Contacts of the strand formed by residues 62 - 68 (chain B) in PDB entry 1KTD
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 GLU 62 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASP* 4.9 9.2 - - - +
24B GLY 4.0 6.8 - - - +
25B SER* 5.6 0.2 + - - -
58B PHE* 3.1 6.9 - - - -
59B TYR* 2.9 35.8 + - + +
60B ASN 3.4 1.6 + - - -
61B LEU* 1.3 86.5 - - + +
63B GLU* 1.3 64.3 + - - +
64B ASN* 3.4 4.3 + - + -
78B THR* 3.7 25.3 - - + +
111C LYS* 3.6 27.8 + - - -
140C ARG* 6.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A HIS* 5.6 0.2 - - - +
56B ARG* 3.0 40.8 + - + +
57B TYR 3.2 14.4 - - - +
58B PHE* 3.7 17.6 - - + -
62B GLU* 1.3 71.2 - - - +
64B ASN* 1.3 59.1 + - - +
65B LEU 3.7 4.5 - - - +
66B ARG* 2.8 42.2 + - - +
77B VAL* 3.2 34.4 - - + +
78B THR* 3.3 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET* 4.5 9.0 - - - +
36B GLU* 5.8 0.2 + - - -
57B TYR* 2.9 15.2 + - - +
58B PHE 3.8 4.0 - - - -
59B TYR* 3.3 43.0 - - - +
62B GLU* 3.4 4.3 + - + +
63B GLU* 1.3 72.5 - - - +
65B LEU* 1.3 72.8 + - - +
76B ALA* 3.8 0.5 - - - -
77B VAL 3.1 16.5 + - - -
78B THR* 2.8 26.3 + - - +
80B LEU* 4.3 10.7 - - + +
81B GLY* 3.1 29.8 - - - +
84B ASP* 5.1 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ARG* 3.7 0.5 - - - -
57B TYR* 2.8 43.9 + - + +
63B GLU* 3.7 3.4 - - - +
64B ASN* 1.3 90.3 + - - +
66B ARG* 1.3 68.2 + - - +
74B PHE* 4.1 7.2 - - + -
75B ARG 2.9 45.1 - - - +
76B ALA* 3.7 5.6 - - - +
77B VAL* 3.7 5.5 - - - +
81B GLY* 3.8 11.9 - - - +
84B ASP* 3.9 21.3 - - + +
85B ALA* 3.9 9.2 - - + +
88B TRP* 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG* 4.4 2.4 - - - +
54B LEU* 4.1 18.3 - - + +
55B VAL* 2.9 15.0 - - - +
56B ARG* 3.7 14.7 - - + +
57B TYR* 4.8 1.8 - - - -
63B GLU* 2.8 36.7 + - - +
65B LEU* 1.3 78.3 - - - +
67B PHE* 1.3 61.4 + - - +
68B ASP* 4.1 9.2 + - - +
74B PHE* 3.4 11.7 - - - -
75B ARG* 3.0 43.1 + - + +
77B VAL* 3.9 13.6 - - + +
800B SO4 3.0 38.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 3.4 8.2 - - + +
54B LEU* 3.3 5.3 - - - -
55B VAL* 2.7 55.7 + - + -
66B ARG* 1.3 75.8 - - - +
68B ASP* 1.3 57.7 - - - +
69B SER* 4.0 23.3 - - - -
72B GLY* 3.6 19.3 - - - -
73B GLU* 3.5 37.0 - - - -
74B PHE* 3.6 37.5 - + + +
95B LEU* 4.5 3.6 - - + -
98B LYS* 3.9 36.1 - - + -
99B ARG* 4.4 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG* 2.9 38.3 + - - +
53B LEU 3.6 2.9 - - - -
54B LEU* 4.0 10.1 - - + -
66B ARG* 4.1 10.5 + - + +
67B PHE* 1.3 75.6 - - - +
69B SER* 1.3 55.9 + - - +
70B ASP* 2.7 35.8 + - - +
71B VAL* 2.7 41.9 + - + +
72B GLY* 3.0 10.0 + - - -
73B GLU 4.5 4.5 + - - -
45D TYR* 4.0 12.8 + - - -
52D ARG* 4.7 0.7 + - - -
----------------------------------------------------------
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