Contacts of the strand formed by residues 66 - 73 (chain A) in PDB entry 5KIY
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 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 3.7 24.9 - - + +
59A LEU 3.2 13.2 - - - +
60A LYS* 3.1 30.7 + - + +
64A ARG 3.6 6.1 + - - +
65A ARG* 1.3 80.8 + - - +
67A ALA* 1.3 63.6 + - - +
91A ASN* 4.3 8.0 - - - +
92A LEU* 3.7 5.3 - - - +
147A ARG* 3.3 50.5 + - - +
150A ASP* 4.3 7.3 - - - +
172A PRO* 5.7 0.2 - - - +
173A TYR* 4.3 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL 3.8 0.2 - - - +
58A LEU* 3.6 5.1 - - - +
59A LEU* 2.8 35.8 + - + +
66A GLU* 1.3 75.7 - - - +
68A VAL* 1.3 62.8 + - - +
69A CYS* 4.3 16.8 - - - -
88A VAL* 4.4 7.0 - - + -
91A ASN* 4.8 5.2 - - + -
92A LEU* 3.4 23.2 - - + +
147A ARG* 4.8 3.1 - - - +
150A ASP* 4.6 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 5.3 1.6 - - - -
56A THR* 4.8 4.3 - - + -
57A VAL 3.3 11.2 - - - +
58A LEU* 3.8 22.2 - - + -
67A ALA* 1.3 70.8 - - - +
69A CYS* 1.3 66.5 + - - +
105A CYS* 4.5 11.4 - - - -
108A VAL* 5.4 1.8 - - + -
145A PRO* 3.5 25.3 - - + +
146A ILE* 3.7 39.0 - - - +
147A ARG* 4.1 6.0 - - + +
150A ASP* 5.0 4.0 + - - +
173A TYR* 4.1 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASN 4.8 2.2 - - - -
37A SER 3.4 16.8 - - - +
39A VAL* 3.7 31.2 - - + -
56A THR* 3.4 6.2 - - - +
57A VAL* 2.8 44.6 + - + +
59A LEU* 4.3 6.7 - - + -
67A ALA* 4.1 10.5 + - - -
68A VAL* 1.3 81.2 - - - +
70A ILE* 1.3 63.3 + - - +
88A VAL* 4.0 22.7 - - - -
145A PRO* 4.0 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 2.8 19.6 + - - +
38A VAL* 3.3 7.1 - - + +
39A VAL* 2.8 32.9 + - - +
54A GLY* 3.6 29.4 - - - +
55A ASP 3.4 4.3 - - - +
56A THR* 4.6 1.8 - - - +
69A CYS* 1.3 78.0 - - - +
71A VAL* 1.3 59.2 + - - +
72A LEU* 4.0 13.9 - - + -
144A ARG* 5.0 0.4 - - - -
145A PRO* 3.7 25.8 - - + -
86B ARG* 3.6 23.8 - - - +
89B MET* 3.4 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 3.3 10.5 - - + +
41A LEU* 3.7 37.2 - - + -
46A MET* 3.9 16.4 - - + -
51A LEU* 4.5 7.0 - - + -
52A PHE 4.2 4.7 - - - +
53A ARG* 4.0 2.3 - - - -
54A GLY 3.0 26.2 + - - -
55A ASP* 3.1 30.6 + - + +
57A VAL* 3.6 27.1 - - + +
69A CYS 4.1 0.6 - - - -
70A ILE* 1.3 71.4 - - - +
72A LEU* 1.3 65.1 + - - +
102A ILE* 5.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASN* 5.7 0.2 - - - +
38A VAL* 3.3 28.0 - - + -
39A VAL 2.8 9.8 + - - +
40A SER* 3.1 6.8 - - - -
41A LEU 2.8 29.8 + - - -
46A MET* 4.0 7.0 - - - -
53A ARG* 4.8 0.9 - - - -
54A GLY* 4.0 14.8 - - - +
70A ILE* 4.0 11.7 - - + -
71A VAL* 1.3 84.3 - - - +
73A SER* 1.3 57.6 + - - +
86B ARG 4.6 3.1 - - - +
89B MET* 3.7 41.1 - - + +
90B GLN* 4.0 18.8 - - + +
93B LEU* 3.7 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU 3.3 6.3 - - - -
43A GLN* 2.8 28.7 - - - -
46A MET* 3.8 13.1 - - - -
53A ARG* 2.7 29.2 + - - +
72A LEU* 1.3 73.0 - - - +
74A ASP* 1.3 58.3 + - - +
90B GLN* 2.7 23.6 + - - +
93B LEU* 3.3 21.7 - - - +
94B ASN* 4.8 2.1 - - - +
97B VAL* 5.7 0.2 - - - +
----------------------------------------------------------
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