Contacts of the helix formed by residues 21 - 31 (chain D) in PDB entry 1GN6
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 21 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D TYR 4.6 0.4 - - - -
17D GLU* 3.9 16.4 - - - -
18D PRO 5.7 0.2 - - - -
20D ILE* 1.3 75.6 - - - +
22D GLY* 1.3 65.6 + - - +
23D GLN* 3.4 13.5 + - - +
24D ILE* 3.1 37.7 + - - +
25D ASN* 3.1 13.2 + - - -
168D LEU* 5.6 0.5 - - - +
169D GLN* 2.7 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D TYR* 3.3 30.3 - - - +
14D GLY* 3.9 3.1 - - - -
17D GLU* 3.0 21.4 + - - +
20D ILE 3.7 0.4 + - - -
21D SER* 1.3 73.0 - - - +
23D GLN* 1.3 63.7 + - - +
25D ASN* 3.8 0.9 - - - +
26D GLU* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C LYS* 4.5 12.0 + - - +
17D GLU* 4.8 0.4 + - - -
21D SER* 3.1 11.2 + - - +
22D GLY* 1.3 77.5 - - - +
24D ILE* 1.3 60.7 + - - +
26D GLU* 3.6 6.4 + - - +
27D LEU* 3.3 29.5 + - + +
168D LEU* 3.8 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C TYR* 6.3 0.2 - - + -
20D ILE* 4.5 10.8 - - + -
21D SER* 3.1 14.7 + - - +
23D GLN* 1.3 75.1 - - - +
25D ASN* 1.3 61.1 + - - +
27D LEU* 3.2 4.3 + - - +
28D HIS* 2.8 44.5 + - + +
164D HIS 3.9 16.4 - - - +
165D ALA* 3.5 28.3 - - - +
166D PHE* 4.2 8.1 - - - -
168D LEU* 4.0 21.5 - - + +
169D GLN* 3.6 47.3 - - + +
170D TYR* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LEU* 5.2 0.2 - - + -
11D TRP* 3.9 21.7 - - + -
13D TYR* 3.1 40.8 + - + +
16D LEU* 3.9 19.8 - - - +
20D ILE* 3.6 20.0 + - - +
21D SER 3.1 11.0 + - - -
22D GLY 3.3 1.3 + - - +
24D ILE* 1.3 77.7 - - - +
26D GLU* 1.3 58.3 + - - +
28D HIS* 3.9 4.4 + - - +
29D HIS* 3.0 32.6 + - - +
79D TRP* 5.4 1.0 + - - -
80D TRP* 3.8 18.2 - - + -
83D LEU* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D TYR* 3.7 35.6 - - + +
22D GLY 3.0 16.8 + - - +
23D GLN* 4.0 6.1 - - - +
25D ASN* 1.3 75.0 - - - +
27D LEU* 1.3 71.1 + - + +
30D SER* 2.7 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C TYR* 3.9 17.5 - - - +
171C LYS* 3.6 29.6 - - + -
172C ASN* 3.7 20.9 - - - +
23D GLN* 3.3 17.4 + - + +
24D ILE* 3.2 4.8 + - + +
26D GLU* 1.3 81.9 - - + +
28D HIS* 1.3 65.5 + - - +
31D LYS* 2.8 37.9 + - + +
32D HIS* 3.1 10.9 + - + -
168D LEU* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ILE* 2.8 31.6 + - + +
25D ASN* 3.9 4.5 + - - +
27D LEU* 1.3 80.2 - - - +
29D HIS* 1.3 56.4 + - - +
32D HIS* 3.3 13.9 + - + +
33D HIS* 2.9 28.4 + - - +
76D HIS* 3.0 14.7 + + - -
79D TRP* 3.4 25.4 + + - -
80D TRP* 3.6 15.8 - + + -
160D ASP* 2.8 19.3 + - - -
164D HIS* 3.2 20.7 + + - +
165D ALA* 4.3 7.1 - - + -
999D FE 2.2 27.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 3.9 28.8 - - + +
7D PRO 2.8 28.3 + - - -
8D ASP* 4.8 3.1 - - - -
9D LEU* 3.4 32.1 - - + +
13D TYR* 2.7 32.9 + + + -
25D ASN 3.0 19.9 + - - +
28D HIS* 1.3 79.5 - - - +
30D SER* 1.3 63.7 + - - +
31D LYS 3.3 0.3 + - - -
33D HIS* 3.6 5.5 - - - +
34D ALA 3.5 17.2 + - - -
80D TRP* 3.7 25.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 5.0 4.5 - - - -
13D TYR* 3.9 14.6 - - - -
26D GLU* 2.7 31.0 + - - +
29D HIS* 1.3 81.2 - - - +
31D LYS* 1.3 78.4 + - - +
34D ALA* 3.7 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C ASN* 3.9 34.5 - - + +
27D LEU* 2.8 39.7 + - + +
30D SER* 1.3 93.1 + - - +
32D HIS* 1.3 67.6 + - - +
33D HIS 3.5 0.2 - - - -
34D ALA* 4.1 1.9 - - - +
35D THR* 3.0 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