Contacts of the strand formed by residues 330 - 334 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ASP 3.8 3.0 + - - +
329A LYS* 1.3 73.8 - - - +
331A ILE* 1.3 65.1 + - - +
363A HIS* 3.3 10.5 - - + +
365A HIS* 3.5 42.3 - - + +
403A GLU 3.1 15.8 + - - -
404A ALA 3.1 21.5 - - - +
406A ASP* 2.8 31.3 + - - +
407A GLY* 3.8 15.9 - - - +
408A ALA* 3.3 7.5 - - + +
409A HIS* 2.8 34.2 + - - -
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Residues in contact with ILE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ILE* 4.7 2.9 - - + -
322A LEU* 3.9 19.5 - - + -
326A VAL* 3.4 30.3 - - + -
329A LYS* 3.8 7.0 - - + +
330A LYS* 1.3 84.7 - - - +
332A ALA* 1.3 66.3 + - - +
333A ILE* 3.7 9.7 + - + -
357A LEU* 4.3 17.3 - - + -
362A ALA* 4.0 8.1 - - + -
363A HIS 2.9 5.5 + - - -
364A LEU* 3.4 11.9 - - + +
365A HIS 2.9 24.1 + - - -
404A ALA 4.7 0.2 - - - -
408A ALA* 4.5 0.2 - - - -
409A HIS* 5.1 0.4 - - + -
410A ALA* 3.7 16.6 - - + +
412A VAL* 3.7 24.9 - - + -
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Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A ILE* 1.3 73.6 - - - +
333A ILE* 1.3 61.7 + - - +
334A LEU* 3.9 3.4 - - + -
365A HIS 3.4 5.8 - - - -
404A ALA* 3.5 32.3 - - + +
405A CYS* 3.9 21.3 - - - -
408A ALA* 4.2 1.4 - - - +
410A ALA 3.0 14.7 + - - +
411A VAL* 3.7 5.3 - - + -
412A VAL* 2.8 32.1 + - - +
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Residues in contact with ILE 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A ILE* 4.3 4.5 - - + -
332A ALA* 1.3 72.4 - - - +
334A LEU* 1.3 62.9 + - - +
335A GLY 3.8 18.8 - - - +
336A PHE* 4.8 2.7 - - + -
350A SER* 4.9 1.1 - - - -
353A ILE* 4.9 4.5 - - + -
354A SER* 4.0 24.0 - - - +
357A LEU* 4.1 23.6 - - + -
364A LEU* 4.2 14.6 - - + -
365A HIS 3.0 7.3 + - - +
366A ILE* 4.0 27.3 - - + +
367A TYR 3.0 26.7 + - - +
412A VAL* 3.5 26.9 - - + +
414A CYS* 4.4 9.2 - - - -
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A ALA* 4.6 4.5 - - + -
333A ILE* 1.3 75.9 - - - +
335A GLY* 1.3 58.8 + - - +
367A TYR* 3.7 18.4 - - + -
401A PRO* 4.1 23.6 - - + +
404A ALA* 4.4 9.9 - - + -
405A CYS* 4.7 5.2 - - - -
411A VAL* 3.6 30.1 - - + -
412A VAL 2.8 12.3 + - - +
413A ILE* 3.4 14.8 - - + -
414A CYS 3.0 25.8 + - - -
415A THR 3.7 0.2 + - - -
420A PHE* 3.5 25.5 - - + -
423A LEU* 3.9 26.9 - - + -
425A TYR* 5.0 1.1 - - - +
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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