Contacts of the helix formed by residues 276 - 291 (chain B) in PDB entry 3KHU
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 276 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ASN* 3.7 7.4 - - - +
274B GLY 3.2 1.0 - - - -
275B SER* 1.3 86.2 - - - +
277B PHE* 1.3 63.3 + - + +
278B GLN 3.6 1.1 - - - -
279B LYS* 3.5 2.3 + - - +
280B ASP* 2.8 40.3 + - - +
501B UPG 1.9 68.0 - - - +
502B UPG 3.6 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ASN* 3.7 36.6 - - + -
227B LEU* 3.7 18.4 - - + -
228B ALA* 4.0 16.8 - - + -
231B ILE* 3.9 18.4 - - + -
265B PHE* 3.9 4.3 - + - -
272B PHE* 3.8 33.0 - + + -
273B GLY 4.6 4.7 + - - +
274B GLY 4.3 3.8 + - - -
276B CYS* 1.3 78.4 - - + +
278B GLN* 1.3 67.8 + - - +
280B ASP* 4.0 2.4 - - - +
281B VAL* 3.0 31.8 + - - +
501B UPG 3.5 61.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 4.1 8.7 - - + -
273B GLY 6.2 0.2 - - - -
274B GLY 4.9 3.4 + - - +
276B CYS 3.6 0.2 - - - -
277B PHE* 1.3 77.5 - - - +
279B LYS* 1.3 65.3 + - - +
281B VAL* 4.1 0.2 - - - +
282B LEU* 2.9 47.9 + - + +
304B ILE* 4.0 27.3 - - + +
307B ASN* 5.1 4.5 + - - -
308B ASP* 4.3 13.5 - - - +
311B ARG* 4.5 11.6 + - - -
347B GLU* 4.0 38.4 + - + +
352B TYR* 4.7 4.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B THR* 3.2 24.4 + - - +
92B PRO* 4.2 4.3 - - - -
93B THR* 3.7 27.5 + - - +
102B ARG 4.8 1.9 - - - +
131B THR* 4.8 6.5 + - - +
275B SER 3.8 19.7 - - - +
276B CYS 3.7 7.4 - - - +
277B PHE 3.3 0.6 - - - -
278B GLN* 1.3 79.7 - - - +
280B ASP* 1.3 60.4 + - - +
282B LEU* 3.8 5.3 - - - +
283B ASN* 3.0 28.1 + - + +
347B GLU* 6.1 0.4 - - - +
502B UPG 5.7 6.3 + - - -
602B EDO 2.7 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B THR* 3.9 14.6 + - - +
220B LYS* 4.4 1.9 - - - +
221B LEU* 3.8 27.0 - - + +
224B ASN* 2.7 39.2 + - + +
276B CYS* 2.8 26.3 + - - +
277B PHE 4.1 1.6 - - - +
279B LYS* 1.3 76.4 + - - +
281B VAL* 1.3 61.5 + - - +
283B ASN* 3.3 3.6 + - - +
284B LEU* 3.0 27.0 + - - +
501B UPG 4.1 3.6 + - - -
502B UPG 5.8 1.6 - - - -
602B EDO 2.8 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ASN 4.8 0.7 - - - +
225B ALA* 3.8 32.3 - - + +
228B ALA* 4.4 13.9 - - + -
277B PHE 3.0 23.4 + - - +
280B ASP* 1.3 73.2 - - + +
282B LEU* 1.3 62.1 + - - +
284B LEU* 3.2 7.3 + - + +
285B VAL* 3.0 30.9 + - + +
300B TRP* 3.7 31.0 - - + +
303B VAL* 4.5 8.7 - - + -
304B ILE* 3.9 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLY 3.9 17.7 - - - +
102B ARG* 4.0 32.3 - - + +
278B GLN* 2.9 49.6 + - + +
279B LYS* 3.9 5.2 - - - +
281B VAL* 1.3 75.4 - - - +
283B ASN* 1.3 58.5 + - - +
285B VAL* 3.3 4.8 + - + +
286B TYR* 2.9 28.2 + - - +
301B GLN* 3.9 23.6 - - - +
304B ILE* 4.2 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ARG 3.3 20.0 + - - +
103B ALA* 4.0 3.2 - - - +
104B ALA* 3.4 27.9 - - - +
133B PRO* 3.6 21.2 - - - +
134B VAL 4.7 0.3 + - - -
