Contacts of the strand formed by residues 43 - 47 (chain X) in PDB entry 2Q4G
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 VAL 43 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406W ASN* 4.0 25.8 - - - +
435W ASP* 2.8 37.3 - - - +
41X LYS* 3.4 8.8 + - - +
42X PRO* 1.3 83.0 - - + +
44X ASN* 1.3 71.2 - - - +
45X THR* 5.2 4.5 - - - +
83X ASP* 5.8 3.8 - - + +
84X CYS 3.5 14.6 - - - +
85X ARG* 5.1 20.4 - - + +
97X TYR* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 44 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435W ASP* 4.9 0.7 - - - -
11X GLN 2.6 23.2 + - - +
12X HIS* 3.1 26.3 - - - -
30X MET* 3.4 23.3 - - + +
35X MET* 3.2 21.0 - - - +
41X LYS* 3.5 6.7 + - + -
43X VAL* 1.3 80.5 - - - +
45X THR* 1.3 71.2 + - - +
46X PHE* 3.4 25.1 - - - -
84X CYS* 3.0 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11X GLN 3.7 0.5 - - - +
12X HIS* 2.9 33.2 + - - +
43X VAL* 5.2 4.0 - - - +
44X ASN* 1.3 77.5 + - - +
46X PHE* 1.3 72.0 + - - +
81X ILE* 3.5 23.1 - - + +
82X THR 3.5 7.6 - - - +
83X ASP* 2.8 27.9 + - - +
120X PHE* 3.6 35.0 - - + -
123X SER* 5.4 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 46 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10X ARG 3.9 14.1 - - - -
11X GLN 3.3 18.6 - - - -
12X HIS 3.4 9.6 - - - -
13X MET 4.4 7.6 - - - -
14X ASP* 4.5 7.4 - - + -
25X TYR* 3.7 34.8 - + + +
29X MET* 3.8 29.2 - - + -
30X MET* 3.9 7.0 - - - -
33X ARG* 4.0 10.8 - - + -
35X MET* 3.5 13.7 - - + -
44X ASN* 3.4 18.2 - - - -
45X THR* 1.3 72.8 - - - +
47X VAL* 1.3 62.4 + - - +
48X HIS* 4.1 2.3 + - - +
81X ILE* 3.2 7.6 - - - +
82X THR* 3.0 34.7 + - - +
84X CYS* 3.9 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8X PHE* 5.3 0.7 - - + -
12X HIS* 2.7 20.9 + - + +
13X MET* 4.2 9.2 - - - +
14X ASP* 3.3 24.2 + - - -
15X SER 3.7 0.5 + - - -
46X PHE* 1.3 74.1 - - - +
48X HIS* 1.3 62.6 + - - +
49X GLU* 3.2 24.4 + - + +
54X VAL* 3.7 27.4 - - + -
79X MET* 4.1 15.0 - - + -
80X HIS 3.9 2.2 - - - -
81X ILE* 4.2 7.9 - - + -
106X ILE* 4.5 4.9 - - + -
120X PHE* 3.5 32.3 - - + -
----------------------------------------------------------
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