Contacts of the helix formed by residues 35 - 50 (chain B) in PDB entry 3CVM
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 SER 35 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 1.3 77.6 - - - +
36B PRO* 1.3 64.1 - - - +
38B GLY 3.1 22.3 + - - -
39B VAL* 3.3 5.7 + - - +
169B LEU* 3.5 7.3 - - - +
322B GLN* 3.0 29.0 + - - -
337B SER* 3.2 31.8 + - - -
371B LEU 2.9 18.3 + - - -
372B PHE* 4.3 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA 4.7 1.3 - - - -
13B SER* 4.3 4.3 - - - +
16B GLY* 3.5 34.6 - - - +
17B VAL* 3.8 3.6 - - + +
34B PHE* 3.4 16.3 - - + +
35B SER* 1.3 84.0 - - - +
37B TYR* 1.3 60.6 + - - +
39B VAL* 3.3 4.2 - - - +
40B ALA* 3.1 25.6 + - - +
370B VAL* 3.3 37.5 - - + +
371B LEU 3.7 9.6 - - - +
372B PHE* 4.1 0.9 - - - -
373B MET* 3.5 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA* 5.1 11.4 - - + -
13B SER* 6.1 0.7 - - - +
35B SER* 3.2 2.6 + - - +
36B PRO* 1.3 78.6 - - - +
38B GLY* 1.3 64.0 + - - +
40B ALA* 3.4 5.9 + - + +
41B SER* 2.8 47.2 + - - -
75B LEU* 5.1 2.4 + - + -
78B LEU* 4.1 24.9 - - + +
79B TYR* 3.6 27.4 - - - +
82B LEU* 4.0 12.8 - - + +
93B THR* 3.6 27.6 + - + +
167B ASN* 4.6 1.3 - - - -
169B LEU* 4.4 16.2 - - + -
369B THR* 3.6 21.3 - - + -
370B VAL 3.2 16.4 + - - +
371B LEU* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER* 3.1 21.9 + - - -
37B TYR* 1.3 79.1 - - - +
39B VAL* 1.3 60.2 + - - +
41B SER* 3.1 12.8 + - - -
42B VAL* 3.2 13.7 + - - +
167B ASN* 3.7 24.5 - - - +
169B LEU* 5.3 0.4 - - - -
337B SER* 4.9 0.9 - - - -
339B THR* 3.7 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 4.3 8.5 - - + -
16B GLY* 4.0 13.9 - - - -
19B VAL* 4.5 9.9 - - + -
34B PHE* 3.7 19.5 - - + -
35B SER 3.3 10.1 + - - +
36B PRO 3.3 11.9 - - - +
38B GLY* 1.3 70.2 - - - +
40B ALA* 1.3 68.9 + - - +
41B SER 3.1 1.8 - - - -
42B VAL* 3.1 9.6 - - + +
43B LEU* 3.0 42.0 + - + +
286B LEU* 4.0 24.7 - - + -
290B LEU* 4.7 3.6 - - + -
322B GLN* 3.7 11.8 - - - +
339B THR* 4.1 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA* 3.5 42.2 - - + +
15B PHE* 4.0 15.9 - - + -
36B PRO 3.1 19.2 + - - +
37B TYR* 3.5 7.4 - - + +
39B VAL* 1.3 78.2 - - - +
41B SER* 1.3 61.3 + - - +
44B ALA* 3.3 22.2 + - - +
62B MET* 3.8 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 2.8 46.5 + - - -
38B GLY 3.2 10.3 - - - -
39B VAL 3.1 0.4 - - - -
40B ALA* 1.3 75.4 - - - +
42B VAL* 1.3 67.4 + - - +
44B ALA* 3.2 14.9 + - - +
45B MET* 3.3 17.7 + - - +
95B ASP* 4.4 8.4 - - - +
117B PHE* 5.1 0.7 - - - -
167B ASN* 3.6 20.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 3.6 2.0 - - - +
39B VAL* 3.1 13.2 - - - +
41B SER* 1.3 78.6 - - - +
43B LEU* 1.3 71.8 + - + +
45B MET* 3.1 13.9 + - - +
46B LEU* 3.0 25.9 + - - +
165B LEU* 4.2 14.7 - - + +
166B VAL 4.1 6.1 - - - +
167B ASN* 3.6 22.4 - - + +
339B THR* 3.2 51.4 - - + +
340B ALA* 4.7 0.4 - - - +
341B VAL* 4.8 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 4.1 16.8 - - + -
39B VAL* 3.0 33.8 + - + +
