Contacts of the strand formed by residues 8 - 14 (chain P) in PDB entry 4R2G
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 PRO 8 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M PHE* 3.8 37.9 - - + -
68M GLY* 4.1 9.2 - - - +
6P VAL* 4.1 5.6 - - + +
7P SER* 1.4 82.1 - - - +
11P LEU* 1.3 59.5 + - - +
12P SER* 5.8 1.1 - - - +
102P THR* 4.9 0.4 - - - -
103P ARG* 3.8 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M PHE 3.8 3.1 - - - +
68M GLY 3.3 28.3 - - - +
69M THR* 3.8 19.5 - - + -
7P SER 3.9 1.6 + - - -
8P PRO* 1.3 73.7 - - - +
12P SER* 1.3 70.1 + - - +
13P VAL* 4.4 8.5 - - + -
19P ALA* 4.8 0.7 - - + -
20P ARG 4.2 18.8 - - - +
21P ILE* 3.5 31.6 - - + -
102P THR* 3.6 16.6 - - + -
103P ARG 3.1 11.1 + - - +
104P LEU* 3.3 19.1 - - + +
105P THR* 2.9 24.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 12 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M ASN* 3.1 20.8 - - - -
67M PHE* 3.3 36.3 + - - +
69M THR* 4.3 3.8 - - - +
8P PRO* 5.3 1.7 - - - +
11P LEU* 1.3 79.2 + - - +
13P VAL* 1.3 67.0 + - - +
105P THR* 3.4 21.1 + - - +
106P LEU* 4.2 21.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 13 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M ASN* 4.2 5.2 - - + -
69M THR* 6.0 1.3 - - + -
11P LEU* 4.4 7.9 - - + -
12P SER* 1.3 79.7 - - - +
14P ALA* 1.3 80.1 + - - +
17P GLU* 4.2 5.2 - - + -
18P THR 3.6 25.4 - - - +
19P ALA* 3.5 26.0 - - + -
78P VAL* 4.2 15.3 - - + -
104P LEU* 3.5 18.4 - - + -
105P THR 3.1 7.8 + - - +
106P LEU* 2.7 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M ASN* 3.7 16.9 - - + +
13P VAL* 1.3 82.7 - - - +
15P LEU* 1.3 58.1 + - - +
16P GLY 3.2 0.5 + - - -
17P GLU* 2.7 52.0 + - + +
78P VAL* 4.0 2.4 - - - +
106P LEU* 3.3 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P VAL 3.6 0.6 + - - -
14P ALA* 1.3 74.1 - - - +
16P GLY* 1.3 61.8 - - - +
17P GLU* 3.4 4.5 + - - +
78P VAL* 3.6 14.4 - - - +
79P GLU* 4.2 10.3 - - - -
80P VAL* 4.3 13.9 - - + +
106P LEU* 2.4 43.9 + - + +
107P SER 3.9 5.2 - - - +
108P GLN* 3.9 27.1 - - - -
109P PRO* 4.3 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 16 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P ALA 3.2 0.6 + - - -
15P LEU* 1.3 74.3 - - - +
17P GLU* 1.3 71.0 + - - +
77P GLY* 3.4 15.1 + - - -
78P VAL* 3.2 21.3 + - - +
----------------------------------------------------------
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