Contacts of the strand formed by residues 21 - 32 (chain D) in PDB entry 6NQN
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 HIS 21 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ALA* 3.3 3.6 - - - -
18D VAL* 2.9 31.9 + - - +
19D ASN* 3.4 23.8 + - + +
20D GLY* 1.3 82.3 - - - +
22D PRO* 1.3 67.8 - - + +
23D PHE* 3.8 6.1 - - - +
51D PRO* 5.3 15.4 - - + +
52D PHE* 5.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLY 3.2 12.6 - - - +
17D ALA* 3.9 5.6 - - + -
20D GLY 3.2 10.8 - - - +
21D HIS* 1.3 91.2 - - + +
23D PHE* 1.3 64.4 + - - +
46D GLU* 5.8 0.2 - - - -
47D GLY* 3.6 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D MET* 3.6 27.8 - - + -
15D GLU* 3.8 1.9 - - - +
16D GLY* 2.9 37.9 + - - +
17D ALA* 3.4 27.6 - - - -
18D VAL* 3.8 2.5 - - + -
21D HIS 3.8 10.8 - - - -
22D PRO* 1.3 75.6 - - - +
24D ALA* 1.3 66.6 + - - +
25D ILE* 4.0 19.7 - - + -
46D GLU* 3.2 22.7 - - - +
47D GLY* 4.1 2.5 - - - +
50D LEU* 3.7 20.6 - - + -
52D PHE* 3.6 19.5 - + + -
57D LEU* 3.6 26.5 - - + -
120D PHE* 4.1 8.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ARG* 3.6 23.3 - - - +
14D MET 3.3 10.5 - - - +
15D GLU* 4.3 4.0 - - + -
23D PHE* 1.3 78.6 - - - +
25D ILE* 1.3 63.2 + - - +
44D VAL 3.6 0.2 - - - -
45D LYS* 2.7 30.8 + - + -
46D GLU* 3.0 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LEU* 4.3 0.9 - - - +
13D ARG* 3.4 3.1 - - - +
14D MET* 2.7 39.7 + - + +
23D PHE* 4.0 18.2 - - + -
24D ALA* 1.3 81.4 - - - +
26D GLU* 1.3 73.3 + - - +
42D LEU* 4.1 7.0 - - + -
43D LYS 3.4 12.1 - - - +
44D VAL* 3.9 14.4 - - + -
45D LYS 4.3 0.4 - - - +
50D LEU* 4.1 10.1 - - + -
54D TYR* 3.9 16.6 - - - +
57D LEU* 3.6 30.1 - - + -
61D PHE* 3.5 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LYS* 5.5 5.8 + - - +
12D LEU* 3.4 9.0 - - - +
13D ARG* 2.8 46.0 + - + +
25D ILE* 1.3 81.7 - - - +
27D GLY* 1.3 59.8 + - - +
41D ASP 4.1 0.2 - - - +
42D LEU* 3.3 2.1 - - - -
43D LYS* 2.8 39.6 + - - +
45D LYS* 3.5 32.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ILE* 5.3 0.4 - - - -
11D LYS* 3.5 3.3 - - - +
12D LEU* 3.0 40.2 + - - +
26D GLU* 1.3 77.8 - - - +
28D VAL* 1.3 69.5 + - - +
40D MET* 5.5 1.1 - - - -
41D ASP 3.2 11.2 - - - -
42D LEU* 3.8 15.0 - - - -
43D LYS* 6.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ILE* 3.3 8.3 - - - +
11D LYS* 4.2 24.0 - - + +
27D GLY* 1.3 79.7 - - - +
29D GLY* 1.3 59.1 + - - +
40D MET* 3.3 3.7 - - - +
41D ASP* 2.8 42.7 + - + +
43D LYS* 6.3 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LYS* 3.4 7.8 - - - +
10D ILE* 2.6 44.0 + - - +
28D VAL* 1.3 76.4 - - - +
30D LEU* 1.3 60.8 - - - +
39D SER 3.2 13.9 - - - -
40D MET* 3.7 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D MET 3.2 14.1 - - - +
9D LYS* 4.1 9.4 - - + +
10D ILE* 4.1 7.0 - - - +
29D GLY* 1.3 76.5 - - - +
31D GLY* 1.3 63.8 + - - +
32D LYS* 6.5 0.2 - - + -
38D GLN* 3.3 2.3 - - - +
39D SER* 2.9 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ASP* 3.8 4.5 - - - +
8D MET* 2.9 33.2 + - - +
30D LEU* 1.3 82.1 - - - +
32D LYS* 1.3 64.6 + - - +
33D PRO* 3.7 1.4 - - - +
37D LYS 3.1 12.6 - - - -
38D GLN* 3.7 2.5 - - - -
68D PHE* 3.5 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D PRO* 3.4 11.2 + - - +
7D ASP* 2.5 41.5 + - - +
30D LEU* 6.5 0.4 - - + -
31D GLY* 1.3 74.9 - - - -
33D PRO* 1.3 67.9 - - - +
34D PHE 3.3 2.2 + - - -
35D GLU* 3.4 23.5 + - + -
36D GLY 3.1 18.2 + - - -
37D LYS* 2.7 22.0 + - + +
68D PHE* 3.8 0.6 - - - -
----------------------------------------------------------
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