Contacts of the strand formed by residues 22 - 28 (chain C) in PDB entry 4NQD
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 PHE 22 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ARG* 3.7 31.0 - - + -
10C LEU 3.2 15.3 - - - -
11C GLY* 4.7 0.2 - - - -
20C PRO* 3.2 1.1 - - - +
21C GLU* 1.3 83.8 - - + +
23C ILE* 1.3 62.2 + - - +
24C SER* 4.0 18.2 - - - -
36C TYR* 3.7 31.4 - + - -
37C ASP* 3.1 5.7 - - - +
38C SER* 2.9 31.6 + - - +
66C LEU* 4.3 5.2 - - + -
69C TRP 4.2 1.3 - - - -
70C GLN* 3.6 46.0 - - + +
73C PHE* 3.7 42.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PHE 4.6 0.2 - - - -
9C ARG* 3.3 3.1 - - - +
10C LEU* 2.8 55.1 + - + +
20C PRO* 4.0 29.8 - - + +
22C PHE* 1.3 84.2 - - - +
24C SER* 1.3 64.3 + - - +
25C VAL* 4.0 14.4 - - + -
35C THR* 4.9 2.9 - - - +
36C TYR 3.4 11.9 - - - +
37C ASP* 4.0 7.4 - - + +
33F SER* 6.0 0.2 - - - +
54F LEU* 4.3 18.2 - - + -
56F PHE* 4.0 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PHE 2.8 16.9 + - - -
9C ARG* 4.0 9.0 - - - -
22C PHE* 4.0 5.1 - - - -
23C ILE* 1.3 75.2 - - - +
25C VAL* 1.3 61.2 + - - +
34C THR 4.5 0.3 - - - -
35C THR* 3.4 3.8 - - - -
36C TYR* 2.8 36.2 + - - +
66C LEU* 3.7 23.8 - - - -
301C 2LJ 2.8 34.2 + - - +
56F PHE* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TYR* 3.5 3.9 - - - -
8C PHE* 2.8 41.2 + - - +
23C ILE* 4.0 8.7 - - + -
24C SER* 1.3 78.5 - - - +
26C GLY* 1.3 72.2 + - - +
27C TYR* 3.6 25.1 - - + +
32C PRO* 4.4 8.7 - - + -
34C THR* 3.4 11.9 - - - +
35C THR* 4.0 17.0 - - - +
46C ARG* 5.7 0.9 - - + -
53F ASP* 6.3 1.8 - - + -
54F LEU 4.8 5.2 - - - +
56F PHE* 3.6 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ARG 3.2 9.9 - - - -
7C TYR* 3.5 12.1 - - - -
25C VAL* 1.3 78.4 - - - +
27C TYR* 1.4 57.4 + - - -
32C PRO* 3.3 7.1 - - - +
33C ILE* 2.8 32.4 + - - -
34C THR* 3.1 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C SER 3.9 0.2 - - - +
5C LEU* 3.4 9.4 - - - +
6C ARG* 2.8 61.8 + - - +
8C PHE* 3.6 39.9 - + - -
25C VAL* 3.6 21.2 - - + +
26C GLY* 1.4 72.0 - - - -
28C VAL* 1.3 63.4 + - - +
29C ASP 3.6 3.8 + - - +
30C SER 4.1 7.6 - - - -
31C HIS 3.2 7.6 - - - +
32C PRO* 3.5 36.3 - - + -
33C ILE* 3.7 3.6 - - - +
54F LEU 4.1 1.4 + - - -
55F SER* 3.2 15.2 + - - -
56F PHE* 3.0 35.3 + + - -
63F TYR* 4.3 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C SER 3.3 9.6 - - - +
5C LEU* 4.1 4.7 - - + -
27C TYR* 1.3 74.8 - - - +
29C ASP* 1.4 66.7 + - - +
31C HIS* 2.8 33.5 + - - +
33C ILE* 3.8 22.4 - - + +
49C TRP* 4.2 4.5 - - + -
165C LEU* 4.2 5.2 - - + -
168C PHE* 3.9 33.9 - - + -
169C LEU* 4.0 16.8 - - + -
176C LEU* 3.8 29.6 - - + -
----------------------------------------------------------
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