Contacts of the helix formed by residues 14 - 28 (chain A) in PDB entry 1WMA
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 LYS 14 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLY 3.8 7.1 - - - +
12A GLY 3.4 1.2 + - - -
13A ASN* 1.3 89.4 - - - +
15A GLY* 1.3 69.5 + - - +
17A GLY 3.5 4.7 + - - -
18A LEU* 3.3 20.8 + - - -
41A ARG* 6.1 2.5 - - - +
233A ASP* 2.7 36.2 + - - +
309A NDP 3.4 68.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LYS* 1.3 80.6 - - - +
16A ILE* 1.3 64.2 + - - -
18A LEU* 3.7 3.7 - - - +
19A ALA 3.3 13.3 + - - -
232A THR* 3.9 12.1 - - - -
243A PRO* 3.9 17.8 - - - +
309A NDP 3.5 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY* 1.3 71.9 - - - -
17A GLY* 1.3 63.2 + - - +
19A ALA* 3.1 9.2 + - - +
20A ILE* 2.9 41.9 + - + +
89A ASN* 3.8 8.5 - - - +
137A VAL* 5.5 1.3 - - + -
227A PRO* 3.6 31.6 - - + -
230A VAL* 3.8 33.9 - - + -
232A THR* 4.1 1.1 - - + +
243A PRO* 4.8 2.9 - - + -
246A GLY* 4.3 20.6 - - - +
247A ALA 4.4 0.2 - - - +
250A PRO* 4.8 2.2 - - + -
309A NDP 2.9 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.8 7.8 - - - +
11A GLY 3.4 8.1 - - - -
12A GLY* 3.9 7.2 - - - -
14A LYS 3.5 2.4 + - - -
15A GLY 3.2 1.2 - - - -
16A ILE* 1.3 78.6 - - - +
18A LEU* 1.3 60.1 + - - +
20A ILE* 3.2 5.6 + - - +
21A VAL* 2.9 27.0 + - - +
89A ASN* 3.4 31.0 - - - +
309A NDP 4.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLY 3.3 21.7 + - - +
13A ASN 3.8 12.3 - - - +
14A LYS* 3.3 19.3 + - - -
15A GLY 3.7 8.7 - - - +
16A ILE 3.3 0.6 - - - -
17A GLY* 1.3 74.9 - - - +
19A ALA* 1.4 59.2 + - - +
21A VAL* 3.2 4.1 + - - +
22A ARG* 2.9 38.6 + - - +
34A LEU* 4.0 7.4 - - + -
45A ALA* 4.1 9.0 - - + +
48A GLN* 3.8 31.4 - - - +
49A LEU* 3.8 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY 3.3 2.6 + - - +
16A ILE 3.1 7.9 + - - +
18A LEU* 1.4 78.6 - - - +
20A ILE* 1.3 61.8 + - - +
22A ARG* 3.4 21.9 + - - +
23A ASP* 3.1 28.5 + - - +
243A PRO* 3.4 44.0 - - + +
244A GLU* 4.0 4.5 - - + +
247A ALA* 3.9 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.8 19.5 - - + -
16A ILE* 2.9 32.7 + - + +
17A GLY* 3.5 7.9 - - - +
19A ALA* 1.3 72.9 - - - +
21A VAL* 1.3 67.0 + - - +
23A ASP* 3.2 2.6 + - - +
24A LEU* 2.9 33.7 + - + +
87A VAL* 4.0 23.3 - - + -
89A ASN* 4.2 9.4 - - + +
137A VAL* 4.7 0.9 - - + -
247A ALA* 3.8 18.4 - - + -
250A PRO* 3.6 27.4 - - + -
251A VAL* 4.1 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.6 29.2 - - + -
12A GLY* 4.4 2.0 - - - +
17A GLY 2.9 20.2 + - - +
18A LEU 3.5 6.7 - - - +
20A ILE* 1.3 76.3 - - - +
22A ARG* 1.3 57.1 + - - +
