Contacts of the helix formed by residues 97 - 117 (chain B) in PDB entry 1XOX
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 THR 97 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU 4.5 2.2 - - - +
95A GLU* 2.7 34.5 - - - +
96A LEU 2.8 15.7 - - - +
97A THR* 4.1 6.8 - - + +
98A LEU* 3.9 3.0 - - - +
91B LYS* 5.3 0.2 - - - +
96B LEU* 1.3 79.3 - - - +
98B LEU* 1.3 65.1 + - - +
99B GLY* 4.2 4.5 - - - -
100B GLU* 3.0 23.5 + - - +
101B PHE* 3.1 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 2.8 57.0 - - + +
94A GLU* 3.8 3.6 - - - -
96A LEU* 3.1 28.9 + - + -
98A LEU* 3.1 44.0 - - + -
101A PHE* 3.7 19.1 - - + -
97B THR* 1.3 69.5 - - - +
99B GLY* 1.3 55.6 + - - +
101B PHE* 2.7 29.6 + - + +
102B LEU* 3.0 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 3.3 41.4 + - - +
97B THR* 3.2 2.1 - - - -
98B LEU* 1.3 78.2 - - - +
100B GLU* 1.3 59.7 + - - +
102B LEU* 3.8 1.7 + - - +
103B LYS* 3.2 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA 5.4 1.4 - - - +
89B VAL* 4.4 11.7 - - + +
91B LYS* 3.2 34.7 + - - -
96B LEU* 4.9 6.1 - - + -
97B THR* 3.0 24.6 + - - +
99B GLY* 1.3 75.0 - - - +
101B PHE* 1.3 64.5 + - - +
103B LYS* 3.6 11.8 + - - +
104B LEU* 3.1 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.7 26.5 - - + -
101A PHE* 6.0 3.8 - + - -
6B LEU* 5.9 0.4 - - + -
10B TRP* 3.4 53.8 - + + -
13B PHE* 3.5 34.3 - + - -
93B PHE* 4.3 23.6 - + - -
96B LEU* 4.9 12.7 - - + +
97B THR 3.1 3.8 + - - +
98B LEU* 2.7 26.4 + - + +
100B GLU* 1.3 72.4 - - - +
102B LEU* 1.3 83.2 + - + +
104B LEU* 3.1 23.6 + - + +
105B ASP* 3.6 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 6.5 0.9 - - + -
5A THR* 5.6 7.4 - - - +
6A LEU* 5.4 13.2 - - + -
93A PHE* 4.4 11.2 - - + -
94A GLU* 4.8 18.4 - - + +
10B TRP* 5.4 8.5 - - + -
98B LEU* 3.0 30.6 + - + +
99B GLY 4.3 2.5 - - - +
101B PHE* 1.3 93.9 - - + +
103B LYS* 1.3 68.5 + - - +
104B LEU 2.9 1.8 - - - -
105B ASP* 2.8 37.9 + - + +
106B ARG* 3.6 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLY 3.2 18.6 + - - +
100B GLU* 3.7 15.7 - - - +
101B PHE 3.3 0.2 - - - -
102B LEU* 1.3 78.7 - - - +
104B LEU* 1.3 65.8 + - + +
106B ARG* 3.4 19.1 + - + +
107B GLU* 3.5 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.5 23.8 - - + -
59B PHE* 3.0 37.3 - - + -
85B ALA* 4.6 16.4 - - + +
86B PHE* 4.5 22.4 - - + -
89B VAL* 5.5 5.6 - - + -
96B LEU* 5.8 6.3 - - + -
100B GLU* 3.1 34.1 - - + +
101B PHE* 3.2 12.3 - - + +
102B LEU 2.9 0.4 - - - -
103B LYS* 1.3 80.2 - - + +
105B ASP* 1.3 57.6 + - - +
106B ARG 3.0 2.2 - - - -
107B GLU* 2.7 25.1 + - + -
108B ARG 3.0 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TRP* 2.7 45.6 + - - -
13B PHE* 4.4 8.1 - - - -
