Contacts of the strand formed by residues 27 - 33 (chain C) in PDB entry 1R6Q
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 MET 27 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 6.2 0.7 - - - -
65A THR* 5.2 8.3 - - + -
25C PRO 4.0 2.7 + - - +
26C SER* 1.3 81.8 - - - +
28C TYR* 1.3 64.1 + - - +
75C VAL* 4.0 17.3 - - + +
76C PHE* 3.4 28.7 - - - +
77C THR* 3.7 25.8 - - + +
106C ALA* 2.9 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU* 2.6 33.0 + - - -
146A GOL 4.0 11.8 + - - -
26C SER* 3.4 14.6 - - - -
27C MET* 1.3 81.0 - - - +
29C LYS* 1.3 65.3 + - - +
30C VAL* 3.8 1.0 + - - +
75C VAL* 3.3 4.4 - - - -
76C PHE* 2.6 38.3 + - - +
78C ALA* 3.6 22.4 - - + -
81C ALA* 3.6 24.3 - - + +
103C LEU* 3.9 23.1 - - + -
104C GLU* 3.3 25.6 - - - -
105C LYS* 3.3 38.2 - - + -
106C ALA 4.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 1.3 74.0 - - - +
30C VAL* 1.3 61.2 + - - +
31C ILE* 4.0 11.6 - - + +
72C ILE* 3.8 33.8 - - + +
74C GLY 3.4 6.1 - - - +
75C VAL* 4.2 16.8 - - + +
103C LEU* 3.2 8.0 - - - +
104C GLU* 2.7 56.4 + - - +
105C LYS 3.5 22.2 + - - -
106C ALA* 4.1 20.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LYS* 1.3 72.2 - - - +
31C ILE* 1.3 58.3 + - - +
51C PHE* 3.7 27.8 - - + -
72C ILE* 3.6 2.6 - - - -
73C CYS* 2.7 33.9 + - + -
74C GLY 2.8 13.6 + - - +
76C PHE* 3.7 24.7 - - + -
81C ALA* 3.8 32.1 - - + +
84C LYS* 4.8 5.2 - - + -
85C VAL* 4.2 7.0 - - + -
101C CYS* 3.7 25.6 - - - -
102C THR 3.5 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LYS* 4.4 9.9 - - + +
30C VAL* 1.3 79.9 - - - +
32C LEU* 1.3 74.7 + - - +
33C VAL* 4.5 3.6 - - + -
70C LYS* 3.9 27.4 - - + -
71C ALA 3.3 13.2 - - - +
72C ILE* 4.3 17.0 - - + -
73C CYS* 4.4 1.1 - - - -
101C CYS* 3.2 9.8 - - - -
102C THR* 2.7 54.8 + - - +
104C GLU* 3.5 42.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ILE* 1.3 79.5 - - - +
33C VAL* 1.3 60.7 + - - +
43C VAL* 4.3 15.0 - - + -
46C VAL* 4.2 13.5 - - + -
47C LEU* 3.8 23.8 - - + -
51C PHE* 5.1 1.1 - - + -
65C VAL* 4.0 18.7 - - + +
70C LYS* 3.2 5.4 - - - +
71C ALA 3.0 29.7 + - - +
73C CYS* 3.6 23.7 - - - -
88C VAL* 4.2 12.6 - - + -
99C LEU* 4.2 18.6 - - + -
100C LEU 3.8 2.7 - - - +
101C CYS* 4.0 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ILE* 4.5 6.1 - - + -
32C LEU* 1.3 76.4 - - - +
34C ASN* 1.3 75.1 + - - +
35C ASP* 3.9 2.3 + - - +
65C VAL* 4.0 3.3 - - - +
69C GLY 3.8 10.1 - - - +
70C LYS* 4.4 6.3 - - + -
99C LEU* 3.6 21.7 - - - +
100C LEU* 2.9 41.2 + - + +
102C THR* 4.2 26.7 - - + +
----------------------------------------------------------
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