Contacts of the strand formed by residues 435 - 440 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276D TYR* 3.4 5.4 - - - -
277D TYR* 2.8 95.4 + + + +
279D LEU 2.8 24.1 + - - -
280D ASN* 5.4 0.2 - - - -
413D ARG* 4.3 17.3 - - + -
414D MET 3.3 13.7 - - - +
415D SER* 3.7 5.4 - - - +
416D PHE* 4.7 1.8 - - - -
429D VAL* 3.3 53.7 + - + -
430D THR* 4.2 11.7 - - + -
432D THR* 3.3 23.6 - - - +
434D CYS* 1.3 73.1 - - - +
436D ILE* 1.3 78.7 + - - +
437D GLU* 4.2 15.0 - - + -
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Residues in contact with ILE 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D ILE* 3.8 23.6 - - + -
275D VAL 3.1 12.3 - - - +
276D TYR* 4.0 19.1 - - + -
296D VAL* 4.4 26.0 - - + -
309D PHE* 4.9 1.1 - - + -
311D LEU* 4.9 0.2 - - + -
334D VAL* 4.7 6.3 - - + -
412D ILE 3.9 0.2 - - - +
413D ARG* 3.3 3.8 - - - -
414D MET* 2.9 63.3 + - + +
416D PHE* 4.1 15.5 - - + -
435D TRP* 1.3 88.2 - - - +
437D GLU* 1.3 61.2 + - - +
438D ILE* 4.1 15.0 - - + -
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Residues in contact with GLU 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D SER 3.8 0.7 - - - +
274D ILE* 3.3 2.3 - - - -
275D VAL* 2.8 41.3 + - + +
277D TYR* 3.6 26.3 + - + -
411D THR* 4.3 13.8 + - - +
412D ILE 3.5 3.6 - - - +
413D ARG* 2.8 48.0 + - + +
435D TRP* 4.2 10.6 - - + -
436D ILE* 1.3 74.6 - - - +
438D ILE* 1.3 65.3 + - - +
439D HIS* 4.1 25.4 + - + +
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Residues in contact with ILE 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D TRP* 5.2 2.0 - - + -
272D CYS* 3.9 16.2 - - + -
273D SER 3.4 2.7 - - - -
274D ILE* 3.9 21.5 - - + -
336D LEU* 3.3 37.9 - - + -
382D ILE* 5.2 2.7 - - + -
410D CYS 3.7 0.3 - - - +
411D THR* 3.0 8.0 - - - -
412D ILE* 2.7 52.7 + - + +
414D MET* 4.0 16.8 - - + -
436D ILE* 4.1 11.0 - - + -
437D GLU* 1.3 77.6 - - - +
439D HIS* 1.3 63.6 + - - +
440D LEU* 3.9 24.7 - - + +
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Residues in contact with HIS 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D CYS* 3.1 7.6 - - - -
273D SER* 2.8 47.7 + - - +
275D VAL* 5.9 5.7 - - + +
410D CYS 3.5 2.9 - - - -
411D THR* 3.3 28.4 - - + +
437D GLU* 4.1 24.5 + - + +
438D ILE* 1.3 76.2 - - - +
440D LEU* 1.3 63.9 + - - +
441D HIS* 3.4 4.4 + - + -
444D LEU* 3.8 22.9 - - + -
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Residues in contact with LEU 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D TRP* 3.8 22.9 - - + +
272D CYS* 3.7 23.6 - - + -
343D VAL* 4.8 11.2 - - + -
383D PHE* 4.4 12.3 - - + -
410D CYS* 2.8 28.6 + - - +
412D ILE* 3.9 31.6 - - + -
438D ILE* 3.9 11.4 - - + +
439D HIS* 1.3 73.2 - - - +
441D HIS* 1.3 58.0 + - - +
442D GLY 3.5 0.9 - - - -
443D PRO* 3.7 23.6 - - + +
444D LEU* 3.0 32.2 + - - +
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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