Contacts of the helix formed by residues 6 - 19 (chain D) in PDB entry 5SY1
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 THR 6 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LYS* 6.4 1.8 - - + -
239B THR* 5.7 9.4 - - + -
5D LEU* 1.3 81.6 - - - +
7D GLU* 1.3 71.9 + - - +
8D GLU* 3.6 8.3 + - - +
9D GLN* 3.4 35.2 + - - +
10D ILE* 3.3 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 7 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D THR* 1.3 80.8 - - - +
8D GLU* 1.3 61.1 + - + +
10D ILE* 3.4 5.8 + - - +
11D ALA* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 8 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B LYS* 4.8 12.4 + - - +
376B ARG* 4.1 32.4 + - - +
6D THR* 3.4 7.9 + - - +
7D GLU* 1.3 80.1 - - + +
9D GLN* 1.3 60.2 + - + +
11D ALA* 2.9 22.7 + - - +
12D GLU* 3.3 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE* 3.6 31.5 - - + +
233B LEU 5.0 1.7 - - - +
235B LYS* 3.5 39.2 - - + +
236B LYS* 4.3 12.7 - - - +
239B THR* 4.6 4.8 + - - +
4D GLN 4.8 0.3 - - - +
5D LEU* 3.3 41.7 - - + +
6D THR* 3.4 24.6 + - - +
7D GLU 3.4 0.2 - - - -
8D GLU* 1.3 78.3 - - + +
10D ILE* 1.3 60.7 + - - +
12D GLU* 4.2 5.3 + - - +
13D PHE* 3.5 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 10 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B ASN* 4.1 18.6 - - + +
621B SER* 5.9 3.1 - - - +
622B LEU* 4.4 20.2 - - + -
5D LEU* 3.6 34.5 - - + +
6D THR 3.3 19.1 - - - +
7D GLU* 3.4 5.3 + - - +
8D GLU 3.2 0.2 - - - -
9D GLN* 1.3 75.0 - - - +
11D ALA* 1.3 59.9 + - - +
12D GLU 3.2 0.9 - - - -
13D PHE* 3.4 6.0 + - - +
14D LYS* 2.9 31.8 + - + +
66D PHE* 4.4 20.9 - - + -
70D LEU* 5.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ARG* 3.7 22.1 - - + +
7D GLU 2.9 18.0 + - - +
8D GLU* 2.9 12.9 + - - +
10D ILE* 1.3 78.7 - - - +
12D GLU* 1.3 56.4 + - - +
14D LYS* 3.4 9.2 - - - +
15D GLU* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B TYR* 4.1 16.9 + - - -
232B ILE* 3.2 36.6 - - + +
372B LYS* 4.8 1.0 - - - +
375B TYR* 4.3 11.0 - - + +
376B ARG* 3.4 45.3 + - + +
557B HIS* 4.8 4.5 - - + -
559B VAL* 4.8 6.4 - - + +
8D GLU 3.3 10.0 + - - +
9D GLN* 4.5 4.7 - - - +
10D ILE 3.2 0.8 - - - -
11D ALA* 1.3 76.0 - - - +
13D PHE* 1.3 66.1 + - + +
15D GLU* 2.8 9.1 + - - +
16D ALA* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B VAL* 4.3 17.9 - - + -
232B ILE* 3.9 35.7 - - + -
233B LEU* 5.6 9.0 - - + -
559B VAL* 3.7 30.3 - - + -
5D LEU* 4.9 8.7 - - + -
9D GLN 3.5 18.4 - - - -
10D ILE* 3.4 7.9 + - - +
12D GLU* 1.3 73.8 - - + +
14D LYS* 1.3 63.4 + - - +
16D ALA* 4.5 1.8 - - - +
17D PHE* 3.1 19.1 + - - +
66D PHE* 3.2 25.1 - - + -
69D PHE* 3.9 14.2 - + + -
70D LEU* 3.5 29.8 - - + -
73D MET* 4.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622B LEU* 5.2 3.0 - - - +
625B SER* 4.8 14.8 + - - -
629B PHE* 5.4 10.3 - - - -
10D ILE* 2.9 20.4 + - + +
11D ALA* 3.4 11.4 - - - +
13D PHE* 1.3 77.8 - - - +
15D GLU* 1.3 60.1 + - - +
17D PHE* 3.7 6.8 + - + +
18D SER* 3.4 19.4 + - - -
66D PHE* 3.6 42.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU 4.9 5.2 - - - +
375B TYR 3.3 25.8 - - - +
376B ARG 4.6 2.3 - - - +
377B GLY* 4.6 11.2 - - - -
389B ILE* 4.1 22.8 - - - +
553B VAL* 5.9 1.9 - - + +
557B HIS* 4.4 13.7 - - + +
11D ALA 3.0 12.0 + - - +
12D GLU 2.8 10.6 + - - +
14D LYS* 1.3 75.3 - - - +
16D ALA* 1.3 59.7 + - - +
18D SER* 2.3 45.2 + - - -
19D LEU* 3.5 14.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B HIS* 4.2 7.4 - - + +
559B VAL* 3.7 37.2 - - + -
560B MET* 4.1 12.7 - - + +
12D GLU 2.8 16.0 + - - +
13D PHE* 4.4 2.7 - - - +
15D GLU* 1.3 73.7 - - - +
17D PHE* 1.3 62.2 + - - +
19D LEU* 3.5 18.8 + - - +
20D PHE* 3.4 21.2 - - - -
69D PHE* 4.9 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D PHE 3.1 20.3 + - - +
14D LYS* 3.8 10.5 - - + +
15D GLU 3.2 0.2 - - - -
16D ALA* 1.3 76.3 - - - +
18D SER* 1.3 65.3 + - - +
20D PHE* 3.2 18.1 + + - +
21D ASP* 3.6 13.0 + - + -
26D GLY* 3.5 42.0 - - - -
27D THR* 4.0 5.4 - - - -
28D ILE* 3.6 33.9 - - + -
64D ILE* 4.1 3.8 - - + -
65D ASP 4.2 7.0 - - - -
66D PHE* 3.8 26.5 - + + -
69D PHE* 3.9 34.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LYS 3.4 10.1 + - - -
15D GLU* 2.3 41.1 + - - -
17D PHE* 1.3 82.9 - - - +
19D LEU* 1.3 62.5 + - - +
20D PHE 3.3 0.7 + - - -
21D ASP* 3.5 21.1 + - - +
22D LYS* 5.2 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ILE* 4.8 9.6 - - + -
553B VAL 3.8 9.9 - - - +
554B SER* 4.3 23.6 - - - +
557B HIS* 3.6 36.3 - - + -
560B MET* 3.6 28.3 - - + +
15D GLU* 3.5 19.9 + - - +
16D ALA* 3.8 11.2 - - - +
17D PHE 3.2 1.2 - - - -
18D SER* 1.3 84.2 - - - +
20D PHE* 1.3 62.4 + - - +
22D LYS* 4.1 23.3 + - - +
36D VAL* 4.4 9.7 - - - +
----------------------------------------------------------
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