Contacts of the helix formed by residues 93 - 108 (chain C) in PDB entry 2X86
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 ASN 93 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ALA* 3.4 13.1 - - + +
78C CYS* 2.8 46.4 + - - -
89C MET* 2.9 29.4 + - - +
92C ASN* 1.3 82.7 + - - +
94C TYR* 1.3 65.0 + - - +
95C GLN 3.7 0.2 - - - -
97C SER* 2.8 32.1 + - - -
140C PHE* 4.0 7.9 - - - -
143C SER* 3.2 29.1 + - - +
144C LYS* 4.6 7.4 - - + +
147C PHE* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C MET 3.7 0.4 + - - -
90C MET* 3.2 36.9 + - + +
93C ASN* 1.3 75.1 - - - +
95C GLN* 1.3 73.4 + - - +
97C SER* 3.2 6.3 + - - -
98C LYS* 2.9 40.5 + - + +
143C SER* 4.1 9.4 - - - +
146C LEU* 3.5 45.6 - - + +
147C PHE* 3.6 27.7 - + + -
150C TYR* 3.7 17.7 - - + +
48D ALA 4.4 0.9 + - - -
49D ASP* 2.5 38.0 + - - -
50D TYR* 3.7 14.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C MET 2.8 15.0 + - - +
91C ASP* 3.3 27.8 - - - +
94C TYR* 1.3 76.9 - - - +
96C TYR* 1.3 63.0 + - - +
98C LYS* 3.0 42.4 + - - +
99C GLU* 3.0 46.9 + - - +
50D TYR 4.1 10.6 - - - +
51D MET* 5.5 5.3 - - - +
55D ASP* 5.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C THR* 5.4 0.9 - - + -
53C LYS* 2.7 41.4 + - + +
54C GLU* 5.5 1.6 - - - -
56C PHE* 3.5 18.1 - + - -
57C LEU* 3.6 33.9 + - + -
74C HIS* 3.9 15.7 - + - +
91C ASP 2.9 13.2 + - - +
92C ASN* 3.1 25.8 - - - +
93C ASN 4.0 0.2 - - - +
94C TYR 3.3 0.2 - - - -
95C GLN* 1.3 74.0 - - - +
97C SER* 1.3 64.3 + - - +
99C GLU* 3.0 17.4 + - - +
100C LEU* 3.0 32.5 + - + +
400C NAP 3.3 38.0 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C HIS* 2.8 32.9 + - - -
76C GLY 5.2 0.2 + - - -
93C ASN* 2.8 22.2 + - - -
94C TYR 3.5 3.8 - - - -
96C TYR* 1.3 79.9 - - - +
98C LYS* 1.3 61.9 + - - +
100C LEU* 3.3 3.7 + - - +
101C LEU* 2.9 24.1 + - - +
111C PHE* 4.1 1.0 - - - -
113C TYR* 5.9 0.5 - - - -
144C LYS* 5.6 3.1 + - - -
147C PHE* 3.6 32.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C TYR* 2.9 31.4 + - + +
95C GLN* 3.0 44.4 + - - +
97C SER* 1.3 76.4 - - - +
99C GLU* 1.3 64.4 + - - +
101C LEU* 3.2 2.7 + - - +
102C HIS* 3.0 36.6 + - + +
147C PHE* 3.5 12.3 - - + -
150C TYR* 3.6 44.8 + - + +
49D ASP* 2.9 30.7 + - - -
50D TYR 4.2 2.4 + - - -
51D MET* 5.3 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LEU* 4.0 14.6 - - + -
60C ILE* 3.9 8.3 - - + +
61C MET* 3.4 44.0 - - + +
95C GLN* 3.0 38.0 + - - +
96C TYR 3.0 10.3 + - - +
98C LYS* 1.3 79.1 - - - +
100C LEU* 1.3 62.1 + - - +
102C HIS* 3.5 7.8 + - - +
103C TYR* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C THR* 4.1 14.1 - - + -
56C PHE* 3.7 24.0 - - + -
57C LEU* 5.2 2.5 - - + -
60C ILE* 3.9 18.2 - - + -
72C ILE* 4.5 13.0 - - + -
