Contacts of the helix formed by residues 31 - 42 (chain B) in PDB entry 3TDM
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 31 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU* 3.8 27.4 - - + +
17B PHE 3.5 6.7 - - - +
18B MET* 4.3 12.6 - - - -
19B VAL* 4.5 0.2 - - - -
29B GLY 3.9 12.3 - - - +
30B ILE* 1.3 84.3 - - - +
32B LEU* 1.3 67.7 + - - +
33B ARG* 4.2 16.4 - - + +
34B ASP* 3.0 24.6 + - - +
35B TRP 2.9 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.6 31.6 - - + -
10B ALA* 3.8 13.7 - - + -
17B PHE* 2.8 51.5 + - + +
19B VAL* 4.1 10.1 - - + +
30B ILE 3.7 0.4 + - - -
31B LEU* 1.3 73.2 - - - +
33B ARG* 1.3 55.2 + - - +
34B ASP 2.7 2.1 + - - -
35B TRP* 2.6 22.4 + - + +
36B VAL* 3.0 19.3 + - + +
49B LEU* 4.2 7.4 - - + -
65B MET* 4.1 10.8 - - + -
68B PHE* 4.2 3.8 - - + -
69B VAL* 3.4 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU* 3.6 32.5 + - - +
31B LEU* 3.2 14.6 - - + +
32B LEU* 1.3 77.7 - - - +
34B ASP* 1.3 73.0 + - - +
36B VAL 4.5 0.9 - - - -
37B VAL* 4.0 14.0 - - - +
68B PHE* 3.7 45.5 - - + -
72B LEU* 3.6 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 4.7 7.0 - - + -
31B LEU* 3.0 31.9 + - + +
32B LEU 2.8 0.8 - - - -
33B ARG* 1.3 91.2 - - - +
35B TRP* 1.3 64.9 + - - +
36B VAL 3.2 1.6 - - - -
37B VAL* 3.5 6.6 + - - +
38B GLU* 3.3 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASN* 5.5 0.6 + - - -
106A ALA* 3.1 37.0 - - + -
107A VAL* 3.7 29.4 - - + +
110A PRO* 3.9 17.7 - - + -
113A ILE* 4.5 4.0 - - + -
6B VAL* 4.7 4.5 - - + +
7B ALA 5.3 1.4 + - - -
8B ILE* 3.7 29.9 - - + +
19B VAL* 4.0 24.7 - - + +
30B ILE* 4.0 19.2 - - + +
31B LEU 2.9 11.2 + - - +
32B LEU* 2.6 14.3 + - - +
34B ASP* 1.3 72.1 - - - +
36B VAL* 1.3 61.6 + - - +
38B GLU* 3.3 26.3 + - + -
39B VAL* 3.0 48.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.8 25.8 - - + -
32B LEU* 3.0 27.1 + - + +
34B ASP 3.2 0.2 - - - -
35B TRP* 1.3 79.0 - - - +
37B VAL* 1.3 62.7 + - - +
39B VAL* 3.9 3.6 - - - +
40B GLU* 3.6 18.0 + - - +
47B ILE* 4.3 9.5 - - + +
49B LEU* 5.4 0.7 - - + -
69B VAL* 4.0 25.4 - - + -
72B LEU* 3.7 31.9 - - + +
73B THR* 3.9 19.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG 4.0 14.8 - - - +
34B ASP* 3.5 9.9 + - - +
35B TRP 3.1 0.4 - - - -
36B VAL* 1.3 76.5 - - - +
38B GLU* 1.3 68.5 + - + +
39B VAL 3.2 0.7 + - - -
40B GLU* 3.4 6.3 + - - +
41B LYS* 3.3 39.3 + - + +
72B LEU* 3.9 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO* 4.8 2.4 - - + +
34B ASP 3.3 14.7 + - - +
35B TRP* 3.3 29.4 + - + +
37B VAL* 1.3 82.5 - - - +
39B VAL* 1.3 57.7 + - - +
41B LYS* 3.4 19.6 + - - +
42B ARG* 2.3 81.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
113A ILE* 4.5 9.3 - - + +
6B VAL* 3.9 22.2 - - + -
8B ILE* 4.8 3.1 - - + -
35B TRP* 3.0 61.0 + - + +
36B VAL* 3.9 6.1 - - - +
37B VAL 3.2 0.2 - - - -
38B GLU* 1.3 74.6 - - - +
40B GLU* 1.3 66.9 + - - +
42B ARG* 3.5 3.3 + - - +
43B GLY 3.4 12.5 + - - -
44B ALA* 3.4 28.6 + - + +
47B ILE* 4.0 20.2 - - + -
75B LEU* 4.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL 3.6 5.1 + - - +
37B VAL* 3.4 8.6 + - - +
39B VAL* 1.3 77.5 - - - +
41B LYS* 1.3 66.1 + - - +
43B GLY* 2.9 14.6 + - - -
44B ALA 4.3 1.1 + - - +
72B LEU 4.3 1.7 - - - +
73B THR* 2.5 39.7 + - - +
74B THR* 2.8 36.8 + - - +
75B LEU* 4.0 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 3.3 29.7 + - + +
38B GLU* 3.5 24.4 + - - +
39B VAL 3.4 0.2 - - - -
40B GLU* 1.3 79.4 - - - +
42B ARG* 1.3 65.8 + - + +
43B GLY* 3.1 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO* 4.0 25.2 - - + +
111A SER* 3.3 30.1 + - - +
113A ILE* 3.8 18.3 - - + +
114A THR* 3.0 42.9 + - - +
117A ALA* 4.9 0.3 - - - +
38B GLU* 2.3 51.6 + - + +
39B VAL 4.0 4.3 - - - +
40B GLU 3.2 0.4 - - - -
41B LYS* 1.3 77.6 - - + +
43B GLY* 1.3 56.8 + - - +
44B ALA 3.7 1.1 - - - -
----------------------------------------------------------
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