Contacts of the strand formed by residues 72 - 77 (chain B) in PDB entry 2D2I
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 LYS 72 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TRP* 3.7 36.2 - - + -
22B PHE* 4.1 19.0 - - + -
27B THR* 5.0 7.1 - - - +
29B LEU 5.1 1.0 + - - -
30B GLU* 5.8 6.1 - - + +
31B VAL 5.7 1.8 - - - +
68B THR* 3.3 1.2 - - - -
69B VAL 2.9 35.7 + - - +
70B ASN 4.4 4.9 - - - +
71B GLY* 1.3 75.4 - - - +
73B THR* 1.3 62.6 + - - +
74B MET* 3.8 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL 4.5 3.6 - - - +
32B VAL* 4.6 4.5 - - - +
66B SER* 4.0 21.1 - - - +
67B ILE 3.6 5.8 - - - +
68B THR* 3.0 27.4 + - - +
71B GLY 3.5 5.8 + - - -
72B LYS* 1.3 74.8 - - - +
74B MET* 1.3 70.0 + - - +
75B LYS* 4.3 3.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 4.1 17.3 - - + -
21B TRP* 5.0 0.9 - - - -
22B PHE* 3.8 20.2 - - + -
31B VAL* 3.4 44.6 - - + +
32B VAL 3.8 8.7 - - - +
33B ALA 4.5 1.1 - - - +
34B ILE* 4.4 10.8 - - + -
66B SER* 3.2 3.4 - - - -
67B ILE* 2.8 53.3 + - + +
69B VAL* 3.6 31.6 - - + +
72B LYS* 3.8 14.1 - - + +
73B THR* 1.3 77.3 - - - +
75B LYS* 1.3 67.4 + - - +
76B ILE* 4.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ARG* 5.4 7.6 - - - +
32B VAL* 3.2 18.6 + - - +
33B ALA* 3.3 1.3 - - - +
34B ILE* 2.8 28.6 + - - +
65B ASN 3.8 7.9 - - - +
66B SER* 4.1 3.8 - - - -
73B THR* 5.6 4.0 - - + +
74B MET* 1.3 73.8 - - - +
76B ILE* 1.3 60.2 + - - +
77B VAL* 5.0 0.2 - - - -
90B TRP* 3.8 63.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 3.4 36.6 - - + +
36B ASN* 5.4 5.2 - - + -
38B SER 5.2 4.7 - - - +
39B ASP 4.7 2.5 - - - -
40B ALA* 4.0 23.1 - - + +
43B ALA* 4.3 12.8 - - + -
64B GLU 5.7 0.2 - - - +
65B ASN* 2.9 33.2 + - - +
66B SER* 3.8 8.5 - - - +
67B ILE* 3.6 32.8 - - + -
74B MET 4.1 0.9 - - - +
75B LYS* 1.3 73.7 - - - +
77B VAL* 1.3 79.7 + - - +
78B CYS* 5.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 5.7 0.2 - - + -
34B ILE 3.0 9.2 + - - +
35B ASN* 3.1 13.3 - - + +
36B ASN 3.1 22.3 + - - -
75B LYS 5.2 0.2 - - - +
76B ILE* 1.3 85.4 - - - +
78B CYS* 1.3 74.6 + - - +
79B ASP* 3.5 22.2 - - - +
85B LEU* 4.0 11.7 - - + -
86B PRO* 4.9 6.7 - - + -
87B TRP* 5.9 2.0 - - + -
90B TRP* 3.1 42.0 - - + -
----------------------------------------------------------
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