Contacts of the strand formed by residues 395 - 398 (chain A) in PDB entry 4KM9
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 PHE 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A LEU* 3.6 39.9 - - + -
267A SER 3.4 6.7 - - - -
268A GLY* 3.7 13.9 - - - -
269A VAL* 3.8 18.8 - - + -
380A LEU* 4.8 7.6 - - + -
383A LEU* 4.7 6.3 - - + -
384A CYS* 3.8 32.8 - - + +
388A ARG* 3.7 12.8 - - + -
389A LEU* 5.5 0.2 - - + -
394A HIS* 1.3 74.3 - - - +
396A THR* 1.3 73.2 + - - +
397A TYR* 3.4 44.9 - + - -
406A ILE 3.9 0.7 - - - +
407A THR* 3.3 1.9 - - - -
408A PHE* 2.7 42.4 + - + +
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Residues in contact with THR 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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267A SER 3.1 10.8 + - - -
268A GLY* 3.0 6.1 - - - -
269A VAL 2.9 26.7 + - - -
394A HIS* 3.7 12.2 + - - -
395A PHE* 1.3 80.0 - - - +
397A TYR* 1.3 75.5 + - - +
398A LYS* 4.1 15.0 - - + -
406A ILE 3.4 2.9 - - - +
407A THR* 3.2 29.5 + - - +
430A TRP* 4.0 20.4 - - + -
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Residues in contact with TYR 397 (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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269A VAL* 3.5 21.3 - - + +
271A ALA* 5.3 2.5 - - + +
273A CYS* 3.7 19.9 - - + -
373A PHE* 3.9 25.4 - + + -
377A SER* 3.6 26.2 - - - -
380A LEU* 3.6 3.9 - - + -
381A ILE* 3.4 34.9 + - + +
384A CYS* 3.5 9.9 - - - +
395A PHE* 3.4 27.3 - + - -
396A THR* 1.3 73.4 - - - +
398A LYS* 1.3 61.5 + - - +
405A ALA* 3.2 5.5 - - - +
406A ILE* 2.7 44.9 + - + +
408A PHE* 3.3 37.0 - + - -
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Residues in contact with LYS 398 (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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269A VAL 3.0 9.6 + - - +
270A SER* 3.3 19.7 + - - +
271A ALA 2.6 36.5 + - - +
273A CYS* 4.1 1.3 - - - -
396A THR* 4.1 16.6 - - + -
397A TYR* 1.3 77.7 - - - +
399A SER* 1.3 59.8 + - - +
404A MET 3.6 5.6 - - - +
405A ALA* 4.2 11.0 - - + -
430A TRP* 4.0 22.2 - - + -
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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