Contacts of the strand formed by residues 330 - 334 (chain D) in PDB entry 3KHU
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 LYS 330 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D ASP 3.8 3.2 + - - +
329D LYS* 1.3 72.3 - - - +
331D ILE* 1.3 65.5 + - - +
363D HIS* 3.3 9.9 - - + +
365D HIS* 3.5 43.1 - - + +
403D GLU 3.1 15.4 + - - -
404D ALA 3.3 21.5 - - - +
406D ASP* 2.7 31.9 + - - +
407D GLY 3.8 16.6 - - - +
408D ALA* 3.3 6.6 - - + +
409D HIS* 2.9 34.7 + - + -
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Residues in contact with ILE 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D ILE* 4.7 2.9 - - + -
322D LEU* 3.9 19.3 - - + -
326D VAL* 3.4 32.3 - - + -
329D LYS* 4.1 7.0 - - + +
330D LYS* 1.3 80.6 - - - +
332D ALA* 1.3 66.4 + - - +
333D ILE* 3.7 10.1 + - + -
357D LEU* 4.4 15.3 - - + -
362D ALA* 4.0 7.9 - - + -
363D HIS 2.9 6.8 + - - +
364D LEU* 3.4 13.1 - - + +
365D HIS 2.8 24.3 + - - -
404D ALA 4.7 2.9 - - - -
408D ALA* 4.5 0.2 - - - -
409D HIS* 5.1 0.4 - - + -
410D ALA* 3.7 13.5 - - + +
412D VAL* 3.7 28.9 - - + -
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Residues in contact with ALA 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D ILE* 1.3 72.0 - - - +
333D ILE* 1.3 62.4 + - - +
334D LEU* 3.9 4.9 + - + -
365D HIS 3.3 6.7 - - - -
404D ALA* 3.2 34.4 + - + +
405D CYS* 3.9 20.9 - - - +
408D ALA* 4.3 1.7 - - + +
410D ALA 3.0 13.4 + - - +
411D VAL* 4.3 2.9 - - - +
412D VAL* 2.8 31.4 + - - +
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Residues in contact with ILE 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D ILE* 3.7 5.1 + - + -
332D ALA* 1.3 73.5 - - - +
334D LEU* 1.3 61.8 + - - +
335D GLY 3.7 19.0 + - - +
336D PHE* 4.9 0.2 - - + -
350D SER* 4.8 3.8 - - - +
353D ILE* 4.9 4.0 - - + -
354D SER* 4.0 23.3 - - - +
357D LEU* 4.0 24.5 - - + -
364D LEU* 4.1 18.4 - - + -
365D HIS 2.9 8.5 + - - +
366D ILE* 3.4 21.2 - - + +
367D TYR 2.9 28.2 + - - +
412D VAL* 3.6 24.2 - - + -
414D CYS* 4.2 14.1 - - + -
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Residues in contact with LEU 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D ALA* 4.5 5.4 - - + +
333D ILE* 1.3 76.9 - - - +
335D GLY* 1.3 59.7 + - - +
367D TYR* 3.7 22.7 - - + -
401D PRO* 4.1 14.6 - - + +
404D ALA* 4.3 12.8 - - + -
405D CYS* 4.5 4.9 - - - -
411D VAL* 3.6 30.3 - - + -
412D VAL 2.9 12.3 + - - +
413D ILE* 3.4 12.6 - - + -
414D CYS 3.0 24.3 + - - -
415D THR 3.7 0.2 + - - -
420D PHE* 3.4 29.4 - - + -
423D LEU* 3.9 27.4 - - + -
425D TYR* 5.1 1.3 - - + +
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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