Contacts of the strand formed by residues 60 - 68 (chain C) in PDB entry 3FTN
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 60 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C VAL* 3.2 7.3 - - - +
35C ALA* 3.1 44.6 + - + +
36C PRO 3.5 0.2 - - - -
37C CYS* 3.2 18.2 - - - +
59C HIS* 1.3 81.3 + - + +
61C ALA* 1.3 61.1 + - - +
119C VAL* 3.8 2.2 - - - +
146C VAL* 3.9 19.0 - - - +
149C PRO* 4.4 4.9 - - + -
150C ASP* 3.3 36.7 - - + +
151C MET* 3.5 13.5 + - - +
346C LYS* 2.9 39.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ALA 3.3 5.6 - - - -
34C VAL* 3.8 11.4 - - + -
59C HIS 4.1 1.2 + - - -
60C GLU* 1.3 77.2 - - - +
62C VAL* 1.3 65.6 + - - +
83C VAL* 3.3 32.6 + - + +
119C VAL* 3.8 28.5 - - + -
124C PHE* 4.0 17.0 - - + -
146C VAL* 3.9 4.5 - - - +
149C PRO* 3.9 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C PRO* 3.6 3.1 - - - +
32C LEU* 2.7 33.0 + - + -
33C ALA* 2.9 15.8 + - + +
61C ALA* 1.3 80.1 - - - +
63C GLY* 1.3 58.6 + - - +
80C ARG* 5.6 0.2 - - + -
81C VAL 3.4 15.3 - - - +
82C VAL* 4.7 7.0 - - + -
83C VAL* 5.3 0.2 - - - -
136C LEU* 3.8 15.0 - - + -
142C LEU* 3.7 29.6 - - + +
145C ALA* 3.6 30.1 - - + +
146C VAL* 3.7 18.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
29C VAL* 3.7 15.0 - - - +
30C ARG 3.0 13.2 - - - -
31C PRO* 4.2 0.7 - - - -
32C LEU* 3.7 11.0 - - - +
62C VAL* 1.3 76.8 - - - +
64C GLU* 1.3 60.8 + - - -
80C ARG* 3.3 5.5 - - - +
81C VAL* 2.9 37.0 + - - +
83C VAL* 4.8 1.8 - - - +
124C PHE* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 3.4 3.1 - - - +
30C ARG* 2.7 68.1 + - + +
32C LEU* 3.9 21.1 - - + +
63C GLY* 1.3 74.8 - - - -
65C VAL* 1.3 73.9 + - - +
66C VAL* 3.3 5.7 + - + -
78C GLY* 4.0 23.7 + - - +
79C ASP 3.5 3.6 - - - -
80C ARG* 4.6 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ALA* 4.6 3.8 - - + -
28C ILE 3.9 4.7 - - - +
29C VAL* 4.4 3.8 - - + -
64C GLU* 1.3 76.6 - - - +
66C VAL* 1.3 60.8 + - - +
67C GLU 4.1 5.2 - - - +
68C VAL* 3.5 31.6 - - + -
75C PHE* 4.6 4.7 - - + -
76C LYS 3.4 23.1 - - - +
77C PRO* 3.2 2.3 - - + +
78C GLY 2.7 27.4 + - - -
79C ASP* 2.8 26.5 + - + +
81C VAL* 3.8 28.3 - - + -
133C LEU* 4.4 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LYS* 4.4 6.5 - - - +
28C ILE* 2.8 20.6 + - + +
30C ARG* 3.7 47.6 - - + +
64C GLU* 3.3 8.7 + - - +
65C VAL* 1.3 73.3 - - - +
67C GLU* 1.3 80.5 + - - +
77C PRO* 3.9 15.9 - - - +
123C PHE* 3.9 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LYS* 4.2 21.7 + - - -
20C PRO 5.2 0.8 - - - +
21C ALA* 5.1 1.1 - - - +
22C PRO* 3.4 33.9 - - + +
27C ALA* 3.3 3.8 - - - -
28C ILE* 2.8 44.5 + - + +
66C VAL* 1.3 86.5 - - - +
68C VAL* 1.3 67.6 + - - +
77C PRO* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PRO* 4.6 7.0 - - - +
26C ASP 3.4 4.5 - - - +
27C ALA* 4.2 8.5 - - + -
65C VAL* 3.5 22.9 - - + -
67C GLU* 1.3 85.1 - - - +
69C GLY* 1.3 69.4 + - - +
72C VAL* 3.8 22.4 - - + +
75C PHE* 3.8 26.7 - - + +
76C LYS* 4.4 1.1 - - - -
77C PRO* 4.4 13.8 - - + +
----------------------------------------------------------
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