Contacts of the helix formed by residues 16 - 26 (chain A) in PDB entry 1CG1
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 GLN 16 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 4.3 7.6 - - + +
7A LEU* 3.8 1.7 - - - -
8A GLY 3.3 26.4 + - - +
14A GLU* 3.0 23.4 + - - +
15A GLY* 1.3 71.4 - - - +
17A GLY* 1.3 53.8 + - - +
19A ILE* 3.0 4.0 + - - +
20A VAL* 2.7 42.0 + - + +
41A HIS* 4.5 4.7 + - + -
222A GLY* 2.9 40.6 - - - +
223A ALA 3.4 1.2 + - - -
224A GLN 3.3 12.2 + - - +
265A ILE* 3.9 22.4 - - + -
432A GDP 2.6 21.4 + - - +
440A IMO 3.6 17.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLN* 1.3 74.5 - - - +
18A LYS* 1.3 64.1 + - - +
20A VAL* 2.9 3.1 + - - +
21A ASP* 2.8 24.9 + - - +
41A HIS* 3.6 26.4 - - - +
42A THR 4.7 0.7 - - - -
43A LEU* 3.6 11.4 - - - +
57A SER* 3.7 12.2 - - - -
221A GLU* 4.8 0.2 - - - -
432A GDP 2.9 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY* 3.7 9.0 + - - +
16A GLN 3.4 0.4 - - - -
17A GLY* 1.3 73.9 - - - +
19A ILE* 1.3 72.9 + - + +
21A ASP* 3.2 7.0 + - - +
22A LEU* 3.0 24.0 + - + +
42A THR 3.7 18.7 + - - +
43A LEU* 4.8 4.0 - - - +
44A VAL 6.1 0.4 - - - +
414A SER* 2.7 24.2 + - - +
416A GLY 2.6 25.4 + - - +
417A PRO 3.5 18.6 - - - +
418A ASP 3.0 15.5 + - - +
419A ARG* 3.9 11.3 - - - -
421A GLU 2.8 10.1 + - - -
422A THR* 2.8 27.8 + - - -
432A GDP 3.7 17.9 + - + +
----------------------------------------------------------
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 VAL* 4.5 5.2 - - + -
15A GLY 3.4 12.2 + - - +
16A GLN 3.0 8.0 + - - +
18A LYS* 1.3 88.0 - - + +
20A VAL* 1.3 61.9 + - - +
22A LEU* 3.5 20.8 + - + +
23A LEU* 3.1 37.3 + - + +
263A LEU* 3.9 14.1 - - + -
265A ILE* 3.8 25.4 - - + -
328A CYS* 3.3 30.5 - - - -
330A THR* 4.5 4.3 - - + -
412A ILE* 4.6 7.0 - - + -
414A SER* 4.7 11.2 - - - -
422A THR* 4.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 3.9 22.2 - - + -
16A GLN* 2.7 24.4 + - + +
19A ILE* 1.3 71.2 - - - +
21A ASP* 1.3 58.9 + - - +
22A LEU 3.2 0.2 + - - -
23A LEU 3.9 0.3 - - - -
24A THR* 2.7 56.6 + - + +
30A VAL* 3.9 17.5 - - + -
57A SER* 3.6 22.2 - - - -
219A MET* 4.1 12.1 - - + -
221A GLU* 3.6 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLY 2.8 8.7 + - - +
18A LYS* 3.8 4.6 - - - +
20A VAL* 1.3 76.8 - - - +
22A LEU* 1.3 53.2 + - - +
24A THR* 2.9 13.6 + - - -
43A LEU* 3.6 39.5 - - + +
45A ILE* 3.9 6.9 - - - +
57A SER 3.7 8.9 + - - +
60A LEU* 4.4 4.3 - - - +
61A ARG* 2.6 40.9 + - - +
419A ARG* 2.6 53.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS* 3.0 16.9 + - + +
19A ILE* 3.7 18.8 - - + +
21A ASP* 1.3 83.5 + - - +
23A LEU* 1.3 68.4 + - + +
24A THR 3.3 0.5 + - - -
25A GLU* 3.6 16.3 + - - +
61A ARG* 3.6 7.6 + - - +
412A ILE* 5.0 1.6 - - + -
419A ARG* 3.2 36.1 - - + +
420A THR* 5.1 3.1 - - + -
422A THR* 3.8 34.5 - - + +
424A ILE* 4.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 4.7 2.9 - - + -
19A ILE* 3.1 34.9 + - + +
22A LEU* 1.3 79.7 - - + +
24A THR* 1.3 58.5 + - - +
25A GLU* 3.0 11.2 + - - +
26A ARG* 3.6 7.3 + - - +
219A MET* 3.8 24.0 - - + -
263A LEU* 4.6 4.3 - - + -
412A ILE* 3.9 20.4 - - + -
424A ILE* 3.9 28.3 - - + -
427A ASP* 4.4 14.9 - - - +
428A PRO* 4.1 23.8 - - + -
429A PHE* 3.4 23.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 2.7 40.1 + - + +
21A ASP* 2.9 17.3 + - - -
22A LEU 3.3 0.2 - - - -
23A LEU* 1.3 71.0 - - - +
25A GLU* 1.3 56.9 + - - +
26A ARG 3.0 2.9 - - - -
27A ALA* 2.8 27.4 + - + +
30A VAL* 3.1 35.7 - - + -
58A GLY* 4.2 3.8 - - - -
61A ARG* 3.0 16.7 - - - +
64A VAL* 3.3 20.3 - - - +
219A MET* 4.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.6 12.9 + - - +
23A LEU 3.0 1.5 - - - +
24A THR* 1.3 77.8 + - - +
26A ARG* 1.3 66.3 + - + +
61A ARG* 3.2 40.7 + - - +
63A ASN* 3.7 15.5 + - - +
419A ARG* 5.6 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 3.6 4.0 + - - +
24A THR 3.0 0.6 - - - -
25A GLU* 1.3 91.4 - - + +
27A ALA* 1.3 61.5 + - - +
28A LYS* 4.0 5.5 + - - +
63A ASN* 4.8 0.9 - - - -
217A PHE* 3.7 44.5 - - + +
427A ASP* 2.7 49.7 + - - -
429A PHE* 3.8 14.9 + - + +
430A ASP* 2.6 30.3 + - - -
----------------------------------------------------------
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