Contacts of the strand formed by residues 59 - 68 (chain F) in PDB entry 1I8F
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 ASN 59 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F GLU 3.4 1.0 - - - +
55F ILE* 3.2 4.8 - - - -
56F ILE 2.7 46.4 + - - +
57F ASP* 2.9 14.9 + - - +
58F GLY* 1.3 77.1 + - - +
60F VAL* 1.3 61.1 + - - +
61F TYR* 3.5 25.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F ARG* 4.0 21.8 - - - +
53F GLU* 3.7 33.2 - - + +
54F GLU 3.4 3.1 - - - +
55F ILE* 4.6 8.1 - - + -
58F GLY 5.0 4.3 - - - +
59F ASN* 1.3 74.7 - - - +
61F TYR* 1.3 66.1 + - - +
62F LYS* 4.0 15.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F GLU* 3.2 2.0 - - - -
54F GLU* 2.7 40.5 + - + +
56F ILE* 3.6 40.6 + - + +
59F ASN* 3.5 37.5 + - + +
60F VAL* 1.3 75.9 - - - +
62F LYS* 1.3 63.8 + - - +
63F ARG* 3.6 35.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E PRO* 6.0 0.3 - - - +
51F ASP 6.1 0.9 - - - +
52F ALA 3.9 6.5 - - - +
53F GLU* 3.9 25.8 - - + +
60F VAL* 3.9 11.5 + - + +
61F TYR* 1.3 71.7 - - - +
63F ARG* 1.3 70.9 + - - +
64F GLY 5.1 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E LEU* 3.4 30.6 - - + +
27E LYS* 4.3 6.9 - - - +
33E GLU* 4.4 9.5 + - - -
75E PHE* 5.1 0.2 - - + -
77E SER* 3.8 16.3 + - - +
78E PRO 3.6 18.9 - - - +
80E PRO* 4.2 11.6 - - - +
52F ALA 2.8 11.7 + - - +
54F GLU* 2.8 30.4 + - + +
56F ILE* 4.9 1.2 - - - +
61F TYR* 3.6 38.4 + - - +
62F LYS* 1.3 81.8 + - - +
64F GLY* 1.3 65.3 + - - +
65F THR 3.4 3.3 + - - -
66F MET* 3.9 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E PRO* 5.2 6.5 - - - -
50F GLU 3.6 0.5 - - - -
51F ASP* 3.1 17.4 + - - -
52F ALA* 2.7 37.5 + - - +
62F LYS* 3.9 1.2 - - - +
63F ARG* 1.3 77.7 - - - +
65F THR* 1.3 60.6 - - - -
66F MET 3.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E THR* 3.5 33.4 - - + +
76E ILE 3.9 0.2 - - - +
77E SER* 3.1 8.5 - - - -
78E PRO* 2.9 41.6 + - + +
48F LEU* 3.8 13.2 - - + -
49F LEU 3.5 6.7 + - - +
50F GLU* 4.6 4.4 - - - +
63F ARG 3.4 2.8 + - - -
64F GLY* 1.3 70.1 - - - -
66F MET* 1.3 63.0 + - - +
67F VAL* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 66 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E PHE* 3.7 42.6 - - + -
76E ILE 3.4 5.6 - - - +
77E SER* 4.2 2.2 - - - -
34F ILE* 3.8 28.0 - - + -
47F LEU 3.6 0.9 - - - +
48F LEU* 3.5 5.2 - - - +
49F LEU* 2.9 38.2 + - + +
52F ALA* 3.9 22.2 - - + -
53F GLU 4.9 0.2 - - - +
54F GLU* 4.6 2.9 - - + -
63F ARG* 3.9 32.1 - - + -
64F GLY 3.6 0.6 + - - -
65F THR* 1.3 75.9 - - - +
67F VAL* 1.3 65.6 + - - +
68F VAL* 3.7 21.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E LEU* 4.2 20.9 - - + +
15E THR* 4.2 9.4 - - + -
16E LEU* 3.7 42.0 - - + -
45E VAL* 6.0 4.9 - - + -
75E PHE* 3.1 5.9 - - - +
76E ILE* 2.8 44.0 + - + +
46F ASN* 5.5 3.1 - - + -
47F LEU 3.2 6.3 - - - +
48F LEU* 4.1 16.8 - - + -
65F THR* 5.4 0.7 - - + -
66F MET* 1.3 74.4 - - - +
68F VAL* 1.3 65.2 - - - +
69F ARG* 5.9 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E LEU 3.6 9.4 - - - +
75E PHE* 4.1 2.7 - - + -
26F VAL* 4.8 5.4 - - + -
28F LEU* 3.7 33.0 - - + -
34F ILE* 4.9 3.4 - - + -
45F VAL 4.3 0.2 - - - +
46F ASN* 3.1 8.0 - - - +
47F LEU* 2.8 44.5 + - + +
49F LEU* 4.1 18.4 - - + -
66F MET* 3.7 28.3 - - + -
67F VAL* 1.3 77.3 - - - +
69F ARG* 1.3 68.4 + - - +
73F VAL* 4.0 9.6 - - + -
----------------------------------------------------------
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