Contacts of the strand formed by residues 66 - 71 (chain B) in PDB entry 2RD1
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 66 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B MSE 4.1 19.3 - - + -
27B THR 4.1 1.8 - - - -
28B THR* 4.6 0.9 - - - +
29B LYS* 5.4 0.4 - - - -
49B THR* 4.5 7.6 - - + +
61B ILE* 4.1 19.5 - - + -
62B ASN 3.8 14.4 - - - +
63B SER* 3.7 17.8 - - - +
64B ASN 3.3 5.3 - - - +
65B ASP* 1.3 78.1 - - - +
67B ALA* 1.3 62.7 + - - +
68B GLN 4.0 12.3 - - - +
69B LEU* 4.0 27.8 - - + -
29C LYS* 4.1 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ALA 4.1 9.4 - - - +
68A GLN* 4.1 19.5 - - + -
27B THR* 2.8 24.0 + - - +
28B THR 3.9 15.0 - - - +
29B LYS* 4.1 2.7 - - - +
65B ASP 3.5 2.8 + - - -
66B VAL* 1.3 74.4 - - - +
68B GLN* 1.3 69.6 + - + +
29C LYS* 4.2 8.5 - - - +
67C ALA* 4.2 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL 3.6 0.6 - - - +
26B MSE 3.2 7.6 - - - +
27B THR* 2.9 45.8 + - + +
66B VAL* 3.6 2.4 - - - -
67B ALA* 1.3 89.4 - - + +
69B LEU* 1.3 62.0 + - - +
70B ILE* 4.0 20.4 - - + +
27C THR* 3.6 20.0 - - - +
28C THR 3.1 22.8 + - - -
29C LYS* 3.4 9.0 - - - +
31C GLY* 3.9 12.7 - - - -
67C ALA* 4.4 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 4.6 10.9 - - + -
25B VAL 3.7 2.5 - - - +
26B MSE 3.6 31.4 - - + +
36B THR* 5.2 0.2 - - + -
39B LYS* 4.2 20.4 + - - +
40B PRO* 3.6 50.7 - - + +
49B THR* 5.1 4.5 - - + -
66B VAL* 4.0 11.9 - - + -
68B GLN* 1.3 71.8 - - - +
70B ILE* 1.3 62.9 + - - +
71B LYS 4.2 0.5 + - - -
29C LYS* 2.8 34.6 + - + +
30C ASN* 3.2 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.2 4.7 - - - -
25B VAL* 2.8 47.7 + - + +
27B THR* 5.9 4.3 - - + -
68B GLN* 4.0 24.7 - - + +
69B LEU* 1.3 83.3 - - - +
71B LYS* 1.3 77.1 + - - +
72B ALA* 3.5 0.4 + - - -
30C ASN 4.4 9.2 - - - +
31C GLY* 4.1 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 3.7 23.2 - - + +
23B ASN 3.9 2.7 - - - +
24B TYR* 3.8 38.0 + - + +
69B LEU 4.2 0.4 + - - -
70B ILE* 1.3 86.7 - - - +
72B ALA* 1.3 70.8 + - - +
73B ASP* 3.9 8.2 + - - +
30C ASN 5.0 2.2 + - - -
----------------------------------------------------------
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