Contacts of the helix formed by residues 318 - 334 (chain D) in PDB entry 3MQ6
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 THR 318 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D ASN 3.6 9.8 + - - -
61D GLY* 3.6 20.3 - - - +
62D MET 3.5 13.9 - - - +
63D ASP* 5.0 0.9 - - - -
64D TYR* 3.9 8.3 - - - -
316D PRO* 3.5 4.0 - - - +
317D PRO* 1.3 93.5 - - + +
319D ALA* 1.3 64.2 + - - +
320D ALA* 3.3 6.4 + - - +
321D ASP* 3.1 27.4 + - + +
322D LEU* 3.2 11.6 + - - +
324D ARG* 4.4 4.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D PRO* 3.4 45.5 - - + +
53D GLY* 3.5 4.3 - - - +
59D ILE 4.6 4.9 - - - +
60D ASN 3.6 6.5 + - - +
62D MET 4.3 2.4 + - - -
64D TYR* 3.8 22.3 - - + -
67D VAL* 5.5 0.7 - - + -
109D VAL* 4.2 6.3 - - + +
318D THR* 1.3 73.2 - - - +
320D ALA* 1.3 63.0 + - - +
322D LEU* 3.2 10.3 + - - +
323D ALA* 3.1 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLY* 4.3 0.8 - - - -
60D ASN* 3.2 27.4 + - + +
61D GLY* 5.4 0.9 - - - -
132D TYR* 3.5 25.4 - - + +
318D THR* 3.2 2.9 - - - +
319D ALA* 1.3 76.0 - - - +
321D ASP* 1.3 60.5 + - - +
323D ALA* 3.2 2.0 + - - +
324D ARG* 2.8 52.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 321 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D TYR* 2.6 29.2 + - - +
317D PRO* 3.3 26.9 - - + +
318D THR* 3.1 19.6 + - + +
320D ALA* 1.3 77.1 - - - +
322D LEU* 1.3 57.2 + - - +
324D ARG* 3.0 33.3 + - - +
325D ARG* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D TYR* 3.9 17.9 - - + +
106D SER* 3.9 29.2 - - - +
109D VAL* 4.0 25.1 - - + -
110D MET* 4.6 14.1 - - + -
278D HIS* 3.8 30.3 - - + +
314D TYR* 3.3 18.9 + - + +
316D PRO* 4.5 6.7 - - + -
318D THR 3.2 8.4 + - - +
319D ALA* 3.3 9.2 - - - +
321D ASP* 1.3 79.6 - - - +
323D ALA* 1.3 61.7 + - - +
325D ARG* 3.3 3.7 + - + +
326D PHE* 3.1 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 323 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLY* 5.3 0.2 - - - -
54D PHE* 4.4 3.8 - - + -
109D VAL* 4.4 8.3 - - + -
113D CYS* 3.7 24.1 - - - -
132D TYR* 3.5 28.9 - - + +
319D ALA 3.1 8.2 + - - +
320D ALA 3.2 7.6 + - - +
322D LEU* 1.3 79.5 - - - +
324D ARG* 1.3 62.6 + - - +
326D PHE* 3.2 3.8 + - - +
327D PHE* 3.1 30.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 324 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D TYR* 3.7 21.7 - - + -
133D SER 6.1 0.9 - - - +
318D THR* 4.4 5.1 + - - +
320D ALA* 2.8 41.0 + - - +
321D ASP* 3.0 42.4 + - - +
323D ALA* 1.3 72.3 - - - +
325D ARG* 1.3 63.6 + - - +
327D PHE* 3.5 8.7 + - - +
328D ALA* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 325 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D GLU* 3.0 42.8 + - - -
278D HIS* 4.1 2.6 + - - -
311D ARG* 3.5 8.2 - - - +
312D GLU* 2.8 35.2 + - - +
314D TYR* 3.2 55.3 - - + +
321D ASP* 2.8 19.4 + - - +
322D LEU* 3.8 5.0 - - - +
323D ALA 3.2 0.2 - - - -
324D ARG* 1.3 78.3 - - - +
326D PHE* 1.3 58.5 + - - +
328D ALA* 3.3 7.6 + - + +
329D PHE* 2.9 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 326 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D MET* 3.7 62.1 - - + -
113D CYS* 3.4 25.1 - - + -
114D ALA* 4.3 1.8 - - - -
