Contacts of the strand formed by residues 18 - 25 (chain Q) 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 LEU 18 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Q PRO* 5.1 0.9 - - + -
12Q VAL* 4.2 19.1 - - + -
17Q THR* 1.3 79.9 - - - +
19Q SER* 1.3 66.3 + - - +
20Q VAL* 3.5 33.0 - - + +
80Q LEU* 4.2 4.7 - - + +
81Q GLN* 3.2 4.0 - - - -
82Q LEU* 2.9 61.6 + - + +
86Q ASP* 4.6 4.9 - - + +
90Q TYR* 4.1 25.6 - - + +
109Q VAL* 3.5 34.3 - - + -
111Q VAL* 6.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 19 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200K VAL* 4.0 7.8 - - - +
202K THR* 4.1 17.5 - - - -
8Q GLY* 4.3 1.4 - - - -
9Q PRO* 3.4 23.6 - - - +
17Q THR 3.9 1.4 + - - -
18Q LEU* 1.3 77.2 - - - +
20Q VAL* 1.3 65.8 + - - +
21Q THR* 5.1 3.1 - - - +
79Q SER* 4.8 1.4 - - - -
80Q LEU 3.4 4.3 - - - -
81Q GLN* 3.0 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Q SER 3.5 7.2 - - - +
8Q GLY* 4.0 11.2 - - - -
9Q PRO* 4.2 0.9 - - + -
18Q LEU* 3.5 20.8 - - + +
19Q SER* 1.3 79.9 - - - +
21Q THR* 1.3 64.9 + - - +
36Q TRP* 3.6 26.2 - - + -
79Q SER* 3.1 3.6 - - - -
80Q LEU* 2.7 53.9 + - + +
90Q TYR* 4.3 8.1 - - + -
107Q THR* 4.3 9.4 - - + -
109Q VAL* 3.9 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 21 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200K VAL* 6.0 1.3 - - + -
6Q GLU* 3.1 7.8 - - - +
7Q SER* 2.9 47.2 + - - -
8Q GLY* 5.4 0.2 - - - -
19Q SER* 5.1 4.5 - - - +
20Q VAL* 1.3 74.1 - - - +
22Q CYS* 1.3 61.8 + - - +
23Q ILE* 5.8 2.7 - - - -
36Q TRP* 3.6 4.6 - - - -
77Q GLN* 3.8 25.4 - - - +
78Q LEU 3.1 7.6 - - - +
79Q SER* 3.3 27.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 22 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4Q LEU* 3.9 20.4 - - - -
5Q GLN 3.5 7.2 - - - -
6Q GLU* 4.0 5.8 - - + -
21Q THR* 1.3 77.0 - - - +
23Q ILE* 1.3 68.9 + - - +
24Q VAL* 4.0 4.4 + - - -
34Q TRP* 5.5 0.2 - - - -
36Q TRP* 3.9 6.3 - - + -
77Q GLN* 3.2 8.1 - - - +
78Q LEU* 2.7 42.2 + - + +
92Q CYS* 2.0 49.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Q GLN 3.6 3.5 - - - +
4Q LEU* 3.6 0.2 - - - -
5Q GLN* 2.9 40.6 + - + +
7Q SER* 5.7 3.8 - - - +
21Q THR* 5.8 2.2 - - - -
22Q CYS* 1.3 74.3 - - - +
24Q VAL* 1.3 72.1 + - - +
25Q SER* 3.9 5.9 + - - +
75Q LYS* 4.2 13.2 - - + +
76Q ASN* 4.0 4.7 - - + +
77Q GLN* 3.8 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Q VAL* 4.2 11.2 - - + -
3Q GLN 3.2 7.6 - - - +
4Q LEU* 4.7 1.3 - - + +
22Q CYS* 4.7 3.6 - - - +
23Q ILE* 1.3 81.3 - - - +
25Q SER* 1.3 65.6 + - - +
27Q GLY 3.3 20.9 - - - +
29Q ILE* 3.9 15.9 - - + +
34Q TRP* 3.7 37.2 - - + -
76Q ASN* 2.8 43.0 + - - +
78Q LEU* 4.0 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 25 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Q VAL* 3.2 7.6 - - - +
3Q GLN* 2.9 51.2 + - - +
4Q LEU 5.5 0.5 - - - -
5Q GLN* 6.0 0.5 - - - +
23Q ILE* 3.9 8.2 + - - +
24Q VAL* 1.3 78.6 + - - +
26Q GLY* 1.3 60.7 + - - +
27Q GLY 3.3 4.4 + - - -
----------------------------------------------------------
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