Contacts of the helix formed by residues 357 - 365 (chain B) in PDB entry 1KHU
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 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355B VAL* 3.9 9.4 + - - -
356B GLN* 1.3 75.7 - - - +
358B ARG* 1.3 53.6 + - - +
359B ASN* 4.0 3.1 + - - +
360B CYS* 3.4 18.0 + - - -
361B ASN* 2.7 47.3 + - - +
368B PRO 5.1 0.2 - - - -
382B ILE* 2.6 27.9 + - - -
411B THR 5.4 0.4 - - - -
412B ILE* 3.5 25.2 - - - +
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Residues in contact with ARG 358 (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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356B GLN* 4.2 16.0 + - - +
357B SER* 1.3 67.5 + - - +
359B ASN* 1.3 57.4 + - - +
361B ASN* 2.9 9.0 + - - +
362B TYR* 2.6 37.5 + - - +
368B PRO* 3.8 37.5 + - + +
369B THR* 4.8 10.9 - - - +
405B GLU 5.7 0.2 - - - -
408B LYS* 3.5 58.3 + - - +
409B MET* 3.6 25.0 + - - +
411B THR 5.4 3.6 + - - -
412B ILE* 5.6 0.6 - - - +
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Residues in contact with ASN 359 (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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357B SER* 3.4 2.7 - - - +
358B ARG* 1.3 77.4 - - - +
360B CYS* 1.3 66.7 + - - +
362B TYR* 3.0 4.7 + - - +
363B HIS* 2.9 23.4 + - - +
383B PHE* 3.2 46.1 - - + +
384B ASN* 2.7 45.7 - - - +
387B GLU* 4.3 8.4 - - - +
388B PHE 4.0 6.9 + - - -
409B MET* 3.6 27.1 + - + +
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Residues in contact with CYS 360 (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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357B SER* 3.2 25.8 + - - +
358B ARG 3.2 0.4 - - - -
359B ASN* 1.3 84.9 - - - +
361B ASN* 1.3 69.1 + - - +
363B HIS* 3.0 15.4 + - - +
364B HIS* 3.1 34.4 + - - -
372B CYS* 4.9 6.3 - - - -
380B LEU* 4.2 19.5 - - - -
381B LYS 3.2 23.8 - - - -
382B ILE* 3.7 12.1 - - - +
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Residues in contact with ASN 361 (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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355B VAL 5.3 0.4 + - - -
356B GLN* 4.5 0.2 - - - +
357B SER 2.7 33.8 + - - +
358B ARG* 3.4 7.0 - - - +
360B CYS* 1.3 74.2 - - - +
362B TYR* 1.3 57.7 + - - +
364B HIS 3.6 0.2 + - - -
365B GLY 3.0 6.2 + - - -
366B PHE* 2.9 42.0 + - + +
367B HIS 3.9 12.3 - - - +
368B PRO* 3.2 20.8 - - + +
370B THR* 2.8 41.2 + - - +
372B CYS* 3.9 19.2 - - - -
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Residues in contact with TYR 362 (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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358B ARG 2.6 19.5 + - - +
359B ASN* 3.3 9.6 - - - +
361B ASN* 1.3 73.5 - - - +
363B HIS* 1.3 65.5 + - - +
365B GLY* 3.5 10.5 + - - -
366B PHE 5.0 1.6 - - - -
387B GLU* 4.7 15.7 - - + -
391B LEU* 3.8 42.1 - - + +
394B GLN* 5.6 2.8 + - - -
409B MET* 5.2 10.3 - - + -
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Residues in contact with HIS 363 (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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359B ASN* 2.9 17.1 + - - +
360B CYS* 3.0 10.5 + - - +
362B TYR* 1.3 81.3 - - - +
364B HIS* 1.3 84.9 + + + +
381B LYS* 5.3 17.2 + - + -
384B ASN* 5.1 17.2 + - + +
387B GLU* 5.8 8.9 + - + +
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Residues in contact with HIS 364 (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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360B CYS* 3.1 33.9 + - - +
363B HIS* 1.3 101.9 - + + +
365B GLY* 1.3 59.7 + - - +
366B PHE* 3.3 49.6 + + + -
380B LEU* 4.2 9.9 - - + +
381B LYS* 4.6 4.3 - - + -
423D GLU* 3.6 26.8 + - - -
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Residues in contact with GLY 365 (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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361B ASN 3.0 5.8 + - - -
362B TYR* 3.5 8.4 + - - -
363B HIS 3.4 2.8 - - - -
364B HIS* 1.3 79.5 - - - +
366B PHE* 1.3 68.9 + - - +
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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