40B ALA 4.4 0.7 - - - +
42B VAL* 1.3 88.3 - - + +
44B ALA* 1.3 61.9 + - - +
46B LEU* 3.3 28.7 + - + +
47B GLN* 3.1 25.3 + - - +
58B ILE* 4.0 8.3 - - + +
62B MET* 3.8 16.4 - - - +
286B LEU* 5.5 0.9 - - + -
290B LEU* 4.2 13.7 - - + -
295B MET* 3.8 26.5 - - - -
298B MET* 4.5 5.6 - - + -
341B VAL* 4.6 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ALA 3.3 15.9 + - - +
41B SER* 3.2 12.2 + - - +
43B LEU* 1.3 74.7 - - - +
45B MET* 1.3 64.5 + - - +
47B GLN* 3.4 20.9 - - - +
48B LEU 4.1 1.6 + - - -
62B MET* 3.9 14.3 - - + +
64B PHE* 5.0 3.6 - - + -
66B ILE* 4.2 8.9 - - + +
75B LEU* 4.3 18.8 - - + -
117B PHE* 3.5 19.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B SER 3.3 11.2 + - - +
42B VAL* 3.1 13.6 + - - +
44B ALA* 1.3 77.8 - - - +
46B LEU* 1.3 62.7 + - - +
48B LEU* 3.2 19.1 + - - +
49B THR* 3.7 4.9 - - - +
95B ASP* 3.5 25.1 - - + +
96B ALA 4.6 1.8 - - - +
97B ILE* 4.1 11.2 - - + -
113B PHE* 3.4 42.6 - - + -
117B PHE* 3.6 26.5 - - + -
119B SER* 2.7 35.2 - - - +
165B LEU* 3.8 13.9 - - + -
166B VAL 4.7 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL 3.0 13.1 + - - +
43B LEU* 3.3 26.0 - - + +
45B MET* 1.3 73.8 - - - +
47B GLN* 1.3 66.7 + - - +
49B THR* 2.9 35.3 + - - +
50B THR* 3.4 10.6 + - + +
58B ILE* 3.6 15.0 - - + -
163B LEU* 6.5 0.2 - - + -
165B LEU* 3.9 11.4 - - + +
298B MET* 3.5 32.5 - - + -
306B PHE* 4.0 16.2 - - + -
317B VAL* 4.8 2.5 - - + -
341B VAL* 4.0 29.8 - - + -
343B VAL* 4.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU 3.1 10.0 + - - +
44B ALA* 3.4 11.2 - - - +
46B LEU* 1.3 76.1 - - - +
48B LEU* 1.3 62.2 + - - +
50B THR* 3.1 27.0 + - - +
55B GLN* 3.5 15.4 + - + -
58B ILE* 3.4 24.5 - - + +
59B GLN* 3.7 23.8 + - + +
62B MET* 3.4 27.3 - - - +
64B PHE* 3.3 24.2 + - - -
66B ILE* 3.2 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B MET 3.2 10.8 + - - +
47B GLN* 1.3 79.7 - - - +
49B THR* 1.3 57.6 + - - +
50B THR 4.2 0.2 - - - +
55B GLN* 5.1 3.0 + - - +
66B ILE* 3.6 15.0 - - + -
67B ASP* 3.0 36.1 - - - +
109B PHE* 3.8 12.7 - - + -
112B HIS* 4.4 10.5 - - + +
113B PHE* 3.4 38.6 - - + -
116B LEU* 3.7 17.0 - - + -
117B PHE* 3.5 25.6 - - + -
308B SER* 3.3 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B MET 3.7 15.3 - - - +
46B LEU* 2.9 18.8 + - - +
48B LEU* 1.3 77.7 - - + +
50B THR* 1.3 57.2 + - - +
109B PHE* 3.9 21.1 - - + -
113B PHE* 4.7 3.4 - - + -
163B LEU* 4.5 17.2 - - + +
165B LEU* 4.6 7.4 - - + -
306B PHE* 3.1 41.4 - - - +
308B SER* 3.7 3.4 - - - -
309B LEU* 3.3 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.4 22.2 + - + +
47B GLN* 3.1 21.9 + - - +
49B THR* 1.3 78.6 - - - +
51B GLY* 1.3 58.4 + - - +
54B THR* 3.9 20.0 - - + -
55B GLN* 3.3 25.3 + - - +
58B ILE* 4.0 5.1 - - + +
298B MET* 5.5 0.2 - - + -
305B ASP 3.3 10.3 - - - +
306B PHE* 3.5 33.2 - - + -
308B SER* 2.9 18.9 + - - -
----------------------------------------------------------
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