Contacts of the strand formed by residues 435 - 440 (chain A) 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 TRP 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A TYR* 3.3 2.7 - - - -
277A TYR* 2.7 92.4 + + + +
279A LEU 2.9 24.2 + - - -
413A ARG* 3.9 29.8 - - + -
414A MET 3.4 13.5 - - - +
415A SER* 3.5 12.3 - - - +
416A PHE* 4.8 1.8 - - - -
429A VAL* 2.9 48.7 + - + -
430A THR* 4.2 9.9 - - + -
432A THR* 3.3 17.3 - - - +
434A CYS* 1.3 75.0 - - - +
436A ILE* 1.3 89.0 + - - +
437A GLU* 4.3 5.2 - - + -
317C VAL* 4.2 9.4 - - + -
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Residues in contact with ILE 436 (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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274A ILE* 3.7 22.9 - - + -
275A VAL 3.1 13.5 - - - +
276A TYR* 3.9 19.5 - - + -
296A VAL* 4.5 22.0 - - + -
309A PHE* 4.9 1.3 - - + -
311A LEU* 4.7 0.2 - - + -
334A VAL* 4.7 2.2 - - + -
336A LEU* 5.0 0.2 - - + -
412A ILE 3.8 0.6 - - - +
413A ARG* 3.4 5.2 - - - -
414A MET* 3.0 62.8 + - + +
416A PHE* 4.3 21.8 - - + -
435A TRP* 1.3 89.9 - - - +
437A GLU* 1.3 58.6 + - - +
438A ILE* 4.4 11.9 - - + -
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Residues in contact with GLU 437 (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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273A SER 3.9 0.9 - - - +
274A ILE* 3.3 3.8 - - - -
275A VAL* 2.9 38.0 + - + +
277A TYR* 4.2 17.1 + - + -
411A THR* 4.0 15.4 + - - -
412A ILE 3.3 8.5 - - - +
413A ARG* 3.0 37.1 + - + +
435A TRP* 4.3 11.6 - - + -
436A ILE* 1.3 76.2 - - - +
438A ILE* 1.3 64.3 + - - +
439A HIS* 4.1 17.7 + - - +
315C SER* 3.1 32.9 + - - -
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Residues in contact with ILE 438 (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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271A TRP* 5.6 1.3 - - + -
272A CYS* 3.7 28.9 - - + -
273A SER 3.5 2.7 - - - -
274A ILE* 3.9 23.3 - - + -
336A LEU* 3.3 28.9 - - + -
382A ILE* 5.2 3.8 - - + -
410A CYS 3.6 1.2 - - - +
411A THR* 3.2 6.5 - - - -
412A ILE* 2.9 48.7 + - + +
414A MET* 3.7 24.5 - - + -
436A ILE* 4.4 7.0 - - + -
437A GLU* 1.3 75.0 - - - +
439A HIS* 1.3 64.5 + - - +
440A LEU* 3.8 12.9 - - + +
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Residues in contact with HIS 439 (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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272A CYS* 2.9 27.7 - - - +
273A SER* 2.8 26.0 + - - +
275A VAL* 6.1 2.7 - - + +
410A CYS 3.7 2.2 - - - -
411A THR* 3.5 23.5 - - + +
437A GLU* 4.1 14.3 + - + +
438A ILE* 1.3 74.7 - - - +
440A LEU* 1.3 61.0 + - - +
441A HIS* 3.6 5.0 + - + +
444A LEU* 3.6 24.5 - - + -
313C LEU* 2.6 42.6 + - + +
314C LEU* 5.5 0.6 - - - +
315C SER* 3.4 23.8 + - - -
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Residues in contact with LEU 440 (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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271A TRP* 3.4 21.8 - - + +
272A CYS* 3.8 19.5 - - + -
343A VAL* 4.6 10.8 - - + -
383A PHE* 5.0 14.1 - - + -
410A CYS* 3.0 37.7 + - - +
412A ILE* 3.9 24.5 - - + -
438A ILE* 3.8 16.8 - - + +
439A HIS* 1.3 70.1 - - - +
441A HIS* 1.3 65.0 + - - +
442A GLY 3.4 1.1 + - - -
443A PRO* 3.7 23.7 - - + +
444A LEU* 3.1 26.7 + - - +
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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