145D VAL* 4.9 0.9 - - + -
147D VAL* 4.0 8.7 - - + -
191D VAL* 4.0 24.2 - - + -
237D LEU* 4.7 5.4 - - + -
322D LEU* 3.1 18.4 + - + +
323D ALA 3.2 3.6 + - - +
325D ARG* 1.3 77.9 - - - +
327D PHE* 1.3 60.7 + - - +
329D PHE* 3.2 18.2 + + + +
330D LEU* 2.9 57.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D PHE* 4.3 3.6 - + - -
113D CYS* 3.2 53.2 - - + -
116D ARG* 4.2 11.7 - - + -
117D TRP* 4.3 9.8 - + + -
126D TRP* 3.7 33.0 - + + -
132D TYR* 3.9 36.6 - + + -
133D SER 5.3 4.7 - - - +
135D PRO* 5.1 7.0 - - + +
323D ALA* 3.1 27.1 + - + +
324D ARG* 3.8 6.1 - - - +
326D PHE* 1.3 77.4 - - - +
328D ALA* 1.3 57.2 + - - +
330D LEU* 3.1 12.5 + - + +
331D ASN* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D ARG 3.1 15.5 + - - +
325D ARG* 3.6 6.5 - - + +
327D PHE* 1.3 77.7 - - - +
329D PHE* 1.3 62.6 - - - +
331D ASN* 3.4 8.0 + - - +
332D GLU* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 329 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D VAL* 6.0 0.7 - - + -
236D SER* 3.6 23.8 - - - -
237D LEU* 4.0 27.6 - - + -
274D GLU* 4.4 5.2 - - + -
276D GLU* 5.1 1.3 - - - -
311D ARG* 3.5 44.9 - - - +
325D ARG* 2.9 19.4 + - + +
326D PHE* 3.5 28.3 - + + +
327D PHE 3.2 0.2 - - - -
328D ALA* 1.3 77.9 - - - +
330D LEU* 1.3 62.0 + - + +
332D GLU* 3.4 2.8 + - - +
333D ARG* 2.7 68.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D CYS 5.0 2.0 - - - +
114D ALA* 5.1 0.4 - - - -
117D TRP* 3.7 41.5 - - + -
145D VAL* 4.1 25.8 - - + -
191D VAL* 4.9 3.1 - - + -
236D SER* 6.3 0.7 - - - -
326D PHE* 2.9 56.1 + - + +
327D PHE* 3.6 10.1 - - + +
329D PHE* 1.3 81.7 - - + +
331D ASN* 1.3 67.1 - - - +
333D ARG* 4.3 0.9 - - - +
334D MET* 2.8 50.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 331 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D TRP* 3.8 12.1 - - + -
135D PRO* 3.4 12.6 - - + +
136D THR* 2.7 46.6 + - - +
137D LEU* 3.0 29.9 + - - +
327D PHE 2.8 17.7 + - - +
328D ALA* 3.6 9.6 + - - +
330D LEU* 1.3 78.9 - - - +
332D GLU* 1.3 61.9 + - - +
335D GLU* 4.2 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D ALA 3.1 15.9 + - - +
329D PHE* 4.0 2.9 - - - +
330D LEU 3.1 0.2 - - - -
331D ASN* 1.3 79.8 - - - +
333D ARG* 1.3 63.4 + - - +
335D GLU* 3.3 25.3 - - - +
336D LEU* 4.0 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D GLY 4.4 11.1 + - - -
235D ILE 3.8 8.3 + - - -
236D SER* 3.3 39.3 + - - +
271D PRO* 5.7 9.7 - - - +
272D LYS 4.3 14.0 + - - -
273D VAL* 5.8 0.2 - - - +
274D GLU* 3.9 17.3 - - - +
329D PHE* 2.7 54.1 + - + +
330D LEU* 4.2 1.8 - - - +
332D GLU* 1.3 74.3 - - - +
334D MET* 1.3 73.7 + - - +
335D GLU 3.5 0.2 + - - -
336D LEU* 3.5 41.2 + - - +
337D VAL* 4.6 6.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D TRP* 3.5 27.1 - - + -
137D LEU* 3.6 6.3 - - + -
143D ARG* 3.3 37.7 + - + +
144D GLN 4.5 0.2 - - - +
145D VAL* 3.8 20.2 - - + -
193D VAL* 4.3 11.9 - - + -
236D SER* 4.8 9.0 - - - -
330D LEU* 2.8 36.6 + - + +
333D ARG* 1.3 82.6 - - - +
335D GLU* 1.3 56.2 + - - +
336D LEU 3.0 2.2 - - - -
337D VAL* 2.8 59.5 + - + +
----------------------------------------------------------
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