Contacts of the helix formed by residues 4 - 11 (chain I) in PDB entry 1FD4
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 ASP 4 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I ILE* 4.0 0.7 - - - +
3I GLY* 1.3 82.3 + - - +
5I PRO* 1.3 73.9 - - + +
6I VAL* 2.8 31.4 + - - +
7I THR* 2.6 31.5 + - - -
8I CYS* 3.1 23.0 + - - +
29I THR 3.5 2.7 + - - +
30I CYS* 3.8 7.6 - - - -
31I GLY* 4.5 0.2 - - - -
3K GLY 4.2 3.1 - - - +
31K GLY* 3.1 37.7 - - - -
32K LEU* 3.5 7.7 - - + +
6L VAL* 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 5 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I ASP* 1.3 90.7 - - + +
6I VAL* 1.3 57.0 + - - +
8I CYS* 3.4 0.9 + - - +
9I LEU* 3.0 37.4 + - + +
15I CYS* 3.6 21.5 - - - -
30I CYS 3.2 17.2 - - - +
32I LEU* 5.6 1.3 - - + -
5J PRO* 3.4 35.7 - - + -
6J VAL* 4.9 6.5 - - + -
9J LEU* 3.8 14.4 - - + -
15J CYS* 5.2 0.4 - - - -
32K LEU* 3.9 9.9 - - + -
6L VAL* 4.3 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 6 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PHE* 4.2 17.9 - - + -
4I ASP* 2.8 13.9 + - - +
5I PRO* 1.3 70.8 - - - +
7I THR* 1.3 65.8 + - - +
9I LEU* 3.3 6.0 + - - +
10I LYS* 2.9 50.3 + - + +
5J PRO* 4.2 16.2 - - + -
30J CYS 4.8 6.5 - - - +
32J LEU* 4.4 8.1 - - + -
32K LEU* 3.4 20.4 - - + -
33K PRO* 4.0 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 7 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I GLY 5.3 1.6 - - - +
2I ILE* 4.0 18.3 - - + +
3I GLY 5.2 0.2 - - - -
4I ASP* 2.6 36.4 + - - -
6I VAL* 1.3 73.6 - - - +
8I CYS* 1.3 64.7 + - - +
10I LYS* 3.6 9.7 + - + +
11I SER* 3.3 19.9 + - - -
3K GLY 4.6 2.8 + - - +
31K GLY 4.1 4.9 + - - -
1O GLY* 3.7 28.5 - - - +
2O ILE* 3.3 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 8 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I ILE* 3.6 7.7 - - + +
4I ASP 3.1 18.5 + - - +
5I PRO 3.5 5.2 - - - +
6I VAL 3.2 0.2 - - - -
7I THR* 1.3 76.2 - - - +
9I LEU* 1.3 59.8 + - - +
11I SER* 2.6 24.8 + - - -
13I ALA* 3.3 13.3 + - - -
14I ILE 3.5 16.2 - - - -
15I CYS* 3.8 4.0 - - - -
30I CYS* 3.6 13.9 - - - -
37I CYS* 2.0 57.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I PRO* 3.0 26.7 + - + +
6I VAL* 3.9 4.3 - - - +
8I CYS* 1.3 73.3 - - - +
10I LYS* 1.3 61.2 + - - +
12I GLY* 2.9 20.1 + - - -
13I ALA 3.5 19.1 - - - +
14I ILE* 4.6 1.3 - - - -
15I CYS* 4.7 4.3 - - - +
15J CYS* 3.8 21.8 - - + +
16J HIS 3.8 8.1 - - - +
17J PRO* 3.7 31.1 - - + +
30J CYS* 3.8 34.3 - - + +
32J LEU* 3.9 16.8 - - + +
35J THR* 3.8 11.2 - - + +
39O LYS* 5.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 10 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PHE* 4.8 8.2 - - - -
36C LYS* 5.9 5.3 - - - +
6I VAL* 2.9 40.2 + - + +
7I THR* 3.7 8.7 - - + +
9I LEU* 1.3 78.2 - - - +
11I SER* 1.3 60.1 + - - +
12I GLY 3.1 0.7 + - - -
32J LEU* 3.7 29.6 - - + +
33K PRO* 5.4 4.4 - - - +
1O GLY 5.0 14.9 - - - +
2O ILE* 6.3 0.4 - - + -
25O LYS* 5.4 6.5 - - + +
26O GLN 6.0 0.4 - - - +
27O ILE* 3.6 26.2 - - + +
39O LYS* 3.5 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 11 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I ILE* 4.4 5.2 - - - +
7I THR 3.3 9.0 + - - -
8I CYS* 2.6 22.3 + - - -
9I LEU 3.2 0.6 - - - -
10I LYS* 1.3 76.8 - - - +
12I GLY* 1.3 58.2 + - - +
13I ALA* 3.5 12.5 + - - +
27I ILE* 4.1 7.8 - - - +
2O ILE* 4.8 2.2 - - - -
11O SER* 4.1 28.1 + - - +
27O ILE* 3.9 24.6 - - - +
39O LYS* 3.7 13.7 - - - +
----------------------------------------------------------
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