Contacts of the helix formed by residues 90 - 108 (chain C) in PDB entry 3SF4
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 ASP 90 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LYS* 3.3 35.5 + - + +
55C SER* 5.4 3.5 + - - -
85C ALA* 3.1 12.2 + - - +
88C ILE* 3.3 24.2 + - + +
89C GLY* 1.3 73.7 - - - +
91C GLN* 1.3 51.7 + - - +
92C LEU* 3.6 8.1 + - - +
93C GLY* 3.1 25.3 + - - -
94C GLU* 2.8 36.8 + - - +
50F LYS* 5.2 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C GLY 3.0 16.3 + - - +
90C ASP* 1.3 71.2 + - - +
92C LEU* 1.3 64.4 + - - +
94C GLU* 3.2 13.8 + - - +
95C ALA 3.0 18.4 + - - -
124C ILE* 3.6 23.6 - - + +
127C GLU* 3.0 29.7 + - - -
128C LEU* 3.8 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ASP* 3.4 7.0 + - - +
91C GLN* 1.3 78.6 - - - +
93C GLY* 1.3 62.0 + - - +
95C ALA* 3.4 7.4 + - + +
96C LYS* 3.2 40.9 + - + +
128C LEU* 3.5 26.3 - - + +
130C ASP* 3.9 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ALA* 3.7 3.6 - - - -
90C ASP* 3.1 27.4 + - - -
92C LEU* 1.3 75.8 - - - +
94C GLU* 1.3 62.4 + - - +
96C LYS* 4.7 0.9 - - - -
97C ALA* 3.0 14.9 + - - +
50F LYS* 2.9 38.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU* 3.5 12.1 - - + +
85C ALA* 3.5 14.5 - - + +
86C ARG* 2.6 52.9 + - + +
90C ASP 2.8 19.4 + - - +
91C GLN* 3.2 13.1 + - - +
93C GLY* 1.3 69.8 - - - +
95C ALA* 1.3 61.9 + - - +
97C ALA 3.1 1.6 + - - -
98C SER* 2.8 34.1 + - - +
120C ARG* 2.9 24.2 + - - +
124C ILE* 3.5 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLN 3.0 12.2 + - - +
92C LEU* 3.5 13.7 - - + +
94C GLU* 1.3 77.2 - - - +
96C LYS* 1.3 63.4 + - + +
98C SER* 3.2 6.0 + - - -
99C GLY 3.2 17.2 + - - -
121C HIS* 3.4 32.0 - - + +
124C ILE* 3.9 29.1 - - + +
125C SER* 4.7 3.6 - - - +
128C LEU* 5.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 3.2 31.1 + - + +
93C GLY* 3.9 4.3 - - - +
95C ALA* 1.3 79.5 - - + +
97C ALA* 1.3 63.5 + - - +
99C GLY* 3.3 2.6 + - - -
100C ASN* 3.1 30.2 + - - +
121C HIS* 4.9 0.6 - - - +
48F GLN* 3.6 46.5 - - + +
49F ALA 2.8 29.0 + - - +
50F LYS* 4.0 22.0 - - + +
51F PRO* 4.4 7.9 - - - +
61F ASP* 4.3 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C HIS* 4.6 3.3 - - - +
81C ASP* 3.3 28.2 + - + +
82C LEU* 3.6 31.2 - - + +
93C GLY 3.0 17.4 + - - +
94C GLU 3.5 4.0 - - - +
96C LYS* 1.3 73.0 - - - +
98C SER* 1.3 62.2 + - - +
100C ASN* 3.3 6.7 + - - +
101C LEU* 2.9 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU* 3.5 19.4 - - - +
94C GLU 2.8 18.8 + - - -
95C ALA* 3.4 8.9 - - - -
97C ALA* 1.3 75.6 - - - +
99C GLY* 1.3 53.1 + - - +
101C LEU* 3.7 0.8 - - - +
102C GLY* 2.7 31.0 + - - -
117C CYS* 3.2 39.8 - - - +
120C ARG* 3.4 20.0 - - - +
121C HIS 3.9 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ALA 3.2 7.7 + - - -
96C LYS 3.3 2.7 + - - -
97C ALA 3.3 0.2 - - - -
98C SER* 1.3 79.5 - - - +
100C ASN* 1.3 57.2 + - - +
102C GLY* 3.2 1.7 + - - -
103C ASN* 2.9 37.3 + - - +
118C CYS* 4.3 7.6 - - - -
121C HIS* 3.7 24.8 - - - +
140C ASN* 4.4 8.5 - - - -
46F VAL 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C SER* 3.7 14.5 + - - -
63C ASN* 3.6 14.8 - - - +
