Contacts of the helix formed by residues 15 - 27 (chain A) in PDB entry 1G1F
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 15 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.2 22.0 + - - +
13A SER* 3.5 21.1 - - - -
14A GLY* 1.3 75.0 - - - +
16A TRP* 1.3 63.6 + - - +
17A ALA* 3.3 3.6 - - - +
18A ALA* 3.2 15.7 + - - -
19A ILE* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 3.6 34.3 - + - -
10A ILE* 3.6 35.9 - - + +
11A ASP* 2.8 31.5 + - - +
14A GLY* 3.5 6.7 + - - -
15A SER* 1.3 77.6 - - - +
17A ALA* 1.3 56.7 + - - +
19A ILE* 3.6 4.6 + - + +
20A TYR* 3.1 31.4 + - - +
264A ALA* 3.7 16.5 - - + +
267A LEU* 4.1 19.1 - - + -
268A ARG* 3.8 35.2 - - + +
271A TYR* 3.7 45.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY 5.2 2.0 + - - +
15A SER* 3.3 1.3 - - - +
16A TRP* 1.3 77.4 - - - +
18A ALA* 1.3 58.2 + - - +
20A TYR* 4.0 1.6 - - - +
21A GLN* 3.1 39.2 + - - +
264A ALA* 4.1 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 3.2 19.8 + - - +
17A ALA* 1.3 77.5 - - - +
19A ILE* 1.3 63.5 + - + +
21A GLN* 3.4 6.9 + - - +
22A ASP* 3.1 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU* 6.4 0.2 - - - -
10A ILE* 3.8 36.8 - - + -
15A SER* 3.0 25.1 + - - +
16A TRP* 4.0 8.3 - - + +
18A ALA* 1.3 75.7 - - + +
20A TYR* 1.3 63.5 + - - +
22A ASP* 3.3 20.1 + - - +
23A ILE* 3.4 14.4 + - - +
247A LYS* 3.9 30.2 - - + +
267A LEU* 4.1 15.7 - - + -
271A TYR* 5.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP 3.1 18.8 + - - +
17A ALA 4.0 2.0 - - - +
19A ILE* 1.3 74.0 - - - +
21A GLN* 1.3 75.0 + - - +
23A ILE* 3.2 11.6 + - + +
24A ARG* 3.2 52.3 + - + +
250A LEU* 5.5 1.8 - - + -
254A ARG* 4.4 7.1 + - - -
261A ILE* 2.7 40.9 + - + -
262A GLN* 3.1 30.9 + - - -
263A THR* 3.9 10.1 - - - -
264A ALA* 3.7 21.5 - - + -
267A LEU* 4.0 22.7 - - + -
1163B PTR 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA* 3.1 27.4 + - - +
18A ALA* 3.8 7.4 - - - +
20A TYR* 1.3 84.4 - - - +
22A ASP* 1.3 58.5 + - - +
24A ARG* 2.9 51.6 + - - +
25A HIS* 3.2 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 3.1 22.3 + - - +
19A ILE* 3.5 16.9 - - - +
20A TYR 3.2 0.2 - - - -
21A GLN* 1.3 76.9 - - - +
23A ILE* 1.3 59.3 + - + +
25A HIS* 3.4 7.6 + - - +
26A GLU* 3.1 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE 3.5 12.1 - - - +
20A TYR* 3.2 12.2 + - + +
22A ASP* 1.3 77.6 - - + +
24A ARG* 1.3 57.1 + - - +
26A GLU* 3.3 5.1 + - - +
27A ALA* 2.9 28.4 + - - +
247A LYS* 4.0 35.0 - - + +
250A LEU* 4.0 25.1 - - + -
251A LEU* 3.5 27.4 - - + +
254A ARG* 4.4 12.6 - - - +
267A LEU* 3.8 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.2 41.7 + - + +
21A GLN* 2.9 39.6 - - - +
22A ASP 3.3 0.2 - - - -
23A ILE* 1.3 76.0 - - - +
25A HIS* 1.3 60.4 + - - +
27A ALA* 3.6 14.7 - - - +
254A ARG* 3.9 15.0 - - - +
1163B PTR 3.1 58.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN 3.2 14.3 + - - +
22A ASP* 3.7 8.7 - - - +
23A ILE 3.3 0.2 - - - -
24A ARG* 1.3 79.5 - - - +
26A GLU* 1.3 67.6 + - - +
27A ALA 3.6 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASP* 3.1 32.7 + - + +
23A ILE* 3.3 6.3 + - - +
25A HIS* 1.3 82.1 - - - +
27A ALA* 1.3 63.8 + - - +
28A SER* 3.7 1.6 + - - -
251A LEU* 4.0 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE 2.9 13.1 + - - +
24A ARG 3.6 12.3 - - - +
25A HIS 3.4 6.1 - - - +
26A GLU* 1.3 78.8 - - - +
28A SER* 1.3 68.2 + - - +
29A ASP* 3.8 3.5 + - - +
251A LEU* 3.9 8.1 - - + -
254A ARG* 3.4 39.3 - - + +
1163B PTR 5.2 4.0 - - - +
----------------------------------------------------------
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