Contacts of the helix formed by residues 261 - 277 (chain I) in PDB entry 5XVO
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 LEU 261 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183I LEU* 3.9 26.2 - - + -
186I ILE* 4.1 17.3 - - + -
187I PHE* 5.8 1.3 - - + -
221I PHE* 3.9 32.3 - - + -
224I LEU* 4.0 13.0 - - + -
247I LEU* 3.4 44.1 + - + +
248I PHE* 5.4 3.2 + - + +
250I ASN 4.2 5.1 + - - -
252I TYR* 4.2 9.4 - - + -
259I MET 3.8 1.0 + - - -
260I PHE* 1.3 74.0 - - - +
262I THR* 1.3 59.8 + - + +
264I ILE* 3.3 13.4 + - + +
265I ALA* 2.9 28.9 + - + +
286I PHE* 5.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 262 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I GLU* 5.7 0.4 - - - +
186I ILE* 4.4 19.1 - - + +
189I ARG* 4.2 22.2 - - - +
248I PHE* 4.4 22.6 - - + +
260I PHE* 4.5 6.9 - - - +
261I LEU* 1.3 77.2 - - - +
263I ASN* 1.3 68.0 + - - +
265I ALA* 3.4 2.6 + - - +
266I THR* 3.1 35.2 + - - +
26P T 4.6 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 263 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259I MET* 4.9 11.8 - - + +
260I PHE* 3.2 29.7 + - - +
262I THR* 1.3 85.2 + - - +
264I ILE* 1.3 63.6 + - - +
266I THR* 2.6 23.6 + - - +
267I ASP* 3.2 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 264 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221I PHE* 3.9 25.6 - - + -
252I TYR* 3.9 21.8 - - + +
254I TYR* 3.6 52.6 - - + -
259I MET* 3.7 33.6 - - + +
260I PHE 3.1 13.1 + - - +
261I LEU* 3.5 13.0 - - + +
263I ASN* 1.3 76.7 - - - +
265I ALA* 1.3 59.3 + - - +
267I ASP* 3.0 4.6 + - - +
268I TYR* 2.8 27.8 + - + +
286I PHE* 4.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 265 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I ILE* 3.4 34.1 - - + +
187I PHE* 3.6 30.5 - - + -
190I GLU* 4.3 2.0 - - - -
261I LEU* 2.9 15.6 + - + +
262I THR 3.7 2.2 - - - +
263I ASN 3.3 0.2 - - - -
264I ILE* 1.3 79.3 - - - +
266I THR* 1.3 59.6 + - + +
268I TYR* 3.8 2.2 - - - +
269I THR* 2.8 33.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 266 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I ILE* 6.2 0.9 - - + -
190I GLU* 3.3 37.3 - - + +
193I GLN* 5.3 2.2 - - - +
262I THR* 3.1 15.6 + - - +
263I ASN* 2.6 28.9 + - - +
265I ALA* 1.3 77.6 - - + +
267I ASP* 1.3 63.1 + - - +
269I THR* 3.9 1.2 - - - -
270I LYS* 3.1 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 267 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254I TYR* 2.7 36.1 + - + -
255I LYS* 4.1 8.3 - - - +
259I MET* 6.0 4.3 - - + -
263I ASN 3.2 7.6 + - - +
264I ILE 3.0 6.5 + - - +
266I THR* 1.3 81.9 + - - +
268I TYR* 1.3 64.4 + - - +
270I LYS* 3.4 18.0 + - - +
271I HIS* 2.9 56.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 268 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108I ILE* 3.9 16.6 - - + +
111I GLN* 3.3 20.5 + - - -
187I PHE* 4.1 9.6 - + - -
217I LEU* 3.6 24.0 - - + -
220I PRO* 3.3 17.9 - - + +
221I PHE* 4.0 20.6 - + + -
254I TYR* 3.6 20.5 + + + +
264I ILE 2.8 22.4 + - - +
265I ALA* 3.8 7.2 - - - +
267I ASP* 1.3 74.6 - - - +
269I THR* 1.3 66.3 + - - +
272I VAL* 3.0 45.0 + - + +
284I PRO* 3.3 39.4 + - + +
286I PHE* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 269 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I PHE* 3.4 21.7 - - - -
