Contacts of the strand formed by residues 18 - 28 (chain H) in PDB entry 1MWA
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 18 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H ARG* 2.9 15.9 + - - +
15H PRO* 5.0 1.4 - - - +
16H GLY 3.1 8.5 + - - +
17H LEU* 1.3 80.3 - - - +
19H GLU* 1.3 63.9 + - - -
20H PRO* 3.9 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H ARG* 3.4 20.5 + - - -
17H LEU 4.3 0.4 + - - -
18H GLY* 1.3 71.8 - - - -
20H PRO* 1.3 76.0 - - + +
75H ARG* 3.7 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 20 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ALA* 5.3 1.8 - - + -
12H VAL 3.2 16.6 - - - +
13H SER* 4.0 13.5 - - - -
14H ARG* 4.2 2.8 + - + +
18H GLY 3.9 2.2 - - - +
19H GLU* 1.3 88.5 - - + +
21H ARG* 1.3 64.7 + - - +
22H TYR* 3.6 1.8 + - + -
38H SER* 3.9 3.3 + - - -
39H ASP* 4.8 0.5 - - - +
75H ARG* 3.1 55.4 + - + +
78H LEU* 3.5 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 21 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H THR 3.8 1.0 - - - +
11H ALA* 3.5 5.0 - - - -
12H VAL* 3.1 43.2 + - + +
14H ARG* 3.4 26.7 - - - +
20H PRO* 1.3 72.1 - - - +
22H TYR* 1.3 61.4 + - - +
23H MET* 2.8 32.4 - - - +
37H ASP* 2.5 32.8 + - - -
38H SER* 3.5 4.3 - - - +
39H ASP* 3.2 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 22 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL* 3.9 24.6 - - + +
10H THR 3.5 10.3 - - - -
11H ALA* 4.3 4.9 - - + -
20H PRO* 3.6 3.8 + - + +
21H ARG* 1.3 75.1 - - - +
23H MET* 1.3 63.8 + - - +
24H GLU* 2.7 46.3 + - + +
36H PHE* 3.9 16.1 - + - -
37H ASP* 3.7 2.4 - - - +
38H SER* 2.8 34.2 + - - +
67H ALA 3.7 13.2 - - - -
70H ASN* 3.1 12.8 - - - +
71H GLU* 3.5 49.6 - - + +
74H PHE* 4.0 25.4 - + + -
75H ARG* 4.6 0.9 - - - +
2P GLN* 5.1 0.2 + - - -
5P PHE* 5.2 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 23 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H PHE 3.8 1.3 - - - +
9H VAL* 3.6 4.9 - - - +
10H THR* 3.0 45.2 + - - +
21H ARG* 2.8 49.6 - - - +
22H TYR* 1.3 77.9 - - - +
24H GLU* 1.3 64.0 + - - +
25H VAL* 4.3 7.6 - - + -
35H ARG* 3.0 33.0 - - + +
36H PHE 3.0 18.8 - - - +
37H ASP* 3.5 13.0 - - + +
53L ASP* 5.7 0.2 - - - -
54L MET* 4.1 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H TYR* 5.4 1.1 - - + -
8H PHE 3.6 4.0 - - - -
9H VAL* 4.4 5.8 - - + -
22H TYR* 2.7 38.7 + - + +
23H MET* 1.3 71.9 - - - +
25H VAL* 1.3 64.7 + - - +
35H ARG* 3.1 4.7 - - - -
36H PHE* 2.7 37.9 + - + +
45H TYR* 2.7 44.9 + - + +
67H ALA* 3.5 11.9 - - - -
70H ASN* 3.4 18.9 + - - +
2P GLN* 3.0 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H TYR* 3.2 4.4 - - - -
8H PHE* 2.6 45.3 + - + +
23H MET* 4.6 7.9 - - + -
24H GLU* 1.3 80.1 - - - +
26H GLY* 1.3 59.5 + - - +
27H TYR* 3.4 36.1 - - + +
32H GLU* 3.6 29.2 - - + +
34H VAL 3.5 4.0 - - - +
35H ARG* 3.6 31.2 - - + +
54L MET 4.9 2.9 - - - +
55L SER* 5.8 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 26 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ARG 3.3 6.3 - - - -
7H TYR* 3.5 19.4 - - - -
25H VAL* 1.3 72.4 - - - +
27H TYR* 1.3 61.4 + - - -
32H GLU* 3.4 6.9 - - - +
33H PHE* 3.1 30.8 + - - -
34H VAL* 2.9 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 27 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H SER 3.7 0.9 - - - +
5H LEU* 3.4 5.7 - - - +
6H ARG* 2.6 45.0 + - + +
8H PHE* 3.5 50.5 - + + +
25H VAL* 3.4 31.9 - - + +
26H GLY* 1.3 76.2 - - - -
28H VAL* 1.3 59.9 + - - +
29H ASP 4.0 0.4 + - - -
30H ASP* 3.7 33.9 - - - +
31H THR 3.4 4.5 - - - +
32H GLU* 3.8 22.0 + - + -
33H PHE* 3.4 6.3 - - - -
55L SER* 3.7 26.2 + - - -
56L PHE 4.7 1.3 + - - -
63L TYR* 4.3 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H SER 3.4 4.3 - - - +
5H LEU* 4.3 5.4 - - + -
27H TYR* 1.3 73.2 - - - +
29H ASP* 1.3 82.1 + - - +
30H ASP 3.0 0.7 - - - -
31H THR* 2.8 26.0 + - - +
33H PHE* 3.7 30.9 - - + -
51H TRP* 4.3 6.3 - - + -
168H LEU* 4.4 7.0 - - + -
171H TYR* 3.9 25.6 - - + -
172H LEU* 4.0 10.1 - - + -
179H LEU* 3.6 32.4 - - + +
----------------------------------------------------------
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