78C HIS* 3.4 24.6 + - + +
81C ASP* 4.9 0.2 + - - -
96C LYS* 3.1 19.5 + - - +
97C ALA* 3.7 7.3 - - - +
99C GLY* 1.3 74.2 - - - +
101C LEU* 1.3 66.1 + - - +
103C ASN* 3.3 2.9 + - - +
104C THR* 3.0 26.2 + - - -
46F VAL 4.6 0.5 - - - +
47F LEU* 3.5 14.4 - - - +
48F GLN* 3.0 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 3.5 46.4 - - + +
78C HIS* 3.9 18.5 - - + +
79C HIS* 3.9 23.8 - - + +
82C LEU* 3.7 25.4 - - + -
97C ALA 2.9 20.8 + - - +
98C SER* 3.9 3.6 - - - +
100C ASN* 1.3 72.7 - - - +
102C GLY* 1.3 58.8 + - - +
104C THR* 3.3 3.2 + - - -
105C LEU* 2.8 45.3 + - + +
117C CYS* 4.0 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C SER 2.7 18.1 + - - -
99C GLY 3.6 1.3 - - - -
101C LEU* 1.3 74.6 - - - +
103C ASN* 1.3 64.8 + - - +
105C LEU* 3.2 1.1 + - - -
106C LYS* 2.9 21.1 + - - +
114C ALA* 3.5 16.2 - - - +
117C CYS* 3.7 16.5 - - - +
118C CYS* 4.0 15.0 - - - -
144C VAL* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C PHE* 4.3 7.4 - - + -
99C GLY 2.9 24.5 + - - +
100C ASN 3.7 4.5 - - - +
101C LEU 3.3 0.2 - - - -
102C GLY* 1.3 74.5 - - - +
104C THR* 1.3 64.1 + - - +
106C LYS* 3.2 12.8 + - - +
107C VAL* 3.2 25.3 + - - +
118C CYS* 4.4 1.5 - - - -
140C ASN* 3.3 22.7 + - - +
143C ASN* 5.2 2.4 - - - +
144C VAL* 5.6 3.3 - - - +
44F MET 3.6 8.7 + - - -
45F CYS* 3.4 28.3 - - - +
46F VAL 3.1 26.4 - - - +
47F LEU* 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C PHE* 3.4 22.5 - - + -
71C TYR* 3.7 13.2 - - + +
74C ALA* 4.0 3.9 - - + +
75C LEU* 3.6 39.5 - - + +
78C HIS* 3.3 17.8 - - - -
100C ASN 3.0 14.9 + - - -
101C LEU* 3.5 10.3 - - - -
103C ASN* 1.3 77.2 - - - +
105C LEU* 1.3 63.7 + - - +
107C VAL* 3.2 6.2 + - - +
108C LEU* 3.1 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 3.4 30.1 - - + -
101C LEU* 2.8 30.0 + - + +
102C GLY 3.6 4.3 - - - +
104C THR* 1.3 73.6 - - - +
106C LYS* 1.3 59.7 + - - +
108C LEU* 3.2 12.5 + - + +
110C ASN* 3.0 51.0 + - + +
113C GLU* 3.8 30.1 - - + +
114C ALA* 3.8 8.5 - - + -
117C CYS* 3.8 26.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLY 2.9 11.9 + - - +
103C ASN* 3.5 13.0 - - - +
104C THR 3.2 0.4 - - - -
105C LEU* 1.3 71.9 - - - +
107C VAL* 1.3 77.9 + - - +
108C LEU 3.0 2.0 - - - -
109C GLY* 3.0 10.8 + - - +
111C PHE* 3.7 32.8 - - + -
114C ALA* 3.8 11.6 - - + +
143C ASN* 3.8 7.1 + - + +
144C VAL* 3.8 28.9 - - + +
147C ALA* 3.7 20.7 - - + +
44F MET* 3.1 39.5 + - - +
45F CYS* 3.9 10.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C PHE* 3.8 24.5 - - + -
71C TYR* 3.9 24.2 - - + -
103C ASN 3.2 12.5 + - - +
104C THR 3.2 8.8 + - - +
106C LYS* 1.3 84.5 - - - +
108C LEU* 1.3 61.6 + - + +
109C GLY 3.3 1.1 + - - -
45F CYS* 4.1 14.8 - - - -
67F GLY* 4.8 0.2 - - - -
68F PRO* 3.4 38.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C TYR* 4.0 28.5 - - + +
72C ALA* 5.1 2.9 - - - +
75C LEU* 3.6 36.3 - - + -
104C THR* 3.1 26.1 + - + +
105C LEU* 3.6 11.2 - - + +
106C LYS 3.0 1.4 - - - -
107C VAL* 1.3 80.2 - - + +
109C GLY* 1.3 58.8 + - - +
110C ASN* 3.3 5.5 + - + +
----------------------------------------------------------
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