190I GLU* 3.8 27.4 - - + +
191I LEU* 3.8 23.1 - - + +
194I THR* 4.5 1.6 - - + -
217I LEU* 3.7 24.4 - - + +
265I ALA 2.8 22.7 + - - -
266I THR 3.9 2.5 - - - -
268I TYR* 1.3 77.7 - - - +
270I LYS* 1.3 65.6 + - - +
271I HIS 3.2 0.2 + - - -
272I VAL* 3.2 2.5 + - - +
273I VAL* 2.9 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 270 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I GLU* 4.8 4.5 - - - +
194I THR* 4.6 16.2 - - + -
266I THR 3.1 13.3 + - - +
267I ASP* 3.4 33.1 + - - +
269I THR* 1.3 80.9 - - - +
271I HIS* 1.3 73.2 + - + +
273I VAL* 3.4 3.7 + - - +
274I LYS* 3.0 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 271 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255I LYS* 6.0 1.8 - - - -
267I ASP* 2.9 50.9 + - - +
269I THR 3.1 0.6 - - - -
270I LYS* 1.3 93.6 - - + +
272I VAL* 1.3 65.6 + - - +
274I LYS* 3.1 8.5 + - + +
275I VAL* 3.0 26.5 + - - +
280I GLU* 3.3 34.9 + - - +
284I PRO* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 272 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104I VAL* 4.0 15.4 - - + +
108I ILE* 4.3 7.4 - - + -
217I LEU* 3.7 26.5 - - + -
268I TYR* 3.0 46.0 + - + +
269I THR* 3.6 9.0 - - - +
271I HIS* 1.3 74.7 - - - +
273I VAL* 1.3 59.8 + - + +
275I VAL* 3.2 7.2 + - - +
276I LEU* 2.9 41.1 + - + +
283I VAL* 5.1 5.2 - - + -
284I PRO* 3.9 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I GLN* 3.7 20.9 - - - +
96I TRP* 4.6 6.3 - - + -
191I LEU* 4.1 16.6 - - + -
194I THR* 4.1 16.6 - - + +
196I CYS* 4.0 20.0 - - - -
269I THR* 2.9 18.9 + - + +
270I LYS* 3.6 9.4 - - - +
271I HIS 3.2 0.2 - - - -
272I VAL* 1.3 78.1 - - + +
274I LYS* 1.3 61.2 + - + +
276I LEU* 3.2 9.2 + - + +
277I ASN* 2.8 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 274 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270I LYS* 3.0 23.4 + - + +
271I HIS* 3.1 10.7 + - + +
273I VAL* 1.3 76.3 - - + +
275I VAL* 1.3 59.5 + - - +
277I ASN* 3.2 11.1 + - - +
278I GLN 3.1 4.0 + - - -
279I GLU* 2.4 64.5 + - + +
280I GLU* 4.1 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 275 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100I ARG* 3.0 40.1 + - - +
104I VAL* 3.6 22.2 - - + -
271I HIS 3.0 17.7 + - - +
272I VAL* 3.6 7.9 - - - +
274I LYS* 1.3 74.5 - - - +
276I LEU* 1.3 64.0 + - - +
278I GLN 3.0 9.2 + - - -
280I GLU* 3.4 24.7 - - + +
281I GLU 4.2 0.2 - - - -
282I GLY 3.6 34.5 - - - +
283I VAL* 4.1 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96I TRP* 3.3 57.1 - - + +
100I ARG* 3.7 17.5 - - + +
101I LYS* 4.0 22.9 - - + +
104I VAL* 3.9 24.0 - - + -
202I LEU* 3.9 26.2 - - + -
213I LEU* 5.4 2.7 - - + -
217I LEU* 5.6 0.7 - - + -
272I VAL* 2.9 35.9 + - + +
273I VAL* 3.6 7.9 - - + +
275I VAL* 1.3 76.9 - - - +
277I ASN* 1.3 62.0 + - - +
278I GLN* 3.1 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 277 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I GLN* 3.1 32.0 + - - -
92I ARG* 3.6 19.6 - - - +
96I TRP* 2.8 29.4 + - - +
273I VAL* 2.8 30.5 + - - +
274I LYS* 3.5 9.0 - - - +
275I VAL 3.2 0.2 - - - -
276I LEU* 1.3 74.4 - - - +
278I GLN* 1.3 69.6 + - - +
279I GLU* 3.7 30.0 + - + +
----------------------------------------------------------
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