER 5.9 2.2 - - - +
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Residues in contact with VAL 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B TRP* 3.5 7.4 - - - -
423B LEU* 1.3 81.8 - - - +
425B GLN* 1.3 60.7 + - - +
426B LEU* 3.9 26.2 - - + -
493B TYR 3.9 0.2 - - - +
494B LYS* 3.5 3.8 - - - -
495B VAL* 2.9 41.1 + - + +
497B LEU* 3.9 34.3 - - + -
502B ALA* 4.2 8.5 - - + -
511B ILE* 5.2 0.7 - - + -
515B LEU* 4.2 9.6 - - + -
517B ARG 3.1 12.6 - - - +
518B HIS* 3.9 19.7 - - + -
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Residues in contact with GLN 425 (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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380B PHE* 3.4 29.6 - - - -
381B TRP* 4.5 5.4 - - + -
424B VAL* 1.3 73.9 - - - +
426B LEU* 1.3 64.6 + - - +
492B VAL* 3.6 27.6 - - + +
493B TYR 3.3 6.1 - - - +
494B LYS* 4.5 12.1 - - + +
515B LEU* 3.7 0.2 - - - -
516B LEU* 2.9 44.9 + - + +
517B ARG* 3.1 32.6 + - + +
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Residues in contact with LEU 426 (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* 5.5 0.7 - - + -
424B VAL* 3.9 24.2 - - + -
425B GLN* 1.3 85.1 - - - +
427B LYS* 1.3 68.7 + - - +
430B THR* 4.3 19.1 - - + -
431B LEU* 4.1 30.1 - - + +
492B VAL* 4.2 4.3 - - - -
493B TYR* 2.7 45.3 + - - +
495B VAL* 4.4 9.9 - - + -
497B LEU* 5.1 2.2 - - + -
511B ILE* 4.2 24.2 - - + -
515B LEU* 3.6 27.8 - - + +
516B LEU* 4.7 1.1 - - - -
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Residues in contact with LYS 427 (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* 1.3 78.4 - - - +
428B GLY* 1.3 64.7 - - - +
429B SER* 3.7 20.4 - - - +
430B THR* 3.3 13.1 + - - +
431B LEU* 3.3 17.3 + - - +
489B MET 4.4 3.6 - - - +
490B ASP 6.1 0.4 - - - -
491B GLU 3.6 7.6 - - - +
492B VAL* 4.4 7.2 - - + +
493B TYR* 4.5 0.2 - - - -
514B GLU* 3.2 38.1 + - - +
516B LEU* 3.9 30.5 - - + +
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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