Contacts of the helix formed by residues 4 - 15 (chain B) in PDB entry 3M18
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 GLY 4 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B VAL 3.8 0.8 + - - -
3B PHE* 1.3 76.8 - - - +
5B ARG* 1.3 60.0 + - - +
6B CYS 3.5 2.5 - - - -
7B GLU* 3.1 20.0 + - - -
8B LEU* 2.9 28.6 + - - +
38B PHE* 4.5 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLY* 1.3 71.9 - - - +
6B CYS* 1.3 73.8 + - - +
8B LEU* 3.2 2.9 + - - +
9B ALA* 3.0 25.6 + - - +
29B VAL* 4.1 11.5 - - + +
38B PHE* 3.8 23.2 - - + -
122B ALA 3.8 4.7 + - - -
123B TRP* 2.8 71.7 + - + +
125B ARG 2.8 29.1 + - - +
126B GLY* 4.7 3.2 - - - -
127B CYS* 3.5 7.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ARG* 1.3 92.8 - - - +
7B GLU* 1.3 65.5 + - - +
9B ALA* 3.3 2.2 + - - +
10B ALA* 3.0 25.3 + - - +
126B GLY 4.3 3.4 - - - -
127B CYS* 2.0 61.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
1B LYS* 2.6 34.7 + - - -
2B VAL 4.6 1.0 - - - +
3B PHE* 3.7 15.2 - - + -
4B GLY* 3.1 28.6 + - - +
5B ARG 3.3 0.2 - - - -
6B CYS* 1.3 78.2 - - - +
8B LEU* 1.3 60.6 + - - +
10B ALA* 3.5 6.4 + - - +
11B ALA* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE* 3.7 28.4 - - + -
4B GLY 2.9 17.5 + - - +
5B ARG* 3.7 4.0 - - - +
6B CYS 3.2 0.2 - - - -
7B GLU* 1.3 74.2 - - - +
9B ALA* 1.3 69.1 + - - +
11B ALA 3.1 0.6 + - - +
12B MET* 2.9 51.1 + - + +
29B VAL* 4.7 4.3 - - + -
32B ALA* 3.6 31.0 - - + -
38B PHE* 3.6 21.5 - - + -
55B ILE* 4.0 14.6 - - + -
88B ILE* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ARG 3.0 14.3 + - - +
6B CYS* 3.3 11.6 + - - +
8B LEU* 1.3 76.4 - - - +
10B ALA* 1.3 57.4 + - - +
12B MET* 3.8 1.4 - - - +
13B LYS* 2.9 31.5 + - - +
25B LEU* 3.7 9.4 - - + +
29B VAL* 3.7 24.6 - - + +
123B TRP 5.0 0.4 - - - +
124B ILE* 4.1 21.1 - - + -
127B CYS* 4.6 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B CYS 3.0 17.5 + - - +
7B GLU* 3.6 7.6 - - - +
9B ALA* 1.3 74.3 - - - +
11B ALA* 1.3 58.6 + - - +
13B LYS* 3.4 7.8 + - - +
14B ARG* 3.0 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE* 4.2 16.4 - - + -
7B GLU 3.1 17.0 + - - +
8B LEU* 3.1 3.1 + - - +
10B ALA* 1.3 78.1 - - - +
12B MET* 1.3 56.5 + - - +
14B ARG* 3.4 8.9 + - - +
15B HIS* 3.0 36.5 + - + -
88B ILE* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 2.9 44.2 + - + +
9B ALA 4.5 0.2 - - - -
11B ALA* 1.3 74.3 - - - +
13B LYS* 1.3 61.6 + - - +
15B HIS* 3.3 4.9 + - - +
16B GLY 3.2 5.0 + - - -
17B LEU* 3.0 47.1 + - + +
25B LEU* 3.7 15.7 - - + -
28B TRP* 3.4 45.8 - - + +
29B VAL* 3.9 8.7 - - - -
32B ALA* 4.1 7.4 - - + -
55B ILE* 5.6 3.4 - - + -
56B LEU* 4.2 17.5 - - + -
88B ILE* 3.9 18.6 - - + -
92B VAL* 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA 2.9 19.0 + - - +
10B ALA* 3.7 6.5 - - - +
12B MET* 1.3 73.9 - - - +
14B ARG* 1.3 64.8 + - - +
16B GLY* 3.2 13.5 + - - -
17B LEU 4.8 1.8 - - - +
18B ASP* 3.7 28.4 + - + +
25B LEU* 3.7 23.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ALA 3.0 18.5 + - - +
11B ALA* 3.5 9.0 - - - +
13B LYS* 1.3 74.7 - - - +
15B HIS* 1.4 86.6 + - + +
16B GLY* 3.4 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 3.0 31.3 + - + +
12B MET 3.3 3.5 + - - +
13B LYS 3.2 0.6 - - - -
14B ARG* 1.4 105.0 + - + +
16B GLY* 1.3 58.7 + - - +
17B LEU 3.5 2.7 - - - -
87B ASP* 4.7 2.2 + - - -
88B ILE* 4.1 17.9 + - + +
89B THR* 3.0 36.5 + - + +
92B VAL* 3.7 25.0 - - + +
96B LYS* 2.8 26.7 + - - -
----------------------------------------------------------
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