Contacts of the helix formed by residues 12 - 22 (chain D) in PDB entry 3N3B
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 GLU 12 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D SER* 3.1 11.9 - - - -
9D SER 2.9 17.9 + - - +
10D SER* 3.9 12.0 - - - +
11D SER* 1.3 77.9 - - - +
13D ASN* 1.3 63.5 + - - +
14D THR 3.5 0.9 - - - -
15D GLN* 3.8 24.8 - - + +
16D ARG* 3.3 38.5 + - + +
27D ARG* 3.6 22.0 + - - +
134D FMN 3.3 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A TYR* 3.9 14.6 - - - -
263A MET 3.8 14.9 - - - +
264A ASN* 5.6 0.8 - - - +
11D SER* 4.2 3.6 + - - -
12D GLU* 1.3 70.7 - - - +
14D THR* 1.3 64.0 + - - +
16D ARG* 3.5 15.6 + - - +
17D PHE 3.1 16.3 + - - -
111D LEU* 3.7 24.1 - - - +
112D MET* 3.3 27.6 + - - +
134D FMN 2.8 59.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D TYR* 4.2 6.3 - - + -
7D PHE 3.4 22.9 + - - +
8D SER* 3.9 0.7 - - - -
13D ASN* 1.3 73.2 - - - +
15D GLN* 1.3 66.5 + - - +
17D PHE* 3.2 6.3 + - - +
18D ILE* 3.0 40.1 + - + +
45D ILE* 3.8 31.2 - - + +
47D PRO* 4.0 7.2 - - + +
81D SER* 4.0 10.8 + - - -
109D PHE* 4.8 5.6 - - + -
111D LEU 4.9 1.6 - - - -
134D FMN 2.8 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D TYR* 2.7 38.6 + - - -
8D SER* 3.1 20.7 + - - +
12D GLU* 3.8 25.4 - - + +
13D ASN 3.3 0.2 - - - -
14D THR* 1.3 76.9 - - - +
16D ARG* 1.3 58.1 + - + +
18D ILE* 3.3 4.5 + - - +
19D GLU* 3.0 67.6 + - - +
27D ARG* 3.4 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLN* 3.1 33.9 + - - +
266A GLY* 4.2 15.2 - - - -
11D SER 2.9 25.9 + - - -
12D GLU* 3.3 31.3 + - + +
13D ASN* 3.5 20.3 + - - +
14D THR 3.3 0.4 - - - -
15D GLN* 1.3 77.5 - - + +
17D PHE* 1.3 64.2 + - - +
19D GLU* 3.8 18.9 - - - +
20D ARG* 3.2 35.3 + - - +
112D MET* 3.4 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ASN 3.1 12.5 + - - +
14D THR* 3.3 11.0 - - - +
16D ARG* 1.3 76.4 - - - +
18D ILE* 1.3 71.7 + - + +
20D ARG* 3.4 4.6 + - - +
21D LEU* 2.9 51.8 + - + +
45D ILE* 4.1 13.7 - - + -
79D ILE* 5.7 0.4 - - + -
109D PHE* 3.6 42.8 - + + -
112D MET 3.2 29.8 + - - +
113D GLY* 4.2 1.3 - - - -
117D ASP* 4.4 10.8 - - + -
118D ILE* 4.2 23.6 - - + +
121D VAL* 3.8 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 5.5 1.1 - - + -
6D TYR* 3.6 59.2 - - + +
14D THR* 3.0 29.5 + - + +
15D GLN* 3.3 7.4 + - - +
17D PHE* 1.3 89.7 - - + +
19D GLU* 1.3 69.9 + - + +
21D LEU* 3.2 19.3 + - + +
22D GLY* 3.3 12.3 + - - -
23D LEU 4.6 8.7 - - - +
25D ALA* 4.3 16.6 - - + +
45D ILE* 3.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D GLN* 3.0 50.3 + - - +
16D ARG* 3.8 20.1 - - - +
17D PHE 3.4 0.2 - - - -
18D ILE* 1.3 79.1 - - + +
20D ARG* 1.3 62.6 + - + +
21D LEU 3.7 0.2 + - - -
22D GLY* 4.0 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLU* 2.8 45.3 + - - +
269A PRO* 4.1 9.1 - - - +
16D ARG* 3.2 23.6 + - - +
17D PHE* 3.7 3.3 - - - +
19D GLU* 1.3 76.2 - - + +
21D LEU* 1.3 63.5 + - - +
22D GLY 3.5 0.2 - - - -
112D MET* 2.8 46.8 + - - +
113D GLY 2.8 19.3 + - - -
114D THR 4.2 4.0 - - - -
115D GLN* 3.9 6.3 + - - +
118D ILE* 3.5 31.9 - - + +
122D ARG* 3.6 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 4.2 21.5 - - + -
17D PHE* 2.9 48.2 + - + +
18D ILE* 3.2 14.8 + - + +
20D ARG* 1.3 78.6 - - - +
22D GLY* 1.3 56.9 + - - +
23D LEU* 3.3 24.3 + - + +
45D ILE* 4.9 0.9 - - + -
118D ILE* 4.0 12.8 - - + +
121D VAL* 4.0 19.5 - - + -
122D ARG* 2.8 57.0 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
18D ILE 3.3 7.9 + - - -
19D GLU 4.0 6.7 + - - -
20D ARG 3.5 2.4 - - - -
21D LEU* 1.3 76.7 - - - +
23D LEU* 1.3 64.2 + - - +
24D PRO* 3.7 4.9 - - - +
122D ARG* 5.0 0.9 - - - -
----------------------------------------------------------
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