24A LEU* 3.2 2.8 + - - +
25A CYS* 2.8 34.2 + - - -
32A VAL* 4.0 17.2 - - + +
33A VAL 4.8 0.4 - - - +
34A LEU* 4.1 37.2 - - + +
49A LEU* 3.6 22.4 - - + -
56A PRO* 4.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 2.9 19.2 + - - +
19A ALA* 3.6 31.6 + - - +
20A ILE 3.2 0.2 - - - -
21A VAL* 1.3 77.0 - - - +
23A ASP* 1.3 66.5 + - - +
25A CYS* 3.3 13.0 + - - +
26A ARG* 3.4 25.6 + - - +
48A GLN* 4.0 15.0 - - - +
49A LEU* 3.7 16.0 - - + +
52A GLU* 2.8 33.9 + - - +
54A LEU* 3.6 24.0 - - + +
243A PRO* 5.8 0.8 - - - +
244A GLU* 3.5 13.5 + - - +
308A AB3 3.1 36.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 3.1 19.4 + - - +
22A ARG* 1.3 81.8 + - - +
24A LEU* 1.3 61.0 + - - +
26A ARG* 3.1 6.3 + - - +
27A LEU* 2.9 38.9 + - + +
244A GLU* 4.6 10.6 - - - +
247A ALA* 3.9 16.8 - - - +
248A GLU* 5.5 3.1 - - - +
251A VAL* 3.8 24.7 - - + +
308A AB3 4.2 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 4.2 16.8 - - + -
9A VAL* 3.7 29.8 - - + -
20A ILE* 2.9 25.9 + - + +
21A VAL 3.7 3.4 - - - +
23A ASP* 1.3 72.5 - - - +
25A CYS* 1.3 66.5 + - - +
27A LEU* 4.8 0.4 - - - -
28A PHE* 2.8 38.1 + - + +
32A VAL* 3.6 17.5 - - + +
85A VAL* 4.8 1.3 - - + -
87A VAL* 4.5 9.6 - - + -
251A VAL* 4.6 6.7 - - + -
254A ALA* 4.2 12.1 - - + -
255A LEU* 3.9 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 2.8 24.4 + - - -
22A ARG* 3.4 11.2 - - - +
23A ASP 3.2 0.2 - - - -
24A LEU* 1.3 77.2 - - - +
26A ARG* 1.3 61.2 + - - +
28A PHE 4.5 5.5 - - - +
32A VAL* 3.8 14.3 - - - +
49A LEU* 4.8 1.3 - - - -
54A LEU* 4.1 24.8 - - + +
55A SER 4.6 2.9 - - - +
56A PRO* 3.9 41.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG* 3.4 25.7 + - - +
23A ASP* 3.1 8.1 + - - +
25A CYS* 1.3 80.3 - - - +
27A LEU* 1.3 62.7 + - - +
28A PHE 3.8 1.1 - - - +
52A GLU* 3.9 24.0 + - - +
54A LEU* 3.9 26.6 - - + +
308A AB3 3.4 96.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP* 2.9 20.6 + - + +
26A ARG* 1.3 81.1 - - - +
28A PHE* 1.3 62.8 + - - +
29A SER* 3.8 4.5 + - - -
251A VAL* 4.4 11.7 - - + -
255A LEU* 3.5 30.9 - - + +
308A AB3 4.0 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A HIS* 3.7 22.9 - + + -
6A VAL 3.6 23.8 - - - -
7A ALA* 3.5 15.5 - - + -
24A LEU* 2.8 42.3 + - + +
25A CYS 4.5 5.5 - - - +
26A ARG 5.0 0.9 - - - +
27A LEU* 1.3 73.2 - - - +
29A SER* 1.3 62.1 + - - +
30A GLY* 3.1 25.4 + - - +
31A ASP 3.4 26.2 - - - -
32A VAL* 4.1 1.6 - - + -
84A ASP* 4.2 5.8 - - + -
85A VAL* 3.7 22.2 - - + -
255A LEU* 3.8 20.0 - - + -
----------------------------------------------------------
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