Contacts of the helix formed by residues 93 - 108 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74I HIS* 6.2 0.2 - - - -
77I ALA* 3.4 12.5 - - + +
78I CYS* 2.8 46.3 + - - +
89I MET* 2.9 29.4 + - - +
92I ASN* 1.3 83.1 + - - +
94I TYR* 1.3 64.5 + - - +
97I SER* 2.8 32.3 + - - -
140I PHE* 4.0 8.1 - - - -
143I SER* 3.2 28.8 + - - +
144I LYS* 4.6 6.9 - - - +
147I PHE* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I MET 3.7 0.2 + - - -
90I MET* 3.2 38.7 + - + +
93I ASN* 1.3 75.6 - - - +
95I GLN* 1.3 73.9 + - - +
97I SER* 3.2 6.3 + - - -
98I LYS* 2.9 39.5 + - + +
143I SER* 4.1 9.6 - - - +
146I LEU* 3.5 45.3 - - + +
147I PHE* 3.6 27.9 - + + -
150I TYR* 3.7 17.6 - - + +
48J ALA 4.3 0.7 + - - -
49J ASP* 2.5 39.5 + - - -
50J TYR* 3.7 13.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90I MET 2.8 15.4 + - - +
91I ASP* 3.3 26.9 - - - +
94I TYR* 1.3 75.9 - - + +
96I TYR* 1.3 64.7 + - - +
98I LYS* 3.0 42.2 + - - +
99I GLU* 3.0 46.3 + - - +
50J TYR 4.1 10.4 - - - +
51J MET* 5.6 3.8 - - - +
55J ASP* 5.8 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I THR* 5.4 0.2 - - + -
30I VAL* 4.1 0.2 - - - +
53I LYS* 2.7 41.3 + - + +
54I GLU* 5.4 1.3 - - - -
56I PHE* 3.5 18.2 - + - -
57I LEU* 3.6 35.3 + - + -
74I HIS* 3.9 15.9 - + - +
91I ASP 2.9 12.0 + - - +
92I ASN* 3.0 26.5 - - - +
94I TYR 3.3 0.4 - - - -
95I GLN* 1.3 74.0 - - - +
97I SER* 1.3 65.0 + - - +
99I GLU* 3.0 17.6 + - - +
100I LEU* 3.0 31.8 + - + +
400I NAP 3.3 36.6 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 97 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74I HIS* 2.8 32.6 + - - -
93I ASN* 2.8 21.7 + - - -
94I TYR 3.2 4.0 + - - -
96I TYR* 1.3 80.0 - - - +
98I LYS* 1.3 60.9 + - - +
100I LEU* 3.3 3.2 + - - +
101I LEU* 2.9 24.6 + - - +
111I PHE* 4.1 0.7 - - - -
113I TYR* 5.9 0.2 - - - -
144I LYS* 5.7 3.3 + - - -
147I PHE* 3.6 33.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I TYR* 2.9 31.9 + - + +
95I GLN* 3.0 44.1 + - - +
97I SER* 1.3 76.0 - - - +
99I GLU* 1.3 64.0 + - - +
101I LEU* 3.2 3.1 + - - +
102I HIS* 3.0 37.9 + - + +
147I PHE* 3.7 11.7 - - + -
150I TYR* 3.6 45.2 + - + +
49J ASP* 2.9 30.9 + - - -
50J TYR 4.3 1.8 + - - -
51J MET* 5.3 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I LEU* 4.0 14.6 - - + -
60I ILE* 3.9 7.8 - - + +
61I MET* 3.4 43.6 - - + +
95I GLN* 3.0 39.0 + - - +
96I TYR* 3.2 10.3 - - - +
98I LYS* 1.3 80.8 - - - +
100I LEU* 1.3 62.3 + - - +
102I HIS* 3.4 7.8 + - - +
103I TYR* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I THR* 4.1 13.7 - - + -
56I PHE* 3.7 24.2 - - + -
57I LEU* 5.2 2.7 - - + -
60I ILE* 3.9 19.3 - - + -
72I ILE* 4.5 12.1 - - + -
74I HIS* 3.3 46.9 - - + +
96I TYR* 3.0 23.8 + - + +
97I SER 3.6 7.9 - - - +
