Contacts of the helix formed by residues 2 - 17 (chain E) in PDB entry 3F5O
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 2 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D GLU* 5.9 0.2 - - - -
3E SER* 1.3 59.7 + - - +
4E MET* 3.5 5.6 + - - +
5E THR* 3.0 35.0 + - - +
6E GLN* 3.0 44.6 + - - +
33E ALA 4.0 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 3 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D SER* 3.7 20.6 + - - -
10D GLU* 2.9 47.0 + - - +
11D VAL* 4.0 10.7 + - - +
2E THR* 1.3 74.0 - - - +
4E MET* 1.3 58.5 + - - +
6E GLN* 3.4 12.0 + - - +
7E SER* 2.8 34.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 4 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E THR* 3.3 4.5 + - - +
3E SER* 1.3 77.2 + - - +
5E THR* 1.3 60.7 + - - +
7E SER* 3.8 5.6 - - - -
8E LEU* 2.8 30.2 + - + +
33E ALA* 3.8 14.1 - - + +
34E ALA* 3.8 34.8 - - - -
35E PRO* 4.5 12.1 - - + -
74E CYS* 3.9 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 5 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E THR* 3.0 29.3 + - - +
4E MET* 1.3 75.2 - - - +
6E GLN* 1.3 59.2 + - - +
9E ARG* 2.9 55.1 + - - +
30E LEU* 3.2 20.2 - - + +
31E VAL 3.9 14.8 - - - +
32E SER* 3.6 7.0 - - - -
33E ALA* 3.0 26.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 6 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D SER* 4.5 16.4 + - - -
2E THR* 3.0 35.3 + - - +
3E SER* 3.7 10.0 - - - +
5E THR* 1.3 76.2 - - - +
7E SER* 1.3 61.9 + - - +
9E ARG* 3.4 21.2 + - - +
10E GLU* 3.2 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 7 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D VAL* 3.6 25.1 - - - +
149D UOC 4.0 25.9 - - - +
3E SER* 2.8 27.4 + - - -
4E MET* 3.8 6.5 - - - -
5E THR 3.3 0.2 - - - -
6E GLN* 1.3 71.5 - - - +
8E LEU* 1.3 65.6 + - - +
10E GLU* 3.1 12.8 + - - +
11E VAL* 3.1 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 8 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E MET* 2.8 21.5 + - + +
7E SER* 1.3 72.5 - - - +
9E ARG* 1.3 63.3 + - - +
11E VAL* 3.2 17.8 + - + +
12E ILE* 2.9 42.5 + - + +
30E LEU* 3.9 18.6 - - + -
33E ALA* 3.7 22.9 - - + -
38E VAL* 3.9 22.0 - - + -
70E MET* 4.2 16.8 - - + +
73E LEU* 4.7 13.7 - - + -
74E CYS* 3.9 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 9 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E THR* 2.9 43.0 + - - +
6E GLN* 3.5 24.2 - - - +
8E LEU* 1.3 77.5 - - - +
10E GLU* 1.3 63.1 + - + +
12E ILE* 4.5 0.7 - - - -
13E LYS* 2.7 66.0 + - + +
30E LEU* 2.8 40.0 + - + +
31E VAL 4.3 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 10 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ILE* 4.9 1.3 - - - +
73D LEU* 5.0 5.6 - - + -
78D GLY 4.3 10.5 - - - +
79D ALA* 5.0 0.9 - - - -
80D PRO* 3.5 27.4 - - + +
149D UOC 3.7 28.0 - - + -
6E GLN* 3.2 13.0 + - + +
7E SER 3.1 8.7 + - - +
9E ARG* 1.3 80.7 - - - +
11E VAL* 1.3 63.0 + - - +
13E LYS* 3.5 10.6 + - - +
14E ALA* 3.2 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 11 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ALA* 3.6 40.4 - - + +
52C ILE* 4.5 7.6 - - + -
149D UOC 4.2 11.7 - - + -
7E SER 3.1 13.7 + - - +
8E LEU* 3.6 21.5 - - + +
10E GLU* 1.3 75.9 - - - +
12E ILE* 1.3 58.2 + - + +
14E ALA* 3.3 2.8 + - - +
15E MET* 2.9 51.2 + - - +
73E LEU* 5.3 8.7 - - + -
149E UOC 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 12 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LEU* 2.9 30.9 + - + +
11E VAL* 1.3 73.4 - - + +
13E LYS* 1.3 92.6 + - - +
15E MET* 3.3 3.7 + - - +
16E THR* 2.9 41.0 + - + +
28E ILE* 4.2 25.6 - - + +
30E LEU* 4.1 23.3 - - + +
40E CYS* 4.8 0.7 - - - -
70E MET* 3.8 35.9 - - + -
149E UOC 6.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 13 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ARG* 2.7 60.4 + - + +
10E GLU* 3.8 12.8 - - - +
12E ILE* 1.3 106.5 - - - +
14E ALA* 1.3 61.8 + - - +
16E THR* 3.6 5.5 + - - +
17E LYS* 3.2 28.4 + - + +
28E ILE 4.8 12.0 + - - -
29E THR* 5.8 0.9 - - - +
30E LEU* 4.7 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ILE* 3.4 43.0 - - + +
80D PRO* 6.4 1.6 - - + -
10E GLU 3.2 12.4 + - - +
11E VAL 3.7 0.2 - - - +
13E LYS* 1.3 78.8 - - - +
15E MET* 1.3 63.1 + - - +
17E LYS* 3.4 18.6 + - - +
18E ALA* 4.2 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 15 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ALA 4.4 1.3 - - - +
52C ILE* 3.7 39.0 - - - +
53C GLY* 4.7 3.6 - - - +
11E VAL* 2.9 38.6 + - - +
12E ILE* 4.1 3.8 - - - +
14E ALA* 1.3 75.7 - - - +
16E THR* 1.3 60.3 + - - +
17E LYS 3.3 0.4 - - - -
18E ALA* 3.5 20.4 - - - +
20E ASN* 4.9 0.7 + - - -
22E GLU* 3.7 17.7 - - + +
73E LEU* 6.1 1.3 - - - -
149E UOC 4.2 33.7 - - + -
51F ALA* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 16 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ILE* 2.9 29.4 + - + +
13E LYS* 4.0 5.6 - - - +
15E MET* 1.3 74.1 - - - +
17E LYS* 1.3 59.2 + - + +
18E ALA 3.2 5.6 - - - +
22E GLU* 3.7 17.9 + - - +
23E ARG* 3.4 20.3 - - - +
25E LEU* 4.0 10.4 + - - +
26E GLY* 2.9 40.8 - - - +
28E ILE* 5.6 0.2 - - - +
70E MET* 6.1 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 17 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D COA 4.0 12.3 + - - -
13E LYS* 3.2 20.2 + - + +
14E ALA* 3.4 13.4 + - - +
15E MET 3.3 0.8 - - - -
16E THR* 1.3 75.9 - - + +
18E ALA* 1.3 65.3 + - - +
19E ARG* 4.0 0.5 + - - +
----------------------------------------------------------
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