Contacts of the strand formed by residues 330 - 334 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C ASP 3.7 2.6 + - - -
329C LYS* 1.3 71.9 - - - +
331C ILE* 1.3 64.0 + - - +
363C HIS* 3.3 7.4 - - - -
365C HIS* 3.5 42.5 - - + +
403C GLU 3.0 16.8 + - - -
404C ALA 3.2 21.5 - - - +
406C ASP* 2.7 30.7 + - - +
407C GLY* 3.7 16.8 - - - +
408C ALA* 3.4 7.7 - - + +
409C HIS* 2.9 33.7 + - + -
604C EDO 4.4 16.4 + - - +
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Residues in contact with ILE 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C ILE* 4.7 2.9 - - + -
322C LEU* 3.9 20.6 - - + -
326C VAL* 3.4 30.5 - - + -
329C LYS* 4.0 6.1 - - + +
330C LYS* 1.3 83.7 - - - +
332C ALA* 1.3 65.6 + - - +
333C ILE* 3.7 9.0 + - + -
357C LEU* 4.4 15.9 - - + -
362C ALA* 4.1 7.6 - - + -
363C HIS 2.9 6.9 + - - -
364C LEU* 3.4 13.4 - - + +
365C HIS 2.9 24.2 + - - -
408C ALA* 4.5 0.2 - - - -
409C HIS* 5.1 0.4 - - + -
410C ALA* 3.7 14.4 - - + +
412C VAL* 3.7 29.4 - - + -
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Residues in contact with ALA 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C ILE* 1.3 71.6 - - - +
333C ILE* 1.3 61.7 + - - +
334C LEU* 4.6 2.7 - - + -
365C HIS 3.4 6.3 - - - -
404C ALA* 3.4 32.8 - - + +
405C CYS* 3.8 21.3 - - - -
408C ALA* 4.3 1.8 - - - +
410C ALA 3.0 14.6 + - - +
411C VAL* 4.2 5.8 - - + -
412C VAL* 2.8 32.1 + - - +
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Residues in contact with ILE 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C ILE* 4.2 4.3 - - + -
332C ALA* 1.3 73.0 - - - +
334C LEU* 1.3 61.4 + - - +
335C GLY 3.8 18.8 - - - +
336C PHE* 4.9 0.4 - - + -
350C SER* 4.8 3.4 - - - -
353C ILE* 4.9 4.0 - - + -
354C SER* 4.0 23.3 - - - +
357C LEU* 4.0 23.3 - - + -
364C LEU* 4.2 15.7 - - + -
365C HIS 2.9 7.4 + - - +
366C ILE* 3.4 24.2 - - + +
367C TYR 2.9 27.4 + - - +
412C VAL* 3.5 25.1 - - + -
414C CYS* 4.2 13.0 - - - -
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Residues in contact with LEU 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C ALA* 4.6 4.7 - - + -
333C ILE* 1.3 76.6 - - - +
335C GLY* 1.3 59.1 + - - +
367C TYR* 3.7 22.0 - - + -
401C PRO* 4.2 13.9 - - + -
404C ALA* 4.4 12.6 - - + -
405C CYS* 4.6 7.0 - - - -
411C VAL* 3.6 29.2 - - + -
412C VAL 2.9 12.1 + - - +
413C ILE* 3.4 12.6 - - + -
414C CYS 3.0 26.5 + - - -
415C THR 3.6 0.2 + - - -
420C PHE* 3.5 28.4 - - + -
423C LEU* 3.8 28.5 - - + -
425C TYR* 5.0 2.7 - - + +
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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