74C HIS* 3.3 46.9 - - + +
96C TYR* 3.0 24.9 + - + +
97C SER 3.6 7.9 - - - +
99C GLU* 1.3 73.8 - - - +
101C LEU* 1.3 66.4 + - - +
103C TYR* 3.1 7.6 + - - +
104C CYS* 2.9 26.3 + - - -
111C PHE* 3.7 12.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
97C SER 2.9 17.3 + - - +
98C LYS 3.5 4.3 - - - +
100C LEU* 1.3 76.7 - - - +
102C HIS* 1.3 60.1 + - + +
104C CYS* 3.3 1.2 + - - +
105C LEU* 2.8 42.0 + - + +
111C PHE* 3.8 30.9 - - + -
147C PHE* 4.0 20.9 - - + -
150C TYR* 4.0 28.5 - - + -
151C VAL* 4.3 9.2 - - + -
154C ILE* 4.3 14.1 - - + -
162C ILE* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LYS* 3.0 35.3 + - + +
99C GLU* 3.9 8.3 - - - +
101C LEU* 1.3 77.9 - - + +
103C TYR* 1.3 63.3 + - - +
105C LEU* 3.3 14.0 + - + +
106C GLU* 3.0 29.3 + - - +
150C TYR* 2.6 38.7 + + - -
154C ILE* 4.5 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ILE* 6.0 0.7 - - + -
60C ILE* 3.5 57.0 - - + -
63C GLY* 4.3 1.1 - - - -
64C GLU 2.6 28.4 + - - -
65C GLU* 3.8 5.0 + - - -
66C PHE* 3.3 18.1 + + - -
69C VAL* 5.6 2.2 - - + +
72C ILE* 4.7 7.0 - - + -
99C GLU 3.2 13.4 + - - +
100C LEU* 3.1 8.0 + - - +
102C HIS* 1.3 78.6 - - - +
104C CYS* 1.3 73.3 + - - +
106C GLU* 4.8 1.1 - - - -
107C ARG* 3.1 78.9 + - - +
109C ILE* 4.1 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ILE* 3.4 37.2 - - - -
100C LEU 2.9 15.2 + - - +
101C LEU* 3.6 7.6 - - + +
103C TYR* 1.3 78.8 - - - +
105C LEU* 1.3 56.1 + - + +
107C ARG 3.0 1.9 + - - -
108C GLU 2.7 31.9 + - - -
109C ILE* 2.9 40.2 + - - +
111C PHE* 3.8 26.9 - - + -
160C SER* 5.0 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
101C LEU* 2.8 31.4 + - + +
102C HIS* 3.5 16.4 - - - +
104C CYS* 1.3 75.9 - - + +
106C GLU* 1.3 64.0 + - - +
108C GLU* 3.3 17.2 + - - +
109C ILE 6.1 0.2 - - - +
111C PHE* 6.3 0.2 - - + -
154C ILE* 3.5 31.9 - - + -
158C ALA* 4.3 13.2 - - + -
159C ASN* 5.3 2.8 - - - +
160C SER* 4.3 15.9 + - - +
161C GLN 5.7 0.2 - - - +
162C ILE* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C HIS* 3.0 19.8 + - - +
103C TYR* 3.8 5.4 - - - +
105C LEU* 1.3 78.4 - - - +
107C ARG* 1.3 80.3 + - + +
108C GLU* 3.4 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C GLY* 3.5 29.5 + - - -
65C GLU* 3.3 37.6 + - - +
103C TYR* 3.1 64.8 + - - +
104C CYS 3.0 1.8 + - - -
106C GLU* 1.3 102.9 + - + +
108C GLU* 1.3 71.2 + - - +
109C ILE* 3.3 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C CYS 2.7 7.0 + - - -
105C LEU 3.3 10.8 + - - +
106C GLU 4.9 2.9 - - - +
107C ARG* 1.3 81.4 - - - +
109C ILE* 1.3 57.6 + - - +
110C PRO* 3.4 10.9 - - - +
159C ASN* 3.9 31.4 + - + +
160C SER* 3.4 25.8 - - - +
----------------------------------------------------------
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