Contacts of the strand formed by residues 19 - 26 (chain D) in PDB entry 2Q6W
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 SER 19 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D PHE* 3.8 17.3 - - - -
13D TYR* 3.2 5.4 - - - -
14D LEU* 2.7 44.0 + - - +
17D ASP* 3.1 22.7 + - - +
18D GLN* 1.3 73.4 - - - +
20D GLY* 1.3 60.8 + - - +
115D PRO 5.2 2.9 - - - -
116D VAL* 5.0 2.9 - - - +
137D PHE* 6.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D PHE* 3.1 13.6 - - - -
13D TYR* 3.8 12.9 - - - -
18D GLN 3.8 3.2 + - - -
19D SER* 1.3 75.8 - - - +
21D GLU* 1.3 63.3 + - - +
36D MET* 3.4 26.7 - - - +
63D ILE* 4.4 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ALA* 5.0 2.1 - - - +
11D GLU* 2.9 5.1 - - - -
12D PHE* 2.8 56.1 + - + -
20D GLY* 1.3 77.6 - - - +
22D PHE* 1.3 73.1 + - - +
23D MET* 3.5 12.5 - - - +
33D HIS* 5.0 1.6 - - + -
34D VAL 5.3 2.5 - - - +
36D MET* 5.0 2.9 - - - -
63D ILE* 3.4 7.0 - - - +
136D VAL* 3.2 22.7 - - + +
137D PHE* 2.3 60.0 + - - +
145D PHE* 5.2 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLN* 3.1 39.3 - - + -
10D ALA 3.4 3.1 - - - -
11D GLU* 3.5 18.2 - - + -
21D GLU* 1.3 78.0 - - - +
23D MET* 1.3 66.7 + - - +
24D PHE* 3.6 16.8 - + - -
32D PHE* 4.1 3.1 - + - -
33D HIS* 3.1 5.0 - - - +
34D VAL* 3.0 35.6 + - + -
36D MET* 4.8 2.2 - - + +
54D PHE* 3.5 35.2 - + - -
59D ALA* 3.3 41.3 - - + -
62D ASN* 3.7 7.2 - - + -
63D ILE* 4.4 7.6 - - + -
27F SER* 3.7 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLN* 3.2 8.3 - - - +
10D ALA* 2.7 46.4 + - + +
21D GLU* 3.5 22.9 - - + +
22D PHE* 1.3 80.7 - - - +
24D PHE* 1.3 82.2 + - - +
25D ASP* 3.9 8.1 - - - +
30D GLU* 3.6 14.6 - - + -
32D PHE 3.2 13.9 - - - +
33D HIS* 3.6 12.1 - - + +
136D VAL* 4.4 1.1 - - + -
137D PHE 4.3 1.1 - - - +
138D LEU* 3.5 30.7 - - + -
139D PRO* 3.6 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ILE* 3.6 22.9 - - + -
8D ILE 3.0 8.1 - - - -
9D GLN* 3.1 28.7 - - + -
22D PHE* 3.6 18.6 - + - -
23D MET* 1.3 80.0 - - - +
25D ASP* 1.3 55.9 + - - +
30D GLU* 3.4 5.4 - - - -
31D ILE* 2.7 36.7 + - + -
32D PHE* 2.8 48.4 + + + +
54D PHE* 4.2 4.3 - + - -
78E TYR* 3.6 15.0 - + - -
82E ASN* 3.8 6.5 - - - -
25F TRP* 3.3 21.5 - + - -
26F ARG 3.5 17.5 - - - -
27F SER* 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D VAL 3.5 0.9 - - - +
7D ILE* 3.1 8.1 - - - +
8D ILE* 2.8 50.0 + - + +
23D MET* 3.9 14.2 - - - +
24D PHE* 1.3 76.4 - - - +
26D PHE* 1.3 60.5 + - - +
27D ASP 4.0 0.9 + - - -
28D GLY* 2.8 46.7 + - - +
29D ASP 3.1 6.8 + - - +
30D GLU* 4.2 0.4 + - - +
31D ILE* 4.2 2.2 - - - -
138D LEU* 4.6 2.6 - - - +
139D PRO* 3.6 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D HIS* 3.1 37.5 - + + -
6D VAL 3.4 4.7 - - - -
7D ILE* 3.8 21.5 - - + -
25D ASP* 1.3 74.5 - - - +
27D ASP* 1.3 69.6 + - - +
28D GLY 3.1 0.7 - - - -
29D ASP* 2.6 34.6 + - - +
31D ILE* 3.8 13.9 - - + +
83E TYR* 5.4 1.3 - + - -
90E THR* 3.7 22.2 - - + -
91E VAL* 3.4 34.5 - - + -
123E TYR* 3.2 25.4 - + - -
153E TRP* 3.6 22.7 - + + -
25F TRP* 6.5 0.2 - + - -
----------------------------------------------------------
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