Contacts of the helix formed by residues 57 - 69 (chain C) in PDB entry 4CFE
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 VAL 57 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PHE* 3.7 37.0 - - + -
52C ILE* 3.4 22.4 - - + +
55C LEU* 3.2 21.2 - - + -
56C ASP* 1.3 80.0 - - - +
58C VAL* 1.3 58.6 + - - +
59C GLY 3.2 2.7 - - - -
60C LYS* 3.5 40.4 - - + +
61C ILE* 3.0 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ILE* 3.7 20.7 + - + +
53C ARG* 4.9 5.6 - - - -
55C LEU 4.9 4.3 - - - +
56C ASP* 4.8 5.8 - - - -
57C VAL* 1.3 82.3 - - - +
59C GLY* 1.3 61.9 + - - +
61C ILE 3.9 0.3 + - - -
62C LYS* 3.7 15.4 + - - +
166D LEU* 3.4 43.2 - - + +
169D ASP* 4.0 12.6 - - + +
170D SER* 3.7 32.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ASP 4.8 2.0 + - - -
57C VAL* 3.2 0.4 - - - +
58C VAL* 1.3 83.3 - - - +
60C LYS* 1.3 62.4 - - - +
61C ILE 3.4 0.7 - - - -
62C LYS* 3.7 11.9 + - - +
63C ARG* 3.5 27.8 + - - +
170D SER* 6.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PHE* 6.3 1.3 - - + -
56C ASP 4.9 5.7 + - - +
57C VAL* 3.2 38.5 + - + +
59C GLY* 1.3 77.9 - - - +
61C ILE* 1.3 64.9 + - + +
63C ARG* 3.6 24.5 + - - +
64C GLU* 3.3 37.0 + - - +
159C GLY 4.9 7.0 - - - +
161C SER 5.4 5.8 - - - +
162C ASN* 6.0 3.1 - - - +
172C TPO 4.8 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PHE* 4.7 17.9 - - + -
47C LEU* 4.4 22.7 - - + -
52C ILE* 3.7 31.2 - - + -
57C VAL* 3.0 22.0 + - + +
58C VAL 4.2 4.7 - - - +
59C GLY 3.4 0.2 - - - -
60C LYS* 1.3 79.2 - - + +
62C LYS* 1.3 65.9 + - - +
64C GLU* 3.2 15.7 + - + +
65C ILE* 3.0 43.6 + - + +
89C PHE* 5.1 4.5 - - + -
166D LEU* 4.4 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C VAL 3.7 8.9 + - - +
59C GLY* 3.8 13.9 - - - +
60C LYS 3.4 0.2 - - - -
61C ILE* 1.3 80.1 - - - +
63C ARG* 1.3 58.3 + - + +
65C ILE* 3.5 3.4 + - - +
66C GLN* 3.0 64.5 + - - +
163D PHE* 4.2 18.3 - - + +
166D LEU* 3.7 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLY 3.5 14.0 + - - +
60C LYS* 3.6 35.0 + - - +
61C ILE 3.2 0.6 - - - -
62C LYS* 1.3 81.1 - - + +
64C GLU* 1.3 63.8 + - - +
66C GLN* 3.3 10.0 + - - +
67C ASN* 2.4 42.6 + - - +
161C SER 4.9 1.4 + - - -
162C ASN* 2.6 38.0 + - - +
163C MET* 3.1 33.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
45C LYS* 5.2 5.5 + - - -
60C LYS* 3.3 26.4 - - + +
61C ILE* 3.2 19.3 + - + +
63C ARG* 1.3 80.8 - - + +
65C ILE* 1.3 53.3 + - + +
67C ASN* 3.7 4.1 - - - +
68C LEU* 2.8 41.1 + - + +
91C MET* 6.2 0.9 - - - -
158C PHE* 4.2 5.2 - - - +
159C GLY* 3.1 39.9 + - - +
161C SER* 3.8 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 5.9 0.4 - - + -
61C ILE* 3.0 37.9 + - + +
62C LYS 3.8 4.3 - - - +
64C GLU* 1.3 77.3 - - + +
66C GLN* 1.3 62.8 + - - +
68C LEU* 4.8 2.7 - - - -
69C LYS* 3.1 32.3 + - + +
79C LEU* 4.9 8.4 - - + +
82C VAL* 4.3 26.9 - - + -
89C PHE* 5.6 3.8 - - + -
91C MET* 4.8 19.7 - - + -
162D VAL* 3.7 24.9 - - + -
163D PHE* 3.8 22.7 - - + -
166D LEU* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LYS* 3.0 52.2 + - - +
63C ARG* 3.7 12.5 - - - +
65C ILE* 1.3 74.8 - - - +
67C ASN* 1.3 62.5 + - - +
69C LYS* 3.6 25.2 - - - +
70C LEU* 3.6 19.4 - - - +
163D PHE* 3.5 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ARG* 2.4 42.6 + - - +
64C GLU* 4.0 4.2 - - - +
65C ILE 3.1 0.2 - - - -
66C GLN* 1.3 84.8 - - - +
68C LEU* 1.3 63.5 + - - +
69C LYS 3.2 2.0 - - - -
70C LEU* 3.4 4.6 + - - +
71C PHE* 3.2 36.0 + - + -
133C HIS* 4.7 3.1 - - - +
135C VAL* 4.2 17.0 - - + +
163C MET* 3.7 34.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
45C LYS* 5.6 3.6 - - - +
64C GLU* 2.8 24.2 + - + +
67C ASN* 1.3 72.8 - - - +
69C LYS* 1.3 60.8 + - - +
70C LEU 3.3 0.6 + - - -
71C PHE* 3.7 29.7 + - + +
76C ILE* 4.9 1.8 - - + -
77C ILE 4.3 14.8 - - - +
78C LYS* 5.7 0.2 - - - -
79C LEU* 3.8 29.8 + - + +
91C MET* 4.0 25.4 - - + -
93C MET* 4.3 13.5 - - + -
158C PHE* 3.8 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ILE* 3.1 24.2 + - + +
66C GLN* 3.6 30.1 - - - +
68C LEU* 1.3 79.7 - - - +
70C LEU* 1.3 91.1 + - + +
71C PHE 4.3 3.9 - - - +
79C LEU* 4.5 20.0 - - + +
163D PHE* 4.6 14.8 - - + -
----------------------------------------------------------
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