Contacts of the strand formed by residues 342 - 347 (chain B) in PDB entry 1KHU
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 GLU 342 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B TYR 3.8 0.7 - - - +
338B TYR* 3.6 2.1 - - - -
339B VAL 2.9 33.0 + - - +
340B GLY 4.2 6.3 - - - +
341B GLY* 1.3 84.7 - - - +
343B VAL* 1.3 64.5 + - - +
344B TYR* 2.8 34.3 + - + -
381B LYS* 3.0 31.5 + - + +
383B PHE 3.3 12.3 - - - +
384B ASN* 3.5 22.9 - - - +
425D HIS* 4.7 7.3 - - - -
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B TRP* 4.0 21.1 - - + -
336B LEU* 6.2 0.9 - - + -
337B TYR 3.1 8.7 - - - +
338B TYR* 3.3 28.0 - - + -
341B GLY 5.5 0.2 - - - -
342B GLU* 1.3 74.9 - - - +
344B TYR* 1.3 63.9 + - - +
381B LYS* 3.7 3.8 - - - +
382B ILE* 3.1 46.7 + - + -
383B PHE* 3.0 34.1 + - + -
412B ILE* 4.9 1.3 - - + -
440B LEU* 4.2 13.0 - - + -
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Residues in contact with TYR 344 (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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335B HIS 3.5 0.7 - - - +
336B LEU* 3.5 8.1 - - - +
337B TYR* 2.6 48.2 + + + +
339B VAL* 3.9 22.7 - - + -
342B GLU* 2.8 41.8 + - + -
343B VAL* 1.3 76.7 - - - +
345B ALA* 1.3 60.4 - - - +
346B GLU 4.2 0.2 - - - -
379B SER* 4.6 3.1 - - - +
380B LEU 3.6 4.0 - - - +
381B LYS* 3.5 36.7 + - + -
382B ILE* 4.5 4.2 - - - +
464C VAL* 4.1 18.8 - - + -
423D GLU 3.0 34.5 - - - -
424D TYR 3.5 5.3 + - - -
425D HIS* 3.3 24.7 - + + +
427D GLN* 5.1 0.7 + - - -
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Residues in contact with ALA 345 (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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334B VAL* 4.4 5.8 - - + -
335B HIS 3.5 4.7 - - - -
336B LEU* 4.4 1.1 - - + -
344B TYR* 1.3 75.3 - - - +
346B GLU* 1.3 59.7 + - - +
374B ILE* 3.9 24.6 - - + +
378B CYS 4.2 0.2 - - - +
379B SER* 3.4 3.3 - - - -
380B LEU 2.9 37.2 + - - +
382B ILE* 3.8 23.6 - - + -
414B MET* 4.2 13.2 - - + -
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Residues in contact with GLU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B VAL* 3.4 5.4 - - - +
335B HIS* 2.7 50.9 + - + +
344B TYR 4.2 0.2 - - - -
345B ALA* 1.3 74.9 - - - +
347B CYS* 1.3 63.2 + - - +
348B LEU* 3.1 19.0 - - + +
374B ILE* 5.1 0.4 - - - -
377B GLY* 4.5 7.0 - - - +
378B CYS 3.6 12.6 - - - +
461C ILE 4.4 2.4 - - - +
462C SER* 2.4 36.0 + - - -
463C SER* 2.8 36.7 + - - +
464C VAL* 4.0 13.9 - - + +
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Residues in contact with CYS 347 (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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333B GLY 3.9 2.5 - - - -
345B ALA 4.3 0.4 - - - -
346B GLU* 1.3 70.1 - - - +
348B LEU* 1.3 62.6 + - - +
349B SER* 4.1 4.9 - - - -
351B SER 3.0 29.4 - - - -
353B ILE* 3.9 25.4 - - + -
374B ILE* 3.6 26.1 - - + +
375B PRO 3.1 22.0 - - - +
376B SER* 3.9 3.6 - - - -
377B GLY* 2.7 32.2 + - - -
378B CYS 3.2 7.9 + - - -
459C ASN* 4.5 0.2 + - - -
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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