Contacts of the helix formed by residues 67 - 88 (chain C) in PDB entry 4FJV
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 67 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C SER* 2.8 32.9 + - - +
64C LEU* 2.8 11.4 + - - +
65C LEU 4.1 6.1 - - - +
66C GLY* 1.3 81.8 - - - +
68C SER* 1.3 58.4 + - - +
69C ARG 3.2 3.0 + - - -
70C GLU* 3.3 35.3 + - + +
71C ILE* 2.8 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C GLY 3.7 4.6 + - - -
67C LYS* 1.3 73.5 - - - +
69C ARG* 1.3 67.0 + - - +
71C ILE* 3.4 9.8 + - - +
72C PHE* 3.0 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLU* 3.0 45.4 + - - +
4A THR 4.7 8.3 + - - -
5A SER* 5.7 6.5 - - - -
67C LYS 3.3 0.8 - - - -
68C SER* 1.3 82.6 + - - +
70C GLU* 1.3 63.1 + - - +
72C PHE* 3.2 8.4 + - - +
73C LYS* 3.1 56.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C TYR* 4.7 11.2 + - - +
63C SER* 5.2 2.4 + - - +
64C LEU* 3.6 23.1 - - + +
67C LYS* 3.3 37.0 + - + +
69C ARG* 1.3 78.6 - - - +
71C ILE* 1.3 62.5 + - - +
73C LYS* 3.4 11.6 + - + +
74C PHE* 3.0 24.4 + - - +
215C SER* 5.3 6.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 3.4 41.7 - - + +
66C GLY 4.3 4.3 - - - +
67C LYS 2.8 30.0 + - - +
68C SER* 3.6 7.6 - - - +
70C GLU* 1.3 78.4 - - - +
72C PHE* 1.3 57.2 + - - +
74C PHE* 3.3 5.5 + - - +
75C LYS* 2.9 28.0 + - + +
106C VAL* 4.8 9.9 - - + +
109C VAL* 3.5 30.1 - - + +
110C GLU* 3.7 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C SER 3.0 13.4 + - - +
69C ARG* 3.5 11.0 - - - +
71C ILE* 1.3 78.3 - - - +
73C LYS* 1.3 70.2 + - + +
75C LYS* 3.2 14.3 + - + +
76C GLU* 3.0 51.2 + - + +
110C GLU* 5.2 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ARG* 3.1 51.0 + - - +
70C GLU* 3.8 10.0 - - + +
72C PHE* 1.3 86.2 - - + +
74C PHE* 1.3 62.9 + - - +
76C GLU* 3.4 16.5 + - - +
77C ARG* 3.3 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C TYR* 3.5 45.3 - + - +
61C LEU* 4.3 5.2 - - + -
64C LEU* 4.0 11.9 - - + -
70C GLU 3.0 18.2 + - - +
71C ILE 3.8 3.4 - - - +
73C LYS* 1.3 73.2 - - - +
75C LYS* 1.3 62.3 + - - +
77C ARG* 3.1 12.4 + - - +
78C VAL* 2.9 51.4 + - + +
102C PHE* 3.9 18.8 - + - -
106C VAL* 3.9 22.4 - - + -
187C LEU* 3.9 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ILE* 2.9 17.2 + - + +
72C PHE* 3.2 15.0 + - + +
74C PHE* 1.3 78.2 - - - +
76C GLU* 1.3 61.7 + - - +
78C VAL* 3.1 8.2 + - - +
79C LEU* 3.0 30.7 + - + +
103C TYR* 3.2 36.5 + - + -
106C VAL* 4.3 19.1 - - + -
107C GLU* 3.1 22.3 + - - -
110C GLU* 3.1 38.9 + - - +
111C LYS* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C PHE* 3.0 44.3 + - + +
73C LYS* 3.5 18.7 - - - +
74C PHE 3.2 0.2 - - - -
75C LYS* 1.3 76.2 - - - +
77C ARG* 1.3 62.3 + - - +
79C LEU* 3.4 20.3 + - + +
80C GLN* 3.4 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LYS 3.3 8.5 + - - +
74C PHE* 3.1 17.1 + - + +
76C GLU* 1.3 78.0 - - - +
78C VAL* 1.3 64.9 + - - +
80C GLN* 3.1 18.4 + - + +
81C THR* 3.3 16.0 + - + +
185C GLN 4.5 3.2 + - - -
186C ALA 4.1 14.4 + - - +
187C LEU* 3.6 32.5 + - + +
188C SER* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C PHE* 2.9 52.6 + - + +
75C LYS* 3.1 9.8 + - + +
77C ARG* 1.3 76.3 - - - +
