Contacts of the helix formed by residues 21 - 31 (chain H) in PDB entry 1GN2
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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H GLU* 3.7 15.5 - - - -
18H PRO 4.5 1.3 + - - -
20H ILE* 1.3 78.6 - - - +
22H GLY* 1.3 64.2 + - - +
23H GLN* 3.2 10.9 + - - +
24H ILE* 3.1 34.6 + - - +
25H ASN* 3.3 10.9 + - - -
168H LEU* 5.7 1.0 - - - +
169H GLN* 2.8 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 22 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H TYR* 3.5 29.3 - - - +
14H GLY* 4.1 1.3 - - - -
17H GLU* 3.3 22.4 + - - -
20H ILE 3.7 0.2 + - - -
21H SER* 1.3 71.1 - - - +
23H GLN* 1.3 67.1 + - - +
25H ASN* 3.2 2.6 + - - +
26H GLU* 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 23 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171G LYS* 4.1 28.1 - - - +
21H SER* 3.2 8.3 + - - +
22H GLY* 1.3 75.3 - - - +
24H ILE* 1.3 64.5 + - - +
26H GLU* 3.7 13.3 - - - +
27H LEU* 3.1 36.7 + - + +
168H LEU* 3.9 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167G TYR* 6.1 0.9 - - + -
20H ILE* 4.1 13.9 - - + -
21H SER* 3.1 19.5 + - - +
22H GLY 3.1 0.4 - - - -
23H GLN* 1.3 76.8 - - - +
25H ASN* 1.3 59.6 + - - +
26H GLU 2.9 0.7 + - - -
27H LEU* 3.0 5.0 + - - +
28H HIS* 2.8 42.7 + - + +
164H HIS 4.2 15.9 - - - +
165H ALA* 3.9 17.0 - - - +
166H PHE* 4.0 23.8 - - - -
168H LEU* 4.2 22.7 - - + +
169H GLN* 3.8 35.4 - - + +
170H TYR* 5.5 0.9 - - + -
177H PHE* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 25 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H TRP* 4.0 8.4 - - + -
13H TYR* 3.0 41.0 + - + +
16H LEU* 3.4 29.8 - - - +
20H ILE* 3.5 26.8 + - - +
21H SER 3.3 4.6 + - - +
22H GLY 3.2 3.9 + - - +
24H ILE* 1.3 79.9 - - - +
26H GLU* 1.3 58.5 + - - +
28H HIS* 3.8 7.2 + - - +
29H HIS* 3.0 32.1 + - - +
79H TRP* 5.3 1.9 + - - -
80H TRP* 3.9 17.9 - - + -
83H LEU* 5.2 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H TYR* 3.6 35.6 - - + +
22H GLY 2.9 17.8 + - - +
23H GLN* 3.7 13.5 - - - +
24H ILE 2.9 1.0 + - - -
25H ASN* 1.3 77.0 - - - +
27H LEU* 1.3 68.2 + - + +
30H SER* 2.7 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167G TYR* 3.8 17.9 - - + +
171G LYS* 3.8 25.8 - - + -
172G ASN* 3.2 25.6 - - - +
23H GLN* 3.1 27.2 + - + +
24H ILE* 3.0 5.1 + - - +
26H GLU* 1.3 81.1 - - + +
28H HIS* 1.3 59.4 - - - +
30H SER* 4.1 0.4 - - - -
31H LYS* 2.8 48.3 + - + +
32H HIS* 3.1 6.1 + - - -
168H LEU* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 28 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167G TYR* 5.1 0.2 + - - -
24H ILE* 2.8 30.4 + - + +
25H ASN* 3.8 2.5 + - - +
27H LEU* 1.3 79.2 - - - +
29H HIS* 1.3 56.5 + - - +
32H HIS* 3.3 15.3 - - + +
33H HIS* 2.9 28.9 + - - +
76H HIS* 3.0 15.9 + + - -
79H TRP* 3.5 23.6 + + - -
80H TRP* 3.6 20.5 - + + -
160H ASP* 2.9 19.3 + - - -
164H HIS* 3.0 24.0 + + - +
165H ALA* 4.3 6.7 - - + +
999H FE 2.4 25.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 29 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LEU* 3.8 29.4 - - + +
7H PRO 2.9 27.6 + - - -
8H ASP* 5.0 4.0 - - - -
9H LEU* 3.4 34.2 - - + +
13H TYR* 2.9 28.3 + + + -
25H ASN 3.0 19.4 + - - +
28H HIS* 1.3 76.9 - - - +
30H SER* 1.3 63.6 + - - +
33H HIS* 3.3 20.4 - - - +
34H ALA 3.3 6.8 + - - -
80H TRP* 3.5 26.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 30 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LEU* 4.9 4.0 - - - -
13H TYR* 4.1 12.3 - - - -
26H GLU* 2.7 29.8 + - - +
27H LEU* 4.1 0.5 - - - -
29H HIS* 1.3 80.9 - - - +
31H LYS* 1.3 80.1 + - - +
34H ALA* 3.5 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172G ASN* 3.6 45.3 - - + +
27H LEU* 2.8 32.8 + - + +
29H HIS 3.3 0.2 - - - -
30H SER* 1.3 92.0 + - - +
32H HIS* 1.3 63.7 + - - +
33H HIS 3.6 0.2 - - - -
34H ALA* 3.9 1.6 - - - +
35H THR* 2.8 31.9 + - - -
----------------------------------------------------------
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