Contacts of the strand formed by residues 6 - 15 (chain C) in PDB entry 1A6Z
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 6 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ARG* 3.8 20.5 + - - +
5C SER* 1.3 81.6 + - - +
7C SER* 1.3 61.6 + - - +
32C ASP* 2.8 31.1 + - - +
103C GLU* 3.6 4.1 - - - +
104C MET* 2.9 37.3 + - + +
105C GLN 6.3 0.9 - - - -
106C GLU* 6.4 0.2 - - - -
169C LEU* 3.7 9.0 - - + +
173C LEU* 3.5 39.2 - - + +
180C LEU* 6.2 0.2 - - + -
181C ASP* 6.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 7 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C HIS* 1.3 76.4 - - - +
8C LEU* 1.3 60.0 + - - +
9C HIS* 3.8 19.6 + - - -
31C VAL* 3.1 4.5 - - - +
32C ASP* 2.7 45.3 + - - -
33C ASP* 4.3 5.2 + - - -
102C CYS 3.6 9.6 - - - -
103C GLU* 4.2 15.0 - - - -
113C TYR* 5.6 2.7 - - - -
169C LEU* 3.5 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 8 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C SER* 1.3 76.4 - - - +
9C HIS* 1.3 65.5 + - - +
10C TYR* 3.6 31.0 - - + +
30C TYR 3.3 13.5 - - - +
31C VAL* 4.9 0.9 - - + -
36C PHE* 3.8 16.8 - - + -
101C GLY* 3.1 2.3 - - - -
102C CYS* 2.8 34.4 + - - +
113C TYR* 4.1 0.3 + - - -
165C CYS* 3.5 35.4 - - - +
168C GLN* 3.7 22.0 - - + +
169C LEU* 3.7 27.3 - - + +
172C LEU* 4.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 9 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C SER* 3.8 15.8 + - - -
8C LEU* 1.3 71.9 - - - +
10C TYR* 1.3 65.4 + - - +
11C LEU* 3.3 28.2 - - + +
28C LEU 3.9 0.2 - - - +
29C GLY* 3.7 0.9 - - - -
30C TYR* 2.9 62.2 + + + +
33C ASP* 3.8 23.3 - - - -
99C ILE* 4.3 7.9 - - + -
100C LEU 3.2 9.6 - - - +
101C GLY* 3.7 0.9 - - - -
113C TYR* 2.9 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 10 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 3.6 23.5 - - + +
9C HIS* 1.3 76.1 - - - +
11C LEU* 1.3 69.0 + - - +
12C PHE* 3.6 23.3 - - + -
28C LEU 3.1 15.5 - - - +
29C GLY* 3.7 13.7 - - - -
36C PHE* 3.5 17.1 - + - -
37C VAL* 4.2 5.2 - - + -
65C LEU* 3.9 4.1 - - + +
68C SER* 6.3 0.2 - - - -
69C LEU* 3.9 27.8 - - + -
72C TRP* 4.0 21.8 - + - -
99C ILE* 3.5 2.3 - - - +
100C LEU* 2.7 43.8 + - + +
101C GLY* 5.6 0.9 - - - -
160C TYR* 3.9 15.3 - - - -
168C GLN* 2.8 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C HIS* 3.3 31.6 - - + +
10C TYR* 1.3 84.8 - - - +
12C PHE* 1.3 62.3 + - - +
13C MET* 5.2 1.8 - - - +
26C GLU 4.0 0.3 - - - +
27C ALA* 3.2 5.4 - - - +
28C LEU* 2.8 43.1 + - + +
30C TYR* 3.9 13.9 - - + -
98C VAL 3.5 3.6 - - - -
99C ILE* 3.5 13.2 - - + -
55D SER* 3.5 25.1 - - - +
56D PHE* 3.6 44.9 - - + +
63D TYR* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TYR* 3.6 26.9 - - + -
11C LEU* 1.3 75.9 - - - +
13C MET* 1.3 63.0 - - - +
25C PHE* 3.6 17.3 - + + -
26C GLU 3.6 3.1 - - - -
27C ALA* 3.5 26.7 - - + -
69C LEU* 4.3 7.6 - - + -
72C TRP* 3.5 49.4 - + + -
76C PHE* 3.9 22.7 - + + -
97C GLN* 3.2 4.4 - - - -
98C VAL* 2.8 48.7 + - + -
100C LEU* 3.6 21.1 - - + -
56D PHE* 3.4 5.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU 5.2 1.6 - - - +
12C PHE* 1.3 76.6 - - - +
14C GLY* 1.3 59.5 + - - +
24C LEU* 4.7 4.2 - - + +
25C PHE* 3.3 3.1 - - - -
26C GLU* 3.0 61.1 + - + +
28C LEU* 4.8 7.4 - - - -
76C PHE* 3.9 4.7 - - - -
96C LEU 3.5 7.2 - - - -
97C GLN* 4.0 15.0 - - + -
33D SER* 6.0 0.2 - - - +
54D LEU* 3.2 53.4 - - + +
55D SER* 3.9 5.2 - - - +
56D PHE* 4.1 12.8 - - + -
62D PHE* 3.2 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C MET* 1.3 76.7 - - - +
15C ALA* 1.3 61.0 + - - +
24C LEU* 3.5 22.7 - - - -
25C PHE* 4.0 0.4 - - - -
76C PHE* 3.5 9.2 - - - -
80C PHE* 3.7 6.5 - - - -
95C THR* 3.4 5.2 - - - -
96C LEU 2.9 30.3 + - - +
97C GLN* 5.7 0.2 - - - +
62D PHE* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLY* 1.3 75.7 - - - +
16C SER* 1.3 61.9 + - - +
17C GLU* 5.2 2.6 - - - +
23C SER* 2.7 31.4 - - - -
24C LEU* 2.8 32.0 + - + +
80C PHE* 3.6 6.7 - - - -
93C SER* 5.5 0.7 - - - +
94C HIS 3.1 10.8 - - - +
95C THR* 4.4 11.2 - - + -
33D SER* 5.8 2.9 - - - +
----------------------------------------------------------
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