79C LEU* 1.3 60.8 + - - +
81C THR* 2.8 32.0 + - + +
99C PHE* 3.3 21.1 - - + -
102C PHE* 3.7 26.5 - - + -
103C TYR* 4.4 20.2 - - + -
106C VAL* 4.3 6.1 - - + -
134C PHE* 5.2 0.2 - - + -
187C LEU* 5.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LYS* 3.0 25.0 + - + +
76C GLU* 3.5 15.0 - - + +
77C ARG 3.1 0.6 - - - -
78C VAL* 1.3 79.1 - - - +
80C GLN* 1.3 62.7 + - + +
81C THR 3.3 0.2 - - - -
82C PRO* 3.3 16.3 - - - +
83C ASN* 4.7 2.6 + - - -
99C PHE* 4.6 9.2 - - + -
103C TYR* 3.9 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLU* 3.4 18.6 + - - +
77C ARG* 3.1 10.4 + - + +
79C LEU* 1.3 81.2 - - - +
81C THR* 1.3 64.4 + - - +
82C PRO* 3.3 2.0 - - - -
83C ASN* 3.1 40.0 + - - +
84C ASP* 3.5 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ARG* 3.3 20.4 - - + +
78C VAL* 2.8 22.2 + - + +
80C GLN* 1.3 74.5 - - - +
82C PRO* 1.3 70.3 - - - +
84C ASP* 3.1 16.2 + - - +
85C LEU* 3.0 25.9 + - - +
99C PHE* 3.7 3.3 - - - -
134C PHE* 3.5 20.8 - - + -
138C LEU* 3.8 31.6 - - + -
186C ALA 5.3 2.5 - - - +
187C LEU* 4.5 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C VAL 3.6 4.5 - - - +
79C LEU 3.3 17.0 - - - +
80C GLN 3.4 1.1 - - - -
81C THR* 1.3 97.4 - - - +
83C ASN* 1.3 57.8 + - - +
85C LEU* 3.2 8.0 + - + +
86C LEU* 2.9 38.8 + - + +
92C GLU* 6.2 0.2 - - + -
95C PHE* 4.0 21.4 - - + -
99C PHE* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LEU 4.7 2.2 + - - -
80C GLN* 3.3 37.2 + - + +
82C PRO* 1.3 78.6 - - - +
84C ASP* 1.3 63.8 + - - +
86C LEU* 3.3 15.4 + - - +
87C ALA* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C GLN* 3.5 7.6 + - - +
81C THR* 3.1 32.2 + - - +
83C ASN* 1.3 77.5 - - - +
85C LEU* 1.3 63.3 + - - +
87C ALA* 3.4 2.6 + - - +
88C ALA* 3.3 10.6 + - - +
138C LEU* 4.3 13.5 - - + +
141C ALA* 3.9 5.1 - - + +
142C PHE 6.1 0.2 - - - +
145C ASN* 3.2 31.1 + - - +
146C ARG* 5.5 5.2 + - - -
186C ALA 5.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C THR 3.0 16.0 + - - +
82C PRO* 3.6 7.0 - - + +
84C ASP* 1.3 74.2 - - - +
86C LEU* 1.3 65.0 + - - +
88C ALA 3.3 5.4 + - - -
89C GLY 3.4 0.2 + - - -
90C PHE* 3.0 33.9 + - + +
95C PHE* 3.7 48.2 - - + -
99C PHE* 5.2 0.7 - - + -
134C PHE* 4.3 21.3 - - + -
137C LEU* 3.7 35.4 - - + +
138C LEU* 3.9 14.4 - - + +
141C ALA* 3.8 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C PRO* 2.9 27.1 + - + +
83C ASN* 3.7 15.5 - - - +
85C LEU* 1.3 76.8 - - - +
87C ALA* 1.3 53.8 + - - +
89C GLY* 2.7 26.9 + - - -
90C PHE 3.7 17.6 - - - +
91C GLU* 5.0 0.7 - - - -
92C GLU* 4.2 15.0 - - + +
95C PHE* 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ASN 2.9 17.7 + - - +
84C ASP* 3.7 7.0 - - - +
86C LEU* 1.3 75.9 - - - +
88C ALA* 1.3 58.4 + - - +
89C GLY 3.3 0.8 + - - -
145C ASN* 3.5 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ASP 3.3 7.3 + - - +
85C LEU 3.3 5.5 + - - +
86C LEU 3.1 1.0 - - - -
87C ALA* 1.3 77.6 - - - +
89C GLY* 1.3 60.4 + - - +
90C PHE* 3.4 7.8 + - + -
141C ALA* 3.7 31.9 - - + +
144C ARG* 3.9 27.8 + - + +
145C ASN* 3.4 14.6 + - - +
----------------------------------------------------------
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