Contacts of the strand formed by residues 393 - 396 (chain A) in PDB entry 5KVI
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 393 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A SER 4.8 2.9 - - - -
280A ARG* 3.1 37.7 + - - +
281A THR 4.5 0.4 - - - -
282A THR* 2.8 28.5 + - - -
293A LEU* 3.8 22.5 - - + +
296A ILE* 3.2 43.7 - - + +
300A VAL* 5.2 0.9 - - + -
302A SER 3.4 1.8 + - - +
303A ILE* 3.4 9.0 - - + -
304A THR 2.8 26.2 + - - -
379A LEU* 3.8 3.3 - - - +
391A THR* 3.6 4.2 + - - -
392A ASP* 1.3 81.6 + - + +
394A ILE* 1.3 86.2 + - - +
395A VAL* 4.1 1.3 - - + -
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Residues in contact with ILE 394 (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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270A ILE* 4.4 5.6 - - + -
280A ARG 3.0 7.2 + - - +
281A THR* 3.2 28.2 - - + +
282A THR 2.7 30.7 + - - -
304A THR 3.3 7.0 - - - +
306A ILE* 3.8 25.4 - - + -
372A VAL* 4.0 17.5 - - + -
379A LEU* 3.6 22.4 - - + -
381A ILE* 3.7 36.3 - - + -
391A THR* 4.2 3.4 - - + -
393A HIS* 1.3 81.7 - - - +
395A VAL* 1.3 69.1 + - - +
396A ALA* 4.1 0.9 - - - +
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Residues in contact with VAL 395 (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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282A THR* 3.3 13.9 - - - +
284A PHE* 4.0 12.1 - - + -
293A LEU* 3.4 40.6 - - + -
303A ILE* 4.0 14.6 - - + -
304A THR 2.8 10.4 + - - +
305A ILE* 3.2 14.1 - - + +
306A ILE* 2.8 31.9 + - - -
315A LEU* 3.8 28.9 - - + -
319A LEU* 4.6 2.7 - - + -
393A HIS* 4.1 0.4 - - + -
394A ILE* 1.3 80.0 - - - +
396A ALA* 1.3 59.8 + - - +
397A ALA 5.2 0.2 - - - +
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Residues in contact with ALA 396 (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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264A PRO* 6.0 0.3 - - - +
265A ARG 5.6 0.8 - - - +
267A LEU* 4.0 26.5 - - + -
270A ILE* 4.8 2.7 - - + -
281A THR* 4.5 9.0 - - + -
282A THR 2.9 15.8 + - - +
283A LEU* 3.6 27.7 - - + +
284A PHE 3.7 13.5 + - - -
306A ILE* 3.6 8.5 - - + +
394A ILE* 4.1 2.5 - - + +
395A VAL* 1.3 73.4 - - - +
397A ALA* 1.3 61.8 + - - +
398A VAL* 3.9 4.9 - - + -
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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