Contacts of the helix formed by residues 356 - 366 (chain B) in PDB entry 3KCZ
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 HIS 356 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239B GLN* 5.7 1.3 - - - -
354B PRO 3.7 3.4 + - - -
355B GLU* 1.3 75.2 - - - +
357B PRO* 1.3 82.4 - - + +
358B LEU* 3.3 48.4 + - + +
359B ASP* 3.1 23.2 + - - +
360B GLN* 3.0 18.1 + - - +
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Residues in contact with PRO 357 (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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349B THR* 4.2 21.5 - - + -
355B GLU 3.7 4.2 - - - +
356B HIS* 1.3 101.0 - - + +
358B LEU* 1.3 58.6 + - + +
360B GLN* 3.2 9.0 + - + +
361B HIS* 2.8 51.2 + - + +
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Residues in contact with LEU 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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234B MET* 3.4 20.2 - - - +
239B GLN* 4.2 29.2 - - + +
242B ILE* 3.9 20.8 - - + +
243B LYS* 3.8 47.8 - - + +
356B HIS* 3.1 26.2 + - + +
357B PRO* 1.3 79.1 - - + +
359B ASP* 1.3 58.9 + - - +
361B HIS* 3.4 13.3 + - + +
362B TYR* 3.0 22.9 + - - +
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Residues in contact with ASP 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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233B SER* 6.0 0.7 - - - -
234B MET* 3.2 37.6 + - - +
355B GLU* 3.7 17.8 - - + +
356B HIS* 3.1 24.7 + - - +
358B LEU* 1.3 74.4 - - - +
360B GLN* 1.3 60.6 + - - +
362B TYR* 3.8 2.8 - - - +
363B ARG* 2.9 31.4 + - - +
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Residues in contact with GLN 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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346B LEU 4.9 0.2 - - - +
348B LYS 2.9 27.2 - - - +
349B THR* 3.4 16.7 - - - +
350B GLU* 4.0 27.0 + - - +
353B SER* 3.6 21.6 + - - -
355B GLU* 3.8 27.9 + - - +
356B HIS 3.0 11.3 + - - +
357B PRO* 3.3 9.9 - - - +
359B ASP* 1.3 74.4 - - - +
361B HIS* 1.3 69.8 + - - +
363B ARG* 3.3 10.2 + - - +
364B ASN* 2.9 42.3 + - - +
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Residues in contact with HIS 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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242B ILE* 3.8 18.2 - - + -
246B CYS* 3.9 31.1 - - + +
346B LEU* 3.9 13.0 + - + +
347B VAL* 3.3 44.4 - - + +
349B THR* 4.3 12.1 - - + -
357B PRO* 2.8 38.3 + - - +
358B LEU* 3.8 11.4 - - + +
360B GLN* 1.3 76.5 + - - +
362B TYR* 1.3 63.6 + - - +
364B ASN* 3.1 12.1 + - - +
365B LEU* 3.2 17.3 + - - +
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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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234B MET* 3.5 22.2 - - + -
238B VAL* 4.3 10.8 - - + -
242B ILE* 4.0 23.0 - - + +
358B LEU 3.0 17.8 + - - +
359B ASP* 3.8 3.4 - - - +
361B HIS* 1.3 75.7 - - - +
363B ARG* 1.3 66.0 - - + +
365B LEU* 3.2 23.2 + - + +
366B HIS* 3.9 1.9 + - - -
367B CYS 3.5 22.1 + - - +
368B ALA* 3.2 9.8 - - - +
369B LEU* 2.9 45.3 + - + -
370B ARG* 5.4 1.4 - - - +
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Residues in contact with ARG 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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350B GLU* 5.1 7.1 + - - -
355B GLU* 2.7 37.4 + - - -
359B ASP 2.9 17.8 + - - +
360B GLN* 3.6 15.0 - - - +
362B TYR* 1.3 79.2 - - - +
364B ASN* 1.3 80.8 + - - +
365B LEU 3.1 1.7 + - - -
366B HIS* 3.1 28.5 + - + +
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Residues in contact with ASN 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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346B LEU* 3.5 42.7 + - + +
348B LYS 5.3 0.8 + - - -
350B GLU* 5.9 0.6 + - - -
360B GLN* 2.9 37.7 + - - +
361B HIS 3.1 5.8 + - - +
363B ARG* 1.3 95.6 + - - +
365B LEU* 1.3 56.9 + - - +
366B HIS* 3.2 23.6 + - - -
440B SER* 4.5 2.8 - - - -
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Residues in contact with LEU 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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242B ILE* 4.0 26.5 - - + -
245B ILE* 4.4 3.1 - - + -
346B LEU* 3.9 17.7 - - + -
361B HIS* 3.2 12.5 + - + +
362B TYR* 3.2 13.4 + - + +
363B ARG 3.1 1.6 + - - -
364B ASN* 1.3 76.2 - - - +
366B HIS* 1.3 68.1 + - - +
367B CYS* 3.2 13.4 + - + +
369B LEU* 4.2 17.0 - - + -
409B LYS* 2.8 18.4 + - - -
436B VAL* 3.9 36.3 - - + +
439B LEU* 4.3 14.8 - - + -
440B SER* 3.4 15.5 - - - +
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Residues in contact with HIS 366 (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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273A ALA* 3.8 29.0 - - + +
362B TYR 3.9 0.8 + - - -
363B ARG* 3.1 26.1 + - + +
364B ASN* 3.2 30.9 + - - -
365B LEU* 1.3 76.8 - - - +
367B CYS* 1.3 56.9 + - - +
409B LYS* 2.9 28.3 + - - +
410B ASP* 3.3 36.2 + - + +
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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