Contacts of the helix formed by residues 4 - 21 (chain B) in PDB entry 2DVL
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 4 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 1.3 76.7 - - - +
5B GLN* 1.3 65.2 + - - +
6B GLU* 3.6 8.4 + - - +
7B GLN* 3.1 37.4 + - - +
8B ARG* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B THR* 1.3 72.3 - - - +
6B GLU* 1.3 59.5 + - - +
8B ARG* 3.0 10.5 + - - +
9B LEU* 2.9 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B THR* 3.2 8.6 + - - +
5B GLN* 1.3 80.5 - - - +
7B GLN* 1.3 67.1 + - + +
9B LEU* 3.0 29.2 + - - +
10B VAL* 3.2 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 3.4 25.9 - - + +
4B THR* 3.1 41.8 + - - +
6B GLU* 1.3 78.0 - - + +
8B ARG* 1.3 61.2 + - - +
10B VAL* 3.5 4.7 + - - +
11B LEU* 3.2 30.7 + - + +
63B ASP* 2.9 32.3 + - - +
65B VAL* 4.4 10.7 - - - +
66B THR* 3.3 22.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 2.7 75.7 + - + +
4B THR 3.1 6.7 + - - +
5B GLN* 3.0 10.8 + - - +
7B GLN* 1.3 75.5 - - - +
9B LEU* 1.3 60.7 + - - +
11B LEU* 3.8 6.7 - - + +
12B ASP* 2.8 39.6 + - - +
15B ARG* 5.5 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLN* 2.9 19.7 + - + +
6B GLU* 3.0 28.9 + - - +
8B ARG* 1.3 73.8 - - - +
10B VAL* 1.3 66.0 + - + +
12B ASP* 3.1 28.5 + - + +
13B ALA* 3.3 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU* 3.2 29.8 + - + +
7B GLN* 3.7 7.0 - - - +
9B LEU* 1.3 77.6 - - + +
11B LEU* 1.3 58.1 + - - +
13B ALA* 2.9 25.1 + - + +
14B VAL* 3.0 22.0 + - + +
48B LEU* 5.2 4.7 - - + -
62B LEU* 3.9 32.3 - - + -
66B THR* 3.7 22.0 - - + -
70B ALA* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 3.8 28.7 - - + -
7B GLN 3.2 18.7 + - - +
8B ARG* 4.0 4.0 - - + +
9B LEU 3.4 0.2 - - - -
10B VAL* 1.3 76.9 - - - +
12B ASP* 1.3 56.4 + - - +
14B VAL* 3.8 7.3 - - + +
15B ARG* 2.9 52.1 + - - +
66B THR* 3.8 31.9 - - + +
69B LEU* 3.9 20.9 - - + +
70B ALA* 3.9 21.5 - - + +
73B GLU* 5.2 3.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG* 2.8 27.8 + - - +
9B LEU* 3.1 22.9 - - + +
10B VAL 3.0 0.2 - - - -
11B LEU* 1.3 77.0 - - - +
13B ALA* 1.3 62.4 + - - +
15B ARG* 3.1 22.9 + - - +
16B ARG* 3.1 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU 3.3 6.2 + - - +
10B VAL* 2.9 11.7 + - + +
12B ASP* 1.3 78.3 - - - +
14B VAL* 1.3 65.9 + - + +
16B ARG* 3.1 13.1 + - - +
17B VAL* 3.0 24.4 + - - +
46B LEU* 4.7 18.9 - - + +
48B LEU* 5.2 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 3.0 22.3 + - + +
11B LEU* 3.9 9.2 - - + +
13B ALA* 1.3 75.8 - - + +
15B ARG* 1.3 58.0 + - - +
17B VAL* 3.0 10.9 - - - +
18B ALA* 2.9 32.2 + - - +
48B LEU* 4.0 28.9 - - + -
70B ALA* 3.9 39.5 - - + +
73B GLU* 3.9 14.1 - - + -
74B LEU* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG* 4.4 5.3 + - - +
11B LEU* 2.9 40.8 + - - +
12B ASP* 3.1 30.9 + - - +
14B VAL* 1.3 77.3 - - - +
16B ARG* 1.3 56.8 + - - +
18B ALA* 3.4 0.5 + - - +
19B ARG* 2.9 79.6 + - - +
73B GLU* 3.8 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASP* 3.1 21.5 + - - +
13B ALA* 3.1 14.5 + - - +
15B ARG* 1.3 79.3 - - - +
17B VAL* 1.3 59.2 + - - +
19B ARG* 3.8 2.6 - - - +
20B GLU* 2.9 70.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA 3.0 10.7 + - - +
14B VAL* 3.0 22.9 - - - +
16B ARG* 1.3 77.6 - - - +
18B ALA* 1.3 58.7 + - - +
20B GLU* 4.8 0.7 - - - -
21B VAL* 2.9 47.9 + - + +
22B LEU* 3.3 4.5 + - + +
42B ALA* 4.2 13.2 - - + +
43B LEU* 3.7 33.9 - - + -
46B LEU* 3.7 22.4 - - + -
48B LEU* 4.0 6.5 - - + -
74B LEU* 4.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL 2.9 19.3 + - - +
15B ARG 3.6 3.6 - - - +
17B VAL* 1.3 79.9 - - - +
19B ARG* 1.3 59.9 + - + +
22B LEU* 3.2 16.1 + - - +
23B TYR 2.9 26.9 + - - -
73B GLU* 4.0 32.8 - - + +
74B LEU* 4.3 9.2 - - + -
77B ALA* 3.6 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG* 2.9 59.8 + - - +
16B ARG* 4.1 2.9 - - - +
18B ALA* 1.3 76.4 - - + +
20B GLU* 1.3 63.1 + - + +
23B TYR* 3.7 11.5 - - + +
24B PRO* 3.2 22.0 - - - +
73B GLU* 3.5 16.3 + - - +
248B ARG* 4.5 8.3 - - - +
252B GLU* 5.2 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 2.9 53.1 + - - +
17B VAL* 4.8 0.7 - - - -
19B ARG* 1.3 82.2 - - + +
21B VAL* 1.3 66.4 + - + +
24B PRO* 3.6 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 2.9 24.9 + - + +
20B GLU* 1.3 87.6 - - + +
22B LEU* 1.3 68.9 + - + +
23B TYR 3.5 0.4 - - - -
24B PRO* 3.4 7.6 - - - +
25B LEU* 3.4 31.4 - - + +
38B PRO* 4.5 1.8 - - + +
39B GLN* 4.0 18.8 - - - +
42B ALA* 3.9 29.8 - - + -
----------------------------------------------------------
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