Contacts of the strand formed by residues 3 - 12 (chain C) in PDB entry 4NQC
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 3 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C MET* 3.8 16.6 - - - +
1C ARG* 3.3 46.2 + - + +
2C THR* 1.3 75.2 + - - +
4C SER* 1.3 62.2 + - - +
28C VAL* 5.3 0.4 - - + -
29C ASP* 2.7 28.8 + - - +
99C GLU* 3.3 5.9 - - - +
100C LEU* 3.0 32.8 + - + +
165C LEU* 4.0 10.1 - - + -
169C LEU* 3.5 48.9 - - + +
176C LEU 3.5 25.5 + - - -
177C GLN* 4.2 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 4 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C THR* 6.0 0.2 - - - -
3C HIS* 1.3 77.3 - - - +
5C LEU* 1.3 64.2 + - - +
6C ARG* 4.8 12.9 + - - +
27C TYR 4.4 0.2 - - - -
28C VAL* 3.3 5.7 - - - -
29C ASP* 2.8 46.4 + - - +
98C CYS 3.2 11.9 - - - -
99C GLU* 3.8 19.9 + - - -
109C PHE* 5.6 1.6 - - - -
165C LEU* 3.6 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 5 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C SER* 1.3 76.0 - - - +
6C ARG* 1.3 63.6 - - - +
7C TYR* 3.9 30.3 - - + -
27C TYR 3.3 13.7 - - - +
28C VAL* 4.1 2.2 - - + -
33C ILE* 3.9 9.9 - - + -
97C GLY* 2.9 23.4 - - - -
98C CYS* 2.9 16.7 + - - +
109C PHE* 4.5 0.2 - - - -
156C TRP* 5.0 0.7 - - + -
161C CYS* 3.5 33.2 - - - +
164C TRP* 3.6 22.9 - - + -
165C LEU* 3.8 20.8 - - + +
168C PHE* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 6 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C SER* 4.8 12.0 + - - +
5C LEU* 1.3 79.0 - - - +
7C TYR* 1.3 65.8 + - - +
8C PHE* 3.4 32.4 - - + -
25C VAL 4.1 0.6 - - - +
26C GLY* 3.2 3.1 - - - -
27C TYR* 2.7 61.4 + - + +
29C ASP 2.9 28.7 + - - +
30C SER* 4.6 4.0 - - - +
95C MET* 4.7 7.4 - - + -
96C ILE 3.1 7.9 - - - +
109C PHE* 4.1 20.9 - - + -
56F PHE 3.4 23.2 + - - -
57F SER* 4.8 0.8 - - - +
58F LYS* 4.7 9.1 - - - +
63F TYR* 4.9 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 7 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LEU* 3.9 28.2 - - + +
6C ARG* 1.3 73.9 - - - +
8C PHE* 1.3 64.7 + - - +
9C ARG* 6.2 2.2 - - + +
24C SER* 5.1 6.5 - - - +
25C VAL 3.4 3.6 - - - +
26C GLY* 3.5 20.6 - - - -
33C ILE* 4.2 3.4 - - + +
34C THR* 3.8 20.0 - - + +
43C LYS* 4.9 12.0 + - - -
94C ARG* 3.9 1.7 - - - +
95C MET* 3.4 2.4 - - - -
96C ILE* 2.8 53.4 + - + +
156C TRP* 4.4 18.2 - + - -
164C TRP* 5.3 4.7 - + + -
168C PHE* 3.4 28.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 8 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ARG* 3.4 43.5 - - + -
7C TYR* 1.3 78.3 - - - +
9C ARG* 1.3 58.9 + - - +
24C SER* 2.8 24.5 + - - -
25C VAL 2.8 20.7 + - - +
27C TYR* 3.7 15.3 - + - -
93C GLN* 5.8 2.0 - - + -
94C ARG* 3.2 9.0 - - - -
95C MET* 3.6 40.2 - - + -
56F PHE* 3.5 48.7 - + + -
57F SER 3.5 22.2 - - - -
58F LYS* 4.1 0.7 - - - -
60F TRP* 4.6 10.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 9 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TYR* 5.9 2.9 - - + +
8C PHE* 1.3 73.2 - - - +
10C LEU* 1.3 60.7 + - - +
22C PHE* 3.8 22.2 - - + -
23C ILE 3.3 4.9 - - - -
24C SER* 3.5 18.0 + - - +
69C TRP* 3.4 62.1 + - - +
72C MET* 5.2 7.7 - - - -
73C PHE* 3.6 31.8 - - + -
93C GLN* 3.1 8.7 - - - +
94C ARG* 2.9 81.7 + - + +
112C TYR* 5.1 1.6 + - - -
56F PHE* 5.3 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ARG* 1.3 73.0 - - - +
11C GLY* 1.3 73.9 + - - +
12C VAL* 4.1 17.3 - - + -
20C PRO 6.0 0.7 - - - +
21C GLU 4.5 0.2 - - - -
22C PHE* 3.2 7.1 - - - -
23C ILE* 2.7 57.3 + - + +
73C PHE* 4.0 3.1 - - - -
91C THR* 4.1 11.9 - - + -
92C TYR 3.4 2.0 - - - +
93C GLN* 3.7 20.9 - - + -
33F SER* 4.0 22.2 - - - +
54F LEU* 4.5 0.9 - - + -
56F PHE* 3.8 28.0 - - + -
62F PHE* 4.1 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 1.3 73.1 - - - +
12C VAL* 1.3 63.0 + - - +
21C GLU 3.3 8.3 - - - -
22C PHE* 4.6 1.8 - - - -
73C PHE* 3.6 17.5 - - - -
77C LEU* 3.8 10.4 - - - +
91C THR* 3.3 6.8 - - - -
92C TYR 2.7 37.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 4.1 26.0 - - + -
11C GLY* 1.3 77.1 - - - +
13C SER* 1.3 63.6 + - - +
15C PRO* 3.6 21.2 - - + +
19C VAL* 4.8 7.4 - - + -
20C PRO 4.2 18.4 - - - +
21C GLU* 2.9 31.6 + - - +
77C LEU* 4.0 2.2 - - - +
89C SER* 3.5 21.5 - - - +
90C HIS 3.6 5.2 - - - +
91C THR* 4.3 11.7 - - + -
33F SER* 4.7 8.5 - - - +
----------------------------------------------------------
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