Contacts of the helix formed by residues 13 - 25 (chain A) in PDB entry 1J9B
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 13 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A CZZ 1.3 71.7 - - - -
14A THR* 1.3 61.9 + - - +
16A ARG* 3.3 25.1 - - - +
17A ASN* 2.9 33.8 + - - -
127A GLU* 3.5 9.2 - - - -
204A SO4 4.6 0.7 - - - -
402A TAS 3.0 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A CZZ 3.0 27.6 + - - -
13A GLY* 1.3 75.6 - - - +
15A SER* 1.3 57.8 + - - +
18A THR* 2.9 33.8 + - - -
95A PRO* 3.9 6.7 - - + -
106A CYS 3.4 25.6 - - - +
107A ARG* 3.8 17.1 + - + +
108A PRO* 4.6 0.2 - - + -
109A SER* 3.6 5.4 - - - +
204A SO4 2.6 39.4 + - - +
402A TAS 3.2 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.2 0.5 - - - +
8A HIS* 2.7 24.0 + - - -
9A ASN* 3.3 33.4 + - - -
12A CZZ 3.0 14.6 + - - -
14A THR* 1.3 77.1 - - - +
16A ARG* 1.3 64.6 + - - +
18A THR* 3.3 2.6 + - - -
19A LEU* 3.0 24.6 + - - +
94A ARG* 4.6 0.4 - - - -
95A PRO* 3.4 29.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A HIS* 4.1 11.9 - - + +
10A PRO* 2.9 33.7 + - + +
11A ALA* 3.4 21.2 + - - +
12A CZZ 3.0 12.0 + - - +
13A GLY* 3.3 17.4 - - - +
15A SER* 1.3 75.9 - - - +
17A ASN* 1.3 63.3 + - - +
19A LEU* 3.3 4.7 + - - +
20A GLU* 3.0 30.3 + - + +
127A GLU* 2.7 45.2 + - - +
402A TAS 4.1 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLY 2.9 22.8 + - - +
16A ARG* 1.3 72.9 - - - +
18A THR* 1.4 57.5 + - - +
20A GLU* 3.3 3.4 + - - +
21A MET* 2.9 35.8 + - + +
109A SER* 3.6 15.3 - - - +
124A PHE* 3.7 10.7 - - + -
126A LYS* 3.5 26.9 - - + +
127A GLU* 2.9 37.3 + - - +
128A ASP* 5.4 1.2 - - - +
204A SO4 2.9 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.1 4.3 - - + -
14A THR 2.9 22.1 + - - -
15A SER 3.6 4.5 - - - -
17A ASN* 1.4 76.1 - - - +
19A LEU* 1.3 61.3 + - - +
21A MET* 3.1 8.2 + - - +
22A ILE* 2.9 23.5 + - + +
95A PRO* 3.4 18.7 - - + +
97A VAL* 3.7 30.1 - - + -
106A CYS* 3.8 2.8 - - + +
109A SER* 3.2 22.3 - - - -
112A VAL* 4.0 19.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
6A ILE* 4.0 16.5 - - + +
8A HIS* 3.7 28.0 - - + +
15A SER 3.0 17.4 + - - +
16A ARG* 3.7 4.7 - - - +
18A THR* 1.3 76.2 - - - +
20A GLU* 1.3 62.0 + - - +
22A ILE* 3.3 3.9 + - - +
23A ARG* 3.0 57.0 + - - +
29A PRO* 3.5 31.6 - - + -
31A ILE* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 3.0 23.4 + - + +
17A ASN* 3.9 2.7 - - - +
18A THR 3.2 0.2 - - - -
19A LEU* 1.3 76.3 - - - +
21A MET* 1.3 58.9 + - - +
23A ARG* 3.1 40.2 + - - +
24A ASN* 2.9 28.2 + - - +
124A PHE* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASN* 2.9 17.3 + - + +
18A THR* 3.1 6.2 + - - +
20A GLU* 1.3 73.9 - - - +
22A ILE* 1.3 66.9 + - - +
24A ASN 3.2 6.1 + - - -
25A SER 3.2 0.5 + - - -
109A SER* 3.3 46.7 - - - +
110A GLU* 3.7 16.2 - - + +
112A VAL* 3.9 11.0 - - + -
113A LEU* 4.1 15.7 - - - -
116A LEU* 3.8 2.4 - - - +
120A GLN* 3.0 36.1 + - - +
124A PHE* 3.6 38.6 - - + -
126A LYS* 5.2 0.2 - - - -
132A VAL* 4.2 12.8 - - + -
133A VAL* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 3.9 17.9 - - + -
6A ILE* 4.1 28.3 - - + -
18A THR 2.9 20.1 + - - +
19A LEU* 3.3 7.2 + - - +
21A MET* 1.3 73.5 - - - +
23A ARG* 1.3 64.6 + - - +
25A SER* 2.7 24.1 + - - -
26A GLY 3.6 0.5 + - - -
27A THR* 3.4 27.6 - - - +
29A PRO* 3.9 19.3 - - + -
97A VAL* 4.0 25.4 - - + -
112A VAL* 4.0 17.0 - - + -
116A LEU* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.0 36.3 + - - +
20A GLU* 3.1 36.0 + - - +
21A MET 3.3 0.2 - - - -
22A ILE* 1.3 77.9 - - - +
24A ASN* 1.3 56.3 + - - +
26A GLY* 2.9 22.2 + - - -
27A THR 3.4 13.1 + - - +
28A GLU* 2.8 42.8 + - - +
29A PRO* 4.4 4.5 - - + -
31A ILE* 3.7 17.2 - - - +
121A LYS* 5.0 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU 2.9 17.5 + - - +
21A MET* 3.2 2.2 + - - +
23A ARG* 1.3 74.8 - - - +
25A SER* 1.3 56.1 + - - +
26A GLY 3.2 0.4 - - - -
120A GLN* 2.7 29.5 - - - +
121A LYS* 2.8 46.0 + - - +
122A GLY* 3.1 27.4 + - - +
123A ALA 3.8 8.6 + - - +
124A PHE* 4.0 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 5.0 0.5 - - - +
21A MET 3.2 3.5 + - - -
22A ILE 2.7 20.5 + - - -
24A ASN* 1.3 77.6 - - - +
26A GLY* 1.3 56.7 + - - +
27A THR* 4.0 10.2 + - - +
116A LEU* 3.9 20.4 - - - +
118A ASP* 3.4 45.5 + - - +
119A ALA 3.9 9.4 - - - +
120A GLN* 3.9 12.1 - - - +
121A LYS* 4.0 6.8 - - - +
----------------------------------------------------------
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