Contacts of the helix formed by residues 4 - 20 (chain B) in PDB entry 2YVE
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 4 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B THR* 1.3 87.7 + - - +
5B LYS* 1.3 64.7 + - - +
6B LYS* 3.7 8.3 + - - +
7B GLU* 3.1 28.1 + - - +
8B MET* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B THR 3.8 0.8 + - - -
4B SER* 1.3 70.0 - - - +
6B LYS* 1.3 66.5 + - - +
8B MET* 3.2 18.9 + - + +
9B ILE* 2.9 32.1 + - + +
36B LEU* 4.3 27.0 - - + +
40B GLY 5.8 0.4 - - - +
44B HIS* 3.3 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B SER* 3.2 8.0 - - - +
5B LYS* 1.3 78.8 - - - +
7B GLU* 1.3 61.6 + - - +
9B ILE* 3.3 10.0 + - - +
10B LEU* 3.1 43.1 + - + +
44B HIS* 4.2 28.8 - - + +
45B PHE* 3.5 28.2 - - + -
54B GLY* 5.1 2.6 + - - -
57B GLU* 5.1 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B THR* 4.7 15.3 + - - +
4B SER* 3.1 25.3 + - - +
6B LYS* 1.3 78.0 - - - +
8B MET* 1.3 57.9 + - - +
10B LEU* 3.2 10.2 + - - +
11B ARG* 2.8 73.6 + - + +
58B LEU* 4.1 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B THR 5.3 5.0 - - - +
4B SER 3.1 13.6 + - - +
5B LYS* 3.2 23.8 + - + +
7B GLU* 1.3 76.5 - - - +
9B ILE* 1.3 66.2 + - - +
11B ARG* 3.4 7.8 + - - +
12B THR* 2.8 41.7 + - - +
34B THR* 4.2 15.7 - - - +
36B LEU* 3.8 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LYS* 2.9 18.9 + - + +
6B LYS 3.5 5.8 - - - +
8B MET* 1.3 84.1 - - + +
10B LEU* 1.3 57.8 + - - +
12B THR* 3.2 4.9 + - - -
13B ALA* 2.9 26.0 + - - +
30B LEU* 3.8 27.1 - - + +
34B THR* 4.3 4.5 - - + -
36B LEU* 3.7 31.4 - - + -
41B LEU* 3.8 16.2 - - + -
44B HIS* 3.6 39.7 - - + -
45B PHE* 3.6 17.9 - - + -
51B LEU* 4.6 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LYS* 3.1 31.6 + - + +
7B GLU* 3.6 7.6 - - - +
9B ILE* 1.3 74.3 - - - +
11B ARG* 1.3 59.9 + - - +
13B ALA* 3.2 4.5 + - - +
14B ILE* 2.9 37.6 + - + +
45B PHE* 3.4 31.4 - - + -
51B LEU* 3.8 10.8 - - + +
54B GLY 3.6 18.4 - - - +
55B MET* 3.6 32.5 - - + +
58B LEU* 3.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLU* 2.8 58.9 + - + +
8B MET* 3.8 6.7 - - - +
9B ILE 3.3 0.2 - - - -
10B LEU* 1.3 71.2 - - - +
12B THR* 1.3 63.4 + - - +
14B ILE* 3.4 9.0 + - - +
15B ASP* 3.1 30.3 + - - +
58B LEU* 3.7 21.9 - - + +
59B LEU* 4.9 6.5 - - - +
62B ASP* 2.7 42.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B MET* 2.8 30.9 + - - +
9B ILE 3.5 8.1 - - - -
11B ARG* 1.3 77.6 - - - +
13B ALA* 1.3 57.5 + - - +
15B ASP 3.3 0.9 + - - -
16B TYR* 3.0 26.0 + - - +
30B LEU* 4.3 1.1 - - + -
33B ALA* 3.7 19.1 - - + +
34B THR* 3.7 22.5 - - + +
2002B GOL 3.2 44.4 + - - +
----------------------------------------------------------
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 ILE 2.9 13.2 + - - +
10B LEU* 3.6 9.2 - - - +
12B THR* 1.3 77.6 - - - +
14B ILE* 1.3 60.7 + - - +
16B TYR* 3.2 7.0 + - - +
17B ILE* 3.1 27.7 + - - +
25B LEU* 4.2 10.1 - - + -
30B LEU* 3.9 23.5 - - + +
51B LEU* 4.5 2.9 - - + -
55B MET* 3.7 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU 2.9 25.9 + - - +
11B ARG* 3.7 10.8 - - - +
13B ALA* 1.3 76.8 - - - +
15B ASP* 1.3 67.9 + - - +
17B ILE* 3.1 20.0 - - - +
55B MET* 3.9 31.9 - - + +
58B LEU* 4.2 17.0 - - + -
59B LEU* 3.9 38.8 - - + -
95B PRO* 3.3 31.7 - - + +
96B GLU 5.3 0.2 - - - +
99B LEU* 4.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG* 3.1 17.0 + - - +
12B THR 3.7 2.9 - - - +
13B ALA 3.3 0.2 - - - -
14B ILE* 1.3 80.9 - - - +
16B TYR* 1.3 63.9 + - - +
18B GLY* 3.2 11.4 + - - -
19B GLU* 3.2 20.8 + - + +
95B PRO* 4.8 6.3 - - - +
2002B GOL 2.5 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B THR 3.0 14.3 + - - +
13B ALA* 3.2 11.9 + - - +
15B ASP* 1.3 76.9 - - - +
17B ILE* 1.3 60.8 + - - +
19B GLU* 3.2 2.8 + - - -
20B TYR* 2.8 67.1 + + + +
21B SER 3.5 20.9 - - - -
24B THR* 2.9 28.1 + - - -
25B LEU* 3.6 29.4 - - + -
29B SER* 3.5 27.3 - - - -
30B LEU* 5.5 0.9 - - + -
33B ALA* 4.6 18.6 - - + -
2002B GOL 4.2 6.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA 3.1 12.0 + - - +
14B ILE 3.1 15.7 - - - +
16B TYR* 1.3 77.5 - - - +
18B GLY* 1.3 62.8 + - - +
20B TYR 3.7 0.9 - - - -
21B SER* 3.5 39.1 + - - +
22B LEU* 3.6 38.4 - - + +
25B LEU* 3.9 17.9 - - + -
55B MET* 4.2 2.5 - - + -
94B ARG* 4.9 0.2 + - - -
95B PRO* 3.7 15.7 - - + +
98B LEU* 3.7 15.9 - - + +
99B LEU* 3.4 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE 3.6 1.2 + - - -
15B ASP 3.2 6.9 + - - -
16B TYR 3.2 0.6 - - - -
17B ILE* 1.3 86.7 - - - +
19B GLU* 1.3 67.3 + - - +
20B TYR 4.5 0.3 - - - +
94B ARG* 2.9 40.2 + - - -
95B PRO* 4.0 20.9 - - - -
98B LEU* 4.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASP* 3.2 15.7 + - + +
16B TYR* 3.2 6.6 + - - +
18B GLY* 1.3 84.4 - - - +
20B TYR* 1.3 83.5 + - + +
94B ARG* 5.6 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 4.4 3.9 - - - +
16B TYR* 2.8 62.8 + + + +
17B ILE 3.7 4.6 - - - +
18B GLY 4.5 1.7 - - - +
19B GLU* 1.3 92.4 - - + +
21B SER* 1.3 67.3 + - - +
24B THR* 3.8 4.7 - - - +
94B ARG* 5.0 7.3 + - - -
----------------------------------------------------------
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