Contacts of the strand formed by residues 32 - 38 (chain D) in PDB entry 6C6S
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 MET 32 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LEU* 3.7 24.2 - - + -
15D GLN* 3.5 25.4 - - - +
18D GLN* 4.0 10.5 - - - +
30D ALA* 3.0 20.8 + - + +
31D PRO* 1.3 70.8 - - - +
33D ILE* 1.3 59.8 + - - +
47D SER* 3.7 22.0 - - - +
48D GLU 3.6 4.9 - - - +
49D PRO* 3.6 30.1 - - + -
100D LYS* 2.4 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PRO 3.8 0.2 + - - -
32D MET* 1.3 74.8 - - - +
34D THR* 1.3 66.6 + - - +
35D LEU* 3.2 37.0 + - + +
47D SER* 4.1 1.6 - - - -
48D GLU 2.8 30.6 + - - +
50D LEU* 3.7 39.5 - - + -
100D LYS* 4.0 29.4 - - + +
103D ASP 3.4 25.6 - - - +
104D ILE* 5.5 1.1 - - + -
105D VAL* 6.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ILE* 1.3 76.1 - - - +
35D LEU* 1.3 59.4 + - - +
45D ALA* 3.7 36.5 - - + +
46D VAL 3.5 7.0 - - - +
47D SER* 3.7 16.3 - - - +
104D ILE* 3.2 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ILE* 3.2 34.9 + - + +
34D THR* 1.3 74.6 - - - +
36D GLU* 1.3 59.9 + - - +
37D LYS* 3.2 8.7 + - - +
45D ALA* 4.2 0.9 - - - -
46D VAL* 2.9 29.8 + - - +
48D GLU* 3.3 34.5 - - + +
49D PRO 4.8 4.7 - - - +
50D LEU* 5.3 2.2 - - - -
104D ILE* 3.6 37.5 - - + +
105D VAL* 3.9 4.3 - - + +
106D ASP* 3.3 17.0 - - - +
107D PRO* 5.1 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D THR 4.1 0.2 + - - -
35D LEU* 1.3 68.0 - - - +
37D LYS* 1.3 58.3 + - - +
38D ILE* 4.6 4.7 - - - +
43D ARG* 3.3 42.3 + - + +
45D ALA* 3.9 16.7 - - + +
104D ILE* 3.7 11.1 - - + +
106D ASP* 2.9 36.9 + - - +
109D THR* 3.2 12.1 + - - -
110D PRO 4.4 5.7 - - - +
111D TYR* 4.0 14.3 - - + -
136D GLU* 3.6 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B C 5.7 5.9 + - - -
35D LEU 3.2 8.4 + - - +
36D GLU* 1.3 75.6 - - - +
38D ILE* 1.3 90.9 + - - +
39D VAL* 3.2 21.7 + - + +
43D ARG* 4.5 1.1 - - - -
44D THR 2.9 35.4 + - - +
46D VAL* 4.9 6.5 - - + -
48D GLU* 4.6 26.3 + - - +
106D ASP* 5.0 1.1 - - - +
109D THR* 3.8 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D GLU* 4.6 3.4 - - - +
37D LYS* 1.3 86.8 - - - +
39D VAL* 1.3 64.0 + - - +
41D GLY* 3.8 24.0 - - - +
42D LYS 3.7 4.5 - - - -
43D ARG* 3.7 28.5 - - + +
109D THR* 3.7 12.4 - - + +
110D PRO* 3.7 31.4 - - + -
156D ASN* 3.8 38.6 - - + +
159D PHE* 5.7 2.7 - - + +
----------------------------------------------------------
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