Contacts of the strand formed by residues 66 - 76 (chain F) in PDB entry 6P59
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 THR 66 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F PRO* 3.3 3.6 - - - +
62F LEU* 2.3 40.8 + - + +
63F GLY 3.3 16.0 + - - -
64F ASN 3.3 11.3 + - - -
65F ASN* 1.3 77.0 + - - +
67F LYS* 1.3 60.5 + - - +
92F TYR* 3.2 42.7 + - + +
93F ILE 3.2 15.0 - - - +
94F ASP* 3.5 19.2 + - - -
95F GLN* 5.6 0.9 - - - +
96F LYS* 4.5 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 67 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLN* 4.7 6.5 + - - +
59F HIS* 3.1 43.8 + - + +
60F ILE 3.3 15.3 - - - +
61F PRO* 3.8 9.9 - - + -
62F LEU* 3.9 2.7 - - - +
66F THR* 1.3 79.9 - - - +
68F ILE* 1.3 64.7 + - - +
69F LYS* 4.9 0.2 - - - -
92F TYR* 3.7 2.1 - - - -
93F ILE* 2.8 69.0 + - + +
95F GLN* 3.7 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F VAL 3.4 2.6 - - - +
59F HIS* 3.5 1.7 - - - -
60F ILE* 2.8 49.2 + - + +
62F LEU* 4.0 13.2 - - + -
67F LYS* 1.3 78.0 - - - +
69F LYS* 1.3 62.7 + - - +
70F VAL* 4.1 21.3 - - + -
90F LEU* 6.0 0.9 - - + -
91F ALA 3.4 16.6 - - - +
92F TYR* 4.4 5.8 - - + -
105F ILE* 4.1 20.2 - - + -
110F ALA* 3.9 12.8 - - + +
113F LEU* 4.1 15.7 - - + -
114F ILE* 3.8 26.0 - - + -
212F LEU* 4.8 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLU* 3.1 31.4 + - - -
77C GLN* 3.2 32.2 - - + +
9F ARG* 4.4 2.6 + - - +
49F PRO* 6.1 0.2 - - - +
57F GLU* 2.7 34.3 + - + +
58F VAL 3.4 4.0 - - - +
59F HIS* 3.3 34.5 - - + +
67F LYS* 4.2 1.4 + - - +
68F ILE* 1.3 73.4 - - - +
70F VAL* 1.3 64.5 - - - +
71F THR* 3.6 10.4 + - - +
89F ALA 3.8 2.3 - - - +
91F ALA* 3.1 36.4 + - + +
93F ILE* 4.0 19.9 - - + +
102F PHE* 4.8 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 70 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F TRP* 3.5 36.6 - - + -
56F SER 3.8 0.9 - - - +
57F GLU* 3.4 5.5 - - - -
58F VAL* 2.9 35.9 + - - +
60F ILE* 4.7 6.1 - - + -
68F ILE* 4.1 11.7 - - + -
69F LYS* 1.3 75.1 - - - +
71F THR* 1.3 66.0 + - - +
72F THR* 3.9 4.2 + - + +
88F ALA* 5.2 1.6 - - + -
89F ALA 3.7 8.5 - - - +
90F LEU* 5.0 7.2 - - + -
212F LEU* 3.8 39.0 - - + -
215F LEU* 4.3 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 71 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLU* 4.0 3.5 + - - +
9F ARG* 3.5 22.2 + - - +
54F SER* 5.2 6.3 - - - +
56F SER 3.7 5.8 - - - +
57F GLU* 3.8 12.1 + - + +
69F LYS* 3.6 20.8 - - - -
70F VAL* 1.3 72.4 - - - +
72F THR* 1.3 66.8 + - - +
73F TYR* 3.5 37.8 + - + +
88F ALA* 3.3 3.6 - - - +
89F ALA* 2.8 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 72 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ILE* 4.4 19.1 - - + -
22F TRP* 4.8 12.8 - - + -
23F HIS* 3.9 22.9 - - + -
54F SER* 3.8 3.5 - - - -
55F HIS* 2.8 38.4 + - - +
56F SER* 2.8 38.0 + - - +
70F VAL* 4.8 6.5 - - + +
71F THR* 1.3 79.8 - - - +
73F TYR* 1.3 58.0 + - - +
87F GLY 3.3 7.0 - - - +
88F ALA* 4.9 5.8 - - + -
215F LEU* 5.2 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 73 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C PHE* 3.9 26.3 - + - -
74C GLN* 4.0 20.6 + - - +
75C GLY 4.9 0.7 + - - -
76C GLU* 3.6 12.0 + - - +
9F ARG* 3.6 23.4 + - - +
11F VAL* 3.9 26.0 - - + -
19F ILE* 4.5 1.4 - - - +
53F TRP* 3.0 25.6 - - + +
54F SER* 4.3 2.7 - - - -
55F HIS* 4.1 2.1 - - - +
71F THR* 3.5 26.0 - - + +
72F THR* 1.3 76.9 - - - +
74F TRP* 1.3 61.6 + - - +
76F LEU* 4.3 15.5 - - + -
85F THR 4.8 0.2 - - - -
86F TYR* 3.3 9.3 - - - +
87F GLY 2.6 41.1 + - - +
89F ALA* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 74 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F HIS* 6.3 0.4 - - - +
52F TRP* 3.2 23.1 + - - -
53F TRP* 2.8 45.5 + - - +
54F SER 4.0 14.5 + - - -
55F HIS* 3.7 16.2 - + + -
73F TYR* 1.3 73.7 - - - +
75F ASN* 1.3 104.7 + - + +
76F LEU* 3.2 5.5 + - - +
85F THR 3.5 5.8 - - - -
86F TYR* 3.7 33.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 75 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLU* 4.2 3.3 - - - +
52F TRP* 3.4 28.0 - - + +
53F TRP* 3.0 20.1 + - + +
74F TRP* 1.3 114.1 - - + +
76F LEU* 1.3 65.8 + - - +
84F GLY* 4.0 20.2 + - - -
85F THR 3.2 5.8 + - - -
86F TYR* 5.2 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLU* 4.1 4.1 - - + +
67C GLN* 3.3 31.4 - - + +
69C PHE* 4.2 19.7 - - + -
11F VAL* 4.7 8.1 - - + -
13F ARG* 4.3 12.1 - - + +
53F TRP* 4.3 9.6 - - + +
73F TYR* 4.3 10.8 - - + -
74F TRP 4.1 5.8 - - - +
75F ASN* 1.3 78.1 - - - +
77F THR* 1.3 68.3 + - - +
78F THR* 3.2 3.8 + - - -
84F GLY* 3.5 4.9 - - - -
85F THR* 2.8 36.6 + - + +
86F TYR 3.6 30.5 - - - +
87F GLY* 3.7 10.1 - - - +
----------------------------------------------------------
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