Contacts of the helix formed by residues 15 - 26 (chain A) in PDB entry 1Q21
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 GLY 15 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLY 3.3 2.2 - - - -
14A VAL* 1.4 76.8 - - - +
16A LYS* 1.3 63.0 + - - +
17A SER 3.3 2.7 - - - -
18A ALA* 3.7 0.5 - - - +
19A LEU* 2.7 40.9 + - - +
116A ASN* 4.0 1.3 + - - -
180A GDP 2.7 41.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.9 27.7 - - + +
9A VAL 3.7 5.4 - - - -
10A GLY 3.3 34.7 + - - +
11A ALA 3.0 20.8 + - - -
12A GLY* 3.7 2.8 - - - -
14A VAL* 3.5 12.1 - - + -
15A GLY* 1.3 78.6 - - - +
17A SER* 1.4 58.4 + - - +
19A LEU* 3.9 5.5 - - - +
20A THR* 2.8 33.4 + - - -
57A ASP* 3.5 10.8 - - - +
58A THR* 3.1 27.4 - - - -
59A ALA* 5.2 1.5 - - - +
81A VAL* 4.4 4.3 - - + -
180A GDP 2.8 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 1.4 74.8 - - - +
18A ALA* 1.3 60.5 + - - +
20A THR* 3.7 0.6 - - - -
21A ILE* 2.8 39.8 + - - +
32A TYR* 3.2 33.9 - - - -
57A ASP* 2.9 25.4 + - - -
173A MG 2.4 27.4 - - - -
180A GDP 3.1 12.0 + - - -
----------------------------------------------------------
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 GLY 3.3 1.1 + - - +
17A SER* 1.3 77.9 - - - +
19A LEU* 1.3 62.2 + - - +
21A ILE* 4.3 3.4 - - - +
22A GLN* 3.0 28.4 + - - +
27A HIS 5.1 0.2 - - - +
28A PHE* 3.6 14.9 - - + -
29A VAL* 4.1 14.5 + - - +
32A TYR* 5.9 0.4 - - - +
146A ALA* 3.4 21.8 - - + -
180A GDP 2.9 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 5.2 1.1 - - + -
15A GLY 2.7 24.6 + - - +
16A LYS* 3.9 4.3 - - - +
18A ALA* 1.3 70.6 - - - +
20A THR* 1.3 66.8 + - - +
22A GLN* 3.2 6.8 + - - +
23A LEU* 2.9 24.4 + - - +
79A LEU* 4.9 8.7 - - + -
81A VAL* 4.0 32.3 - - + -
114A VAL* 4.1 13.7 - - + -
116A ASN* 3.5 25.6 - - + +
144A THR* 3.5 14.4 - - + +
146A ALA* 4.2 4.7 - - + -
152A VAL* 3.9 26.6 - - + +
155A ALA* 5.9 1.1 - - + -
156A PHE* 3.9 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.5 22.5 - - - +
16A LYS 2.8 18.1 + - - -
17A SER* 3.7 6.3 - - - -
19A LEU* 1.3 76.5 - - - +
21A ILE* 1.3 65.7 + - + +
23A LEU* 2.9 13.1 + - - +
24A ILE* 3.0 21.3 + - + +
40A TYR* 3.9 36.8 - - + -
55A ILE* 4.3 15.5 - - + -
57A ASP* 4.0 14.4 + - + +
156A PHE* 4.1 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER* 2.8 28.9 + - - +
18A ALA* 4.3 2.0 - - - +
20A THR* 1.3 76.8 - - - +
22A GLN* 1.3 58.4 + - - +
24A ILE* 4.4 4.7 - - - -
25A GLN* 2.8 50.9 + - - +
26A ASN 3.7 0.3 + - - -
27A HIS* 3.8 12.5 - - + +
29A VAL* 3.6 34.5 - - + -
32A TYR* 3.9 28.9 - - + -
40A TYR* 4.0 31.9 - - + +
57A ASP* 5.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA 3.0 21.9 + - - +
19A LEU* 3.3 7.6 - - - +
21A ILE* 1.3 79.5 - - - +
23A LEU* 1.3 59.7 + - - +
26A ASN 3.1 9.4 + - - -
27A HIS* 3.4 23.7 + - - +
28A PHE* 3.8 18.2 - - - +
146A ALA* 2.6 35.9 + - + +
147A LYS 4.1 3.6 + - - -
148A THR 4.7 0.2 - - - -
149A ARG* 2.7 70.9 + - + +
152A VAL* 4.4 10.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
19A LEU 2.9 13.4 + - - +
20A THR 3.5 5.4 - - - +
22A GLN* 1.3 83.0 - - - +
24A ILE* 1.3 68.9 + - + +
26A ASN* 4.2 1.7 + - - +
42A LYS* 3.7 19.8 + - + -
44A VAL* 6.2 0.7 - - + -
53A LEU* 4.6 11.0 - - + -
55A ILE* 3.5 32.1 - - + -
149A ARG* 3.5 12.2 + - - +
152A VAL* 4.2 4.9 - - + +
153A GLU* 4.2 30.1 - - + -
156A PHE* 3.7 37.9 - - + -
157A TYR* 4.4 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR* 3.1 20.9 - - + +
21A ILE* 3.8 4.7 - - - +
23A LEU* 1.3 81.7 - - + +
25A GLN* 1.4 81.6 + - + +
40A TYR* 4.0 28.3 - - + -
41A ARG 3.9 18.4 - - - +
42A LYS* 2.8 53.0 + - + +
55A ILE* 4.0 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 2.8 21.8 + - - +
24A ILE* 1.4 91.6 - - + +
26A ASN* 1.3 71.8 + - - +
27A HIS* 2.8 48.5 + - + +
40A TYR* 4.1 18.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE 3.7 0.2 + - - -
22A GLN* 3.1 21.8 + - - +
23A LEU 4.2 1.7 + - - +
24A ILE 3.6 2.0 - - - +
25A GLN* 1.3 79.5 - - - +
27A HIS* 1.4 59.0 + - - +
42A LYS* 5.9 2.7 - - - +
149A ARG* 3.2 33.4 + - - +
----------------------------------------------------------
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