Contacts of the strand formed by residues 272 - 278 (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 CYS 272 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270D HIS* 3.1 4.4 - - - +
271D TRP* 1.3 124.2 - - + +
273D SER* 1.3 61.7 + - - +
274D ILE* 3.7 28.3 - - - -
288D HIS* 4.1 1.2 - - - -
289D ALA* 3.3 32.2 + - - +
294D VAL* 5.0 0.2 - - - -
336D LEU* 5.0 0.4 - - - -
438D ILE* 3.9 5.8 - - + -
439D HIS 3.1 15.3 - - - +
440D LEU* 3.7 8.1 - - + -
441D HIS* 3.9 10.0 - - - -
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Residues in contact with SER 273 (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* 1.3 73.2 - - - +
274D ILE* 1.3 62.7 + - - +
275D VAL* 5.8 2.2 - - - +
286D ALA* 5.8 2.9 - - - -
287D PHE 3.5 6.3 - - - -
288D HIS* 3.9 19.7 - - - -
437D GLU 3.8 1.0 - - - +
438D ILE* 3.4 1.7 - - - -
439D HIS* 2.8 47.1 + - - +
441D HIS* 3.3 25.2 + - - -
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Residues in contact with ILE 274 (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* 3.7 24.0 - - - -
273D SER* 1.3 81.6 - - - +
275D VAL* 1.3 69.3 + - - +
286D ALA* 3.8 1.8 - - - +
287D PHE* 3.1 52.9 + - + +
294D VAL* 4.4 2.7 - - + -
296D VAL* 4.4 9.4 - - + -
309D PHE* 3.6 23.0 - - + -
336D LEU* 3.8 19.5 - - + -
436D ILE* 3.8 32.5 - - + -
437D GLU 3.3 8.3 - - - +
438D ILE* 3.9 11.4 - - + -
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Residues in contact with VAL 275 (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* 5.8 2.5 - - - +
274D ILE* 1.3 79.7 - - - +
276D TYR* 1.3 63.1 + - - +
277D TYR* 3.5 27.9 - - + +
282D ARG* 3.0 51.6 - - + +
286D ALA* 4.4 7.2 - - + +
309D PHE* 4.7 0.7 - - - -
436D ILE* 3.1 9.2 - - - -
437D GLU* 2.8 44.2 + - + +
439D HIS* 5.9 5.8 - - + +
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Residues in contact with TYR 276 (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 4.4 0.2 + - - -
275D VAL* 1.3 74.8 - - - +
277D TYR* 1.3 73.1 - - - +
278D GLU* 2.5 41.3 + - + -
282D ARG* 3.4 11.0 - - - +
283D VAL* 2.8 62.5 + - + +
285D GLU 5.4 0.4 + - - -
309D PHE* 4.3 18.7 - - + -
311D LEU* 3.9 24.9 - - + -
314D LEU* 3.6 19.5 - - + -
327D ARG* 3.5 13.1 + - - +
330D ILE* 4.7 2.2 - - + +
416D PHE* 4.8 1.3 - + - -
434D CYS* 3.4 23.6 - - + -
435D TRP 3.4 16.8 - - - -
436D ILE* 4.0 10.5 - - + -
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Residues in contact with TYR 277 (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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275D VAL* 3.5 28.1 - - + +
276D TYR* 1.3 88.8 - - - +
278D GLU* 1.3 63.9 + - - +
279D LEU 4.0 3.1 - - - +
280D ASN 4.3 8.1 - - - -
281D ASN 3.2 22.7 - - - +
282D ARG* 3.7 19.2 - - + +
283D VAL 4.3 0.9 - - - +
434D CYS* 3.6 0.7 - - - -
435D TRP* 2.8 90.7 + + + +
437D GLU* 3.6 20.8 + - + -
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Residues in contact with GLU 278 (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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276D TYR* 2.5 26.7 + - + +
277D TYR* 1.3 76.8 - - - +
279D LEU* 1.3 73.6 - - - +
281D ASN* 2.8 24.5 + - - +
283D VAL* 3.3 16.4 - - + -
316D ASN* 2.7 26.5 - - - +
319D ARG* 2.6 48.1 + - - -
323D ILE* 3.4 18.5 - - + +
327D ARG* 3.2 6.2 - - - -
433D PRO 3.0 13.5 - - - +
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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