99I GLU* 1.3 75.1 - - - +
101I LEU* 1.3 66.9 + - - +
103I TYR* 3.1 7.6 + - - +
104I CYS* 2.9 26.2 + - - -
111I PHE* 3.7 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I SER 2.9 17.7 + - - +
98I LYS 3.5 3.6 - - - +
100I LEU* 1.3 75.8 - - - +
102I HIS* 1.3 60.6 + - + +
104I CYS* 3.3 1.2 + - - +
105I LEU* 2.8 40.9 + - + +
111I PHE* 3.8 30.5 - - + -
147I PHE* 4.0 20.6 - - + -
150I TYR* 4.0 28.7 - - + -
151I VAL* 4.3 9.6 - - + -
154I ILE* 4.3 13.9 - - + -
162I ILE* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 102 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I LYS* 3.0 34.4 + - + +
99I GLU* 3.9 8.3 - - - +
101I LEU* 1.3 76.9 - - + +
103I TYR* 1.3 63.4 + - - +
105I LEU* 3.3 13.7 + - + +
106I GLU* 3.0 31.0 + - - +
150I TYR* 2.6 38.5 + + - -
154I ILE* 4.5 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I ILE* 6.0 0.7 - - + -
60I ILE* 3.5 56.3 - - + -
63I GLY* 4.3 0.4 - - - -
64I GLU 2.6 28.2 + - - -
65I GLU* 3.9 5.4 + - - -
66I PHE* 3.3 17.7 + + - -
69I VAL* 5.6 2.7 - - + +
72I ILE* 4.8 7.0 - - + -
99I GLU 3.2 13.9 + - - +
100I LEU* 3.1 9.1 + - - +
102I HIS* 1.3 76.8 - - - +
104I CYS* 1.3 72.7 + - - +
106I GLU* 4.8 1.8 - - - -
107I ARG* 3.1 79.4 + - - +
109I ILE* 4.1 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 104 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ILE* 3.4 37.2 - - - -
100I LEU 2.9 15.2 + - - +
101I LEU* 3.6 6.7 - - + +
103I TYR* 1.3 79.1 - - - +
105I LEU* 1.3 56.4 + - + +
107I ARG 3.0 1.9 + - - -
108I GLU 2.7 32.1 + - - -
109I ILE* 2.9 40.9 + - - +
111I PHE* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I LEU* 2.8 31.0 + - + +
102I HIS* 3.5 15.7 - - - +
104I CYS* 1.3 78.0 - - + +
106I GLU* 1.3 62.3 + - - +
108I GLU* 3.3 17.2 + - - +
109I ILE 6.1 0.2 - - - +
111I PHE* 6.3 0.4 - - + -
154I ILE* 3.6 33.0 - - + -
158I ALA* 4.3 13.7 - - + -
159I ASN* 5.2 3.2 - - - +
160I SER* 4.3 15.0 + - - +
161I GLN 5.7 0.2 - - - +
162I ILE* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102I HIS* 3.0 19.2 + - - +
103I TYR* 3.8 5.0 - - - +
105I LEU* 1.3 79.1 - - - +
107I ARG* 1.3 80.0 + - + +
108I GLU* 3.4 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I GLY* 3.5 29.3 + - - -
65I GLU* 3.3 36.8 + - - +
103I TYR* 3.1 64.0 + - - +
104I CYS 3.0 2.2 + - - -
106I GLU* 1.3 101.3 + - + +
108I GLU* 1.3 70.6 + - - +
109I ILE* 3.2 24.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104I CYS 2.7 4.8 + - - -
105I LEU 3.3 10.6 + - - +
106I GLU 4.9 2.7 - - - +
107I ARG* 1.3 81.5 - - - +
109I ILE* 1.3 58.4 + - - +
110I PRO* 3.4 10.9 - - - +
159I ASN* 3.9 30.7 + - + +
160I SER* 3.4 27.1 - - - +
----------------------------------------------------------
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