Contacts of the helix formed by residues 7 - 14 (chain A) in PDB entry 2PWA
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 PRO 7 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 3.8 2.2 - - - +
5A ASN 4.5 1.1 - - - +
6A ALA* 1.3 90.3 - - + +
8A TRP* 1.3 67.1 + - + +
9A GLY* 3.1 3.1 - - - +
10A LEU* 3.0 29.3 + - + +
11A ALA 3.2 7.3 + - - -
81A THR* 3.8 17.9 - - + +
82A TYR* 3.8 32.1 - - + +
208A ILE* 6.0 2.7 - - + -
209A LEU* 4.2 28.9 - - + +
229A HIS* 6.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ALA 3.4 3.8 + - - -
7A PRO* 1.3 73.4 - - + +
9A GLY* 1.3 61.1 + - - +
11A ALA* 3.3 8.5 + - - +
12A ARG* 2.8 47.2 + - + +
20A THR 4.9 7.4 - - - +
183A SER* 3.5 13.9 - - - -
184A ASP 3.2 22.0 - - - -
185A ARG* 3.5 73.8 - - + +
204A PRO* 3.4 22.7 - - + -
206A THR 3.0 30.7 + - - -
207A ASP* 3.1 18.0 + - - +
208A ILE* 3.7 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 3.0 3.2 + - - +
8A TRP* 1.3 89.6 - - - +
10A LEU* 1.3 60.6 + - - +
12A ARG* 3.2 2.4 + - - +
13A ILE* 3.1 21.7 + - - +
204A PRO* 3.5 35.4 - - - +
208A ILE* 4.8 2.7 - - - +
229A HIS* 3.8 13.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 3.8 13.0 - - - +
6A ALA* 4.2 1.1 - - + -
7A PRO* 3.0 22.8 + - + +
9A GLY* 1.3 73.3 - - - +
11A ALA* 1.3 66.1 + - - +
12A ARG 3.3 0.3 + - - -
13A ILE* 3.3 11.0 + - - -
14A SER 3.5 1.9 + - - -
23A TYR* 3.1 40.3 - - + -
76A THR 4.9 0.2 - - - +
81A THR 3.7 13.7 - - - +
82A TYR 3.7 29.2 - - - +
83A GLY 3.6 20.0 - - - +
84A VAL* 3.6 31.4 - - + -
86A LYS* 3.8 0.4 - - - +
229A HIS* 4.1 11.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ALA* 4.8 0.2 - - + -
7A PRO 3.2 8.2 + - - +
8A TRP* 3.5 7.4 - - - +
10A LEU* 1.3 77.9 - - - +
12A ARG* 1.3 63.0 + - - +
14A SER* 3.1 16.0 + - - -
15A SER* 3.4 13.3 + - - -
20A THR* 3.4 34.9 + - - +
21A SER* 3.7 21.3 - - - +
22A THR 3.7 14.5 - - - +
23A TYR* 4.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TRP* 2.8 45.4 + - + +
9A GLY* 3.5 6.1 - - - +
10A LEU 3.2 0.2 - - - -
11A ALA* 1.3 73.2 - - - +
13A ILE* 1.3 63.2 + - - +
14A SER 3.2 0.2 + - - -
15A SER* 2.8 39.0 + - - +
16A THR 3.6 3.4 + - - -
17A SER 3.5 14.8 + - - +
18A PRO* 3.6 24.4 - - - +
19A GLY 5.1 0.9 - - - +
20A THR* 5.1 1.1 - - - -
183A SER* 5.8 0.4 - - - +
185A ARG 5.4 0.7 - - - -
187A ASP* 2.8 42.3 + - - +
204A PRO* 4.3 5.8 - - + -
257A ASN* 3.6 4.7 + - - +
260A ASP* 3.1 23.2 + - - -
272A LEU* 3.5 24.2 - - + +
273A ALA 4.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLY 3.1 9.2 + - - +
10A LEU* 3.3 6.6 + - - +
12A ARG* 1.3 75.5 - - + +
14A SER* 1.3 56.0 + - - +
15A SER 3.5 0.2 - - - -
23A TYR* 4.5 12.8 - - + +
84A VAL* 5.1 7.9 - - + -
204A PRO* 3.5 31.9 - - + -
229A HIS* 3.7 33.7 - - + +
233A LEU* 4.6 11.7 - - + -
272A LEU* 6.0 0.2 - - + -
273A ALA* 2.8 41.5 - - + +
274A TYR* 3.3 4.4 - - - -
275A ASN* 2.8 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU 3.5 5.5 + - - -
11A ALA 3.1 9.9 + - - -
12A ARG 3.1 0.6 - - - -
13A ILE* 1.3 79.1 - - - +
15A SER* 1.3 58.3 - - - +
22A THR 3.5 8.5 + - - -
23A TYR* 3.8 4.7 - - - -
24A TYR* 3.1 54.6 + - - +
274A TYR* 3.8 8.7 + - - -
275A ASN* 3.4 14.6 - - - +
277A TYR* 5.4 1.8 - - - +
----------------------------------------------------------
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