221B LEU* 3.6 16.9 - - + +
279B LYS* 3.0 18.1 + - + +
280B ASP 3.5 5.2 - - - +
281B VAL 3.2 0.2 - - - -
282B LEU* 1.3 76.2 - - - +
284B LEU* 1.3 59.2 + - - +
286B TYR* 3.3 6.1 + - - +
287B LEU* 2.8 31.2 + - - +
602B EDO 4.0 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 4.9 5.6 - - + -
240A LEU* 4.7 9.6 - - + -
218B LEU* 3.9 28.3 - - + -
221B LEU* 4.5 15.0 - - + +
222B ALA* 4.8 8.3 - - - -
225B ALA* 3.9 27.4 - - + -
280B ASP 3.0 13.0 + - - +
281B VAL* 3.4 9.9 - - - +
283B ASN* 1.3 78.1 + - - +
285B VAL* 1.3 63.1 + - - +
287B LEU* 3.3 15.9 + - + +
288B CYS* 3.0 29.1 + - - -
300B TRP* 4.0 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ARG* 3.9 18.8 - - - +
281B VAL* 3.0 21.1 + - + +
282B LEU* 3.6 10.1 - - + +
284B LEU* 1.3 75.7 - - - +
286B TYR* 1.3 64.1 + - - +
288B CYS* 3.1 10.3 + - - +
289B GLU* 3.0 29.9 + - - +
297B ALA* 3.7 18.8 - - + +
300B TRP* 4.0 10.5 - - + +
301B GLN* 3.7 48.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B MET* 4.6 5.8 + - + +
99B GLY* 3.7 24.4 - - - -
102B ARG* 4.0 36.5 - - + +
103B ALA* 3.6 26.5 - - + -
135B ARG* 5.2 5.8 - - - -
282B LEU 2.9 17.1 + - - +
283B ASN* 3.3 8.7 + - - +
285B VAL* 1.3 74.5 - - - +
287B LEU* 1.3 68.0 + - + +
289B GLU* 3.1 10.0 + - + +
290B ALA* 2.9 36.5 + - + +
320D ASP* 4.9 5.7 + - - -
324D ASN* 3.2 23.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 4.2 20.0 - - + -
244A THR* 5.0 0.9 - - + -
134B VAL* 3.7 44.4 - - + +
135B ARG* 3.7 29.2 - - - +
218B LEU* 4.9 0.9 - - + -
221B LEU* 5.2 2.0 - - + -
283B ASN* 2.8 16.5 + - - +
284B LEU* 3.4 22.0 - - + +
286B TYR* 1.3 81.2 - - - +
288B CYS* 1.3 62.5 + - - +
290B ALA* 3.4 3.2 + - - +
291B LEU* 3.1 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 3.1 33.4 - - - -
284B LEU* 3.0 25.5 + - - -
285B VAL* 3.1 7.8 + - - +
287B LEU* 1.3 74.3 - - - +
289B GLU* 1.3 64.2 + - - +
291B LEU* 3.2 6.0 + - - -
293B LEU* 2.8 49.2 + - + +
296B VAL* 3.5 23.6 - - - -
297B ALA* 3.7 11.7 - - + +
300B TRP* 4.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ARG* 2.9 42.8 + - - +
285B VAL* 3.0 21.8 + - - +
286B TYR* 3.1 9.3 + - + +
288B CYS* 1.3 76.0 - - - +
290B ALA* 1.3 64.2 + - - +
292B ASN* 3.1 18.7 + - - +
293B LEU 4.8 2.9 - - - +
294B PRO* 5.5 4.9 - - + -
297B ALA* 3.8 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ARG* 4.1 23.0 + - - +
286B TYR* 2.9 33.5 + - + +
287B LEU* 3.7 6.7 - - - +
289B GLU* 1.3 77.8 - - - +
291B LEU* 1.3 60.9 + - - +
292B ASN* 3.3 7.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 4.2 10.8 - - + -
243A ALA* 4.4 22.3 - - + +
244A THR* 3.6 24.7 - - + -
135B ARG* 3.6 24.9 - - - +
287B LEU* 3.1 43.4 + - + +
288B CYS 3.2 2.9 + - - +
289B GLU 3.1 0.6 - - - -
290B ALA* 1.3 77.8 - - + +
292B ASN* 1.3 73.5 + - - +
293B LEU* 3.3 16.0 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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