Contacts of the helix formed by residues 41 - 53 (chain A) in PDB entry 2B7O
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 PRO 41 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR 4.4 1.6 - - - +
40A TRP* 1.3 91.6 - - + +
42A ALA* 1.3 59.8 + - - +
43A ASP* 3.5 17.5 - - - +
44A GLN* 3.2 33.5 + - - +
45A ALA* 3.0 26.6 + - - +
164A HIS 5.3 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP 3.6 2.5 + - - -
41A PRO* 1.3 72.8 - - - +
43A ASP* 1.3 58.0 + - - +
45A ALA* 3.7 6.6 - - - +
46A LEU* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO* 3.5 18.1 - - - +
42A ALA* 1.3 79.1 - - - +
44A GLN* 1.3 78.7 + - - +
46A LEU* 3.6 8.8 + - - +
47A ALA* 3.1 27.4 + - - +
1B MSE 5.4 8.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 4.9 0.2 - - - +
41A PRO* 3.2 33.1 + - + +
43A ASP* 1.3 88.9 + - - +
45A ALA* 1.3 65.4 + - - +
47A ALA* 3.2 7.7 + - - +
48A MSE 3.0 27.0 + - - +
164A HIS 5.2 1.4 + - - -
165A ASP* 5.0 3.4 + - - -
166A PRO* 3.4 33.9 - - + +
0B ALA* 3.6 17.8 - - + +
1B MSE 3.7 34.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 3.7 11.7 - - + +
41A PRO 3.0 17.4 + - - +
42A ALA* 3.7 8.1 - - - +
44A GLN* 1.3 77.3 - - - +
46A LEU* 1.3 61.8 + - - +
48A MSE 3.3 1.6 + - - +
49A ARG* 2.9 30.4 + - - +
166A PRO* 4.0 12.4 - - - +
169A LEU* 4.7 1.6 - - - +
253A ASP* 3.6 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA 2.9 21.7 + - - +
43A ASP* 3.7 9.2 - - + +
45A ALA* 1.3 72.3 - - - +
47A ALA* 1.3 62.3 + - - +
49A ARG* 3.4 33.7 + - - +
50A THR* 2.8 39.3 + - - +
53A GLU* 6.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASP 3.1 15.5 + - - +
44A GLN* 3.2 6.9 + - - +
46A LEU* 1.3 78.5 - - - +
48A MSE 1.3 62.9 + - + +
50A THR* 3.4 8.1 + - - -
51A VAL* 3.3 24.2 + - - +
3B TRP* 3.7 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 3.2 27.8 - - + -
44A GLN 3.0 19.7 + - - +
45A ALA 3.8 3.4 - - - +
47A ALA* 1.3 74.8 - - - +
49A ARG* 1.3 64.0 + - - +
51A VAL* 3.2 14.3 + - - +
52A LEU* 3.2 25.4 + - - +
166A PRO* 3.1 31.0 - - + +
167A SER* 2.4 53.8 - - - +
169A LEU* 3.9 13.0 - - + -
170A VAL* 3.6 14.3 - - + +
0B ALA* 4.2 12.6 - - + +
3B TRP* 5.2 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA* 2.9 20.4 + - - +
46A LEU* 3.5 37.5 - - + +
48A MSE 1.3 75.4 - - - +
50A THR* 1.3 58.4 + - - +
52A LEU* 3.1 4.5 + - - -
53A GLU* 3.0 46.7 + - - +
169A LEU* 4.8 2.6 - - + +
253A ASP* 3.3 44.5 + - + +
256A ARG* 3.0 52.6 - - - +
257A ALA* 3.6 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU 6.1 1.3 - - - +
14A SER* 5.4 13.6 - - - -
46A LEU* 2.8 26.0 + - - +
47A ALA* 3.5 12.4 - - - -
49A ARG* 1.3 73.8 - - - +
51A VAL* 1.3 69.3 + - - +
53A GLU* 3.3 30.4 + - - +
54A SER* 4.2 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 3.8 28.3 - - + -
10A ASP 4.4 10.3 - - - +
11A GLN* 5.6 1.3 - - - -
12A LEU 6.1 0.7 - - - +
47A ALA 3.3 13.0 + - - +
48A MSE 3.2 13.8 + - - +
50A THR* 1.3 78.5 - - + +
52A LEU* 1.3 68.0 + - + +
53A GLU 3.3 0.5 + - - -
54A SER* 3.5 15.7 + - - -
55A VAL* 3.6 14.0 - - + +
170A VAL* 3.9 24.2 - - + -
1001A CE1 5.5 4.9 - - + -
3B TRP* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A MSE 3.2 10.5 + - - +
49A ARG* 3.1 9.0 + - - +
51A VAL* 1.3 79.3 - - + +
53A GLU* 1.3 57.5 + - - +
54A SER 3.2 3.5 + - - -
55A VAL* 3.4 15.0 - - + +
169A LEU* 3.6 40.8 - - + +
170A VAL* 4.0 17.9 - - + +
173A TYR* 3.6 35.4 - - + -
254A TYR* 4.2 11.4 - - + -
257A ALA* 3.8 7.0 - - + -
258A MSE 2.8 41.4 - - + +
260A ARG* 2.9 14.9 + - - -
1001A CE1 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 4.7 6.6 - - - +
46A LEU* 6.0 0.9 - - - +
49A ARG* 3.0 36.7 + - - +
50A THR* 3.6 25.3 + - - +
51A VAL 3.3 1.2 - - - -
52A LEU* 1.3 77.0 - - - +
54A SER* 1.3 59.4 + - - +
256A ARG 5.3 1.8 - - - +
257A ALA* 3.7 21.3 - - - +
260A ARG* 3.3 20.0 + - - +
----------------------------------------------------------
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