Contacts of the strand formed by residues 363 - 367 (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 HIS 363 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328D ASP* 3.3 43.2 + - + -
329D LYS 2.7 13.7 + - - +
330D LYS* 3.3 9.8 + - + +
331D ILE 2.9 25.5 + - - +
361D GLY 3.7 4.0 + - - -
362D ALA* 1.3 69.6 - - - +
364D LEU* 1.3 63.9 + - - +
365D HIS* 3.6 12.7 - - + +
393D ARG 4.0 15.5 + - - -
394D LEU* 3.4 29.3 - - + +
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Residues in contact with LEU 364 (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* 3.4 19.1 - - + +
333D ILE* 4.1 9.9 - - + -
354D SER* 3.5 48.7 - - - +
357D LEU* 4.0 15.9 - - + -
358D MET* 4.0 15.3 - - + -
362D ALA* 3.9 26.9 - - + +
363D HIS* 1.3 72.3 - - - +
365D HIS* 1.3 63.1 + - - +
366D ILE* 4.0 16.6 - - + -
394D LEU 2.9 10.4 + - - +
395D VAL* 4.8 4.3 - - + -
396D THR* 2.8 28.2 + - - +
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Residues in contact with HIS 365 (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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330D LYS* 3.5 41.5 + - + +
331D ILE 2.8 10.1 + - - +
332D ALA* 3.3 3.8 - - - -
333D ILE 2.9 22.6 + - - -
363D HIS* 3.6 20.1 - - - +
364D LEU* 1.3 79.9 - - - +
366D ILE* 1.3 62.8 + - - +
396D THR* 3.2 36.5 + - + +
398D SER* 3.6 16.6 + - - +
403D GLU 4.6 1.6 + - - -
404D ALA* 3.6 21.4 - - - +
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Residues in contact with ILE 366 (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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333D ILE* 3.4 20.9 - - + +
336D PHE* 3.7 33.7 - - + -
354D SER* 4.3 7.4 - - - +
364D LEU* 4.2 13.7 - - + -
365D HIS* 1.3 75.2 - - - +
367D TYR* 1.3 63.6 + - - +
376D ILE* 4.0 23.5 - - + +
380D LEU* 3.6 31.4 - - + -
395D VAL* 4.1 9.6 - - + -
396D THR 2.9 12.9 + - - +
397D ILE* 3.7 11.6 - - + +
398D SER* 2.9 24.8 + - - +
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Residues in contact with TYR 367 (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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333D ILE 2.9 10.0 + - - +
334D LEU* 3.7 14.3 - - + -
335D GLY 2.9 27.7 + - - -
365D HIS 3.9 0.8 + - - -
366D ILE* 1.3 76.3 - - - +
368D ASP* 1.3 68.6 + - - +
369D PRO* 3.4 39.4 - - + +
398D SER* 3.8 13.7 - - - +
399D LYS 3.5 18.8 - - - -
400D ASP* 3.6 21.8 - - + -
401D PRO* 3.8 25.0 - - + +
404D ALA* 4.4 4.9 - - + -
419D MET* 3.6 27.7 - - + +
420D PHE* 4.0 11.2 - + - -
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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