Contacts of the strand formed by residues 62 - 68 (chain C) in PDB entry 3OFN
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 62 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 5.1 13.9 - - + -
55C VAL 3.2 14.8 - - - +
56C GLU* 3.7 30.1 + - + -
57C PHE* 4.5 5.1 - - - -
60C GLY 3.7 16.7 + - - -
61C VAL* 1.3 83.9 - - - +
63C GLY* 1.3 52.9 + - - +
77C LEU* 3.7 2.4 - - - -
78C PHE* 2.8 48.0 + - + +
79C GLY 5.1 0.2 - - - +
113C LEU* 5.3 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 3.2 11.4 - - - +
55C VAL* 2.9 43.1 + - - +
57C PHE* 4.5 1.1 - - - -
62C LYS* 1.3 75.2 - - - +
64C MET* 1.3 60.7 + - - +
75C ILE* 3.8 3.6 - - - -
76C VAL 3.1 14.6 - - - -
77C LEU* 4.3 0.4 - - - -
78C PHE* 4.0 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLU* 3.8 26.9 - - + +
53C GLU 3.5 3.6 - - - -
63C GLY* 1.3 74.1 - - - +
65C ALA* 1.3 60.9 + - - +
66C LEU* 3.1 39.2 + - + -
75C ILE* 3.3 4.7 - - - +
76C VAL* 2.9 43.8 + - + +
78C PHE* 3.8 17.0 - - + -
97C VAL* 3.6 32.3 - - + -
131C ALA* 6.4 0.4 - - + -
132C GLN* 6.2 3.1 - - + -
243C PRO* 5.8 0.7 - - - -
246C TYR* 4.6 8.7 - - + +
247C LEU* 4.0 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 3.8 24.7 - - + -
50C GLN 4.2 8.3 - - - +
51C ALA* 3.8 1.6 - - - -
52C GLU* 2.7 32.8 + - - -
53C GLU 3.0 12.6 + - - +
63C GLY 4.3 0.2 - - - -
64C MET* 1.3 68.2 - - - +
66C LEU* 1.3 60.9 + - - +
67C ILE 3.6 0.7 - - - -
68C LEU* 4.4 5.3 - - + +
73C VAL* 3.7 22.0 - - + -
74C GLY 3.4 7.9 - - - -
75C ILE* 3.7 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ALA* 5.7 3.5 - - - +
52C GLU* 3.8 18.5 - - + +
64C MET* 3.1 37.6 + - + +
65C ALA* 1.3 75.0 - - - +
67C ILE* 1.3 66.2 + - + +
68C LEU* 4.3 1.9 + - - +
74C GLY 3.0 6.7 + - - +
76C VAL* 3.7 28.3 - - + -
246C TYR* 4.8 10.8 - - + +
283C LEU* 3.8 24.2 - - + -
287C LEU* 4.2 18.4 - - + -
289C ARG* 4.7 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 1.3 86.7 - - + +
68C LEU* 1.3 64.7 + - - +
69C GLU* 3.7 34.1 - - + +
73C VAL* 3.2 10.6 - - - +
74C GLY* 2.8 39.0 + - - +
287C LEU* 4.1 42.8 - - + +
289C ARG* 4.2 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 4.0 35.2 - - + +
50C GLN 4.3 1.8 - - - +
51C ALA* 3.9 39.7 - - + +
65C ALA* 4.4 7.9 - - + +
66C LEU 4.3 1.1 + - - -
67C ILE* 1.3 80.9 - - - +
69C GLU* 1.3 64.6 + - - +
70C PRO* 4.9 0.2 - - - +
72C GLN 4.2 2.0 - - - -
73C VAL* 4.2 13.7 - - + -
----------------------------------------------------------
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