Contacts of the strand formed by residues 430 - 434 (chain B) in PDB entry 4KMH
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 TRP 430 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A VAL* 3.8 36.2 - - + +
63A GLY* 3.3 33.9 - - - -
64A GLY* 4.2 2.5 - - - -
65A PRO* 4.1 19.3 - - + -
396B THR* 3.8 20.0 - - + -
398B LYS* 3.8 16.2 - - - -
403B ASP 5.4 3.8 - - - +
405B ALA* 3.5 26.4 - - + +
407B THR* 2.7 26.6 + - - +
417B PHE* 4.2 2.8 - - - -
426B ALA* 3.1 4.4 - - - -
427B HIS 3.0 36.6 + - - +
428B GLY 3.3 0.6 - - - -
429B PRO* 1.3 78.8 - - + +
431B LEU* 1.3 71.2 + - - +
432B GLN* 3.9 4.8 + - + -
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Residues in contact with LEU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B TRP* 3.5 34.1 - - + +
366B LEU* 3.9 22.4 - - + -
369B VAL* 4.3 7.2 - - + -
371B LEU* 3.8 21.5 - - + -
405B ALA 2.7 11.6 + - - +
406B ILE* 3.4 6.4 - - + -
407B THR* 2.7 32.9 + - - -
424B TYR* 4.5 3.1 - - + -
425B ALA 3.4 31.0 - - - +
426B ALA* 4.0 3.6 - - + -
429B PRO 3.5 0.6 + - - -
430B TRP* 1.3 75.4 - - - +
432B GLN* 1.3 57.2 + - - +
433B ILE* 3.4 35.0 - - + -
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Residues in contact with GLN 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE 4.9 0.2 + - - -
58A VAL* 4.8 13.7 - - - +
59A LYS 5.4 0.4 - - - +
62A LEU* 4.5 12.5 - - - +
407B THR* 3.3 20.0 - - + +
409B VAL* 4.8 7.9 - - + +
415B GLY 4.9 1.0 + - - -
416B ALA* 3.6 15.2 - - - +
417B PHE* 3.0 62.8 + - + +
418B ALA* 3.4 14.0 + - + +
423B PRO 3.2 4.5 - - - +
424B TYR* 3.7 1.6 - - - -
425B ALA 2.7 37.3 + - - +
430B TRP* 4.8 3.6 - - + -
431B LEU* 1.3 76.9 - - - +
433B ILE* 1.3 60.8 + - - +
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Residues in contact with ILE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B VAL* 5.3 0.4 - - + -
371B LEU* 4.2 17.7 - - + -
406B ILE* 3.8 13.2 - - + -
407B THR 2.9 15.0 + - - +
408B PHE* 3.6 9.3 - - + -
409B VAL* 2.9 30.5 + - - +
423B PRO 3.3 4.7 - - - +
424B TYR* 4.0 19.7 - - + -
431B LEU* 3.4 26.9 - - + -
432B GLN* 1.3 73.2 - - - +
434B LEU* 1.3 60.1 + - - +
435B LEU* 3.5 42.6 + - + +
469B LEU* 4.1 13.9 - - + -
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Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B VAL* 3.5 11.4 - - + +
410B SER 3.2 26.7 - - - +
411B THR* 4.1 19.3 - - + -
413B VAL* 5.0 2.9 - - + -
416B ALA* 5.3 0.4 - - + -
418B ALA* 3.4 26.4 - - + +
419B THR* 3.7 23.6 - - - +
420B GLU* 3.9 27.6 - - + +
423B PRO* 2.8 28.9 + - - +
424B TYR* 4.9 0.2 - - - -
432B GLN 4.1 0.6 + - - -
433B ILE* 1.3 71.3 - - - +
435B LEU* 1.3 76.0 + - - +
436B THR* 4.4 2.0 - - + +
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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