101B PHE* 3.6 12.8 + - - +
102B LEU* 2.8 24.8 + - + +
104B LEU* 1.3 77.4 - - - +
106B ARG* 1.3 65.5 + - - +
108B ARG* 3.6 6.9 + - - +
109B ALA* 3.2 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU 3.6 6.4 + - - -
103B LYS* 3.4 14.5 + - + +
104B LEU 3.0 0.2 - - - -
105B ASP* 1.3 83.0 - - - +
107B GLU* 1.3 59.4 + - + +
109B ALA* 3.9 3.9 - - - +
110B LYS* 3.0 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B PHE* 3.5 17.9 - - + -
83B GLY 4.8 4.9 - - - +
85B ALA* 3.8 21.0 - - + +
103B LYS* 3.5 25.9 + - - +
104B LEU* 2.7 18.6 + - + +
106B ARG* 1.3 71.5 - - - +
108B ARG* 1.3 66.8 + - - +
110B LYS* 2.9 17.2 + - - +
111B ASN* 2.8 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA 4.8 14.6 + - - -
10B TRP* 6.3 0.8 - - - -
12B PRO* 5.8 7.0 - - - +
13B PHE* 4.3 19.5 - - - -
58B PHE* 4.8 15.9 - - - +
59B PHE* 3.5 36.5 - - + +
61B PHE* 4.3 20.0 - - + -
104B LEU 3.0 5.2 + - - +
105B ASP* 3.9 11.6 + - - +
107B GLU* 1.3 78.1 - - - +
109B ALA* 1.3 65.9 + - - +
111B ASN* 3.1 13.6 + - - +
112B LYS* 3.1 20.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASP 3.2 14.9 + - - +
106B ARG* 4.1 4.5 - - - +
108B ARG* 1.3 81.3 - - - +
110B LYS* 1.3 62.9 + - - +
112B LYS* 3.4 9.6 + - - +
113B ILE* 3.3 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ARG* 3.0 31.9 + - + +
107B GLU* 2.9 19.0 + - - +
109B ALA* 1.3 73.9 - - - +
111B ASN* 1.3 65.7 + - - +
113B ILE* 3.2 13.3 + - + +
114B ALA* 3.2 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B PHE 3.6 4.0 - - - +
60B CYS* 3.6 29.2 + - - +
61B PHE* 3.5 23.2 - - + -
83B GLY* 3.6 26.2 - - - +
107B GLU* 2.8 25.3 + - - +
108B ARG 3.6 7.0 - - - +
110B LYS* 1.3 77.0 - - - +
112B LYS* 1.3 63.1 + - - +
114B ALA* 3.1 23.7 + - - +
115B LYS* 3.3 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE* 3.3 36.0 - - + -
108B ARG* 3.1 20.5 + - + +
109B ALA* 3.5 14.8 - - - +
110B LYS 3.2 0.2 - - - -
111B ASN* 1.3 76.7 - - - +
113B ILE* 1.3 62.8 + - + +
115B LYS* 3.3 33.1 + - - +
116B GLU* 3.8 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ALA* 3.3 22.8 + - + +
110B LYS* 3.2 12.4 + - + +
112B LYS* 1.3 77.9 - - + +
114B ALA* 1.3 66.9 + - - +
116B GLU* 3.0 23.4 + - + +
117B THR* 3.0 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LYS 3.2 9.1 + - - +
111B ASN* 3.1 19.6 + - - +
113B ILE* 1.3 81.1 - - - +
115B LYS* 1.3 62.4 + - - +
117B THR* 2.8 25.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE* 3.4 50.8 - - + -
63B GLU* 5.9 0.8 + - - -
111B ASN 3.3 9.9 + - - +
112B LYS* 3.4 24.5 - - - +
113B ILE 3.1 0.2 - - - -
114B ALA* 1.3 81.0 - - - +
116B GLU* 1.3 64.3 + - + +
117B THR* 4.7 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LYS* 3.8 12.1 + - - +
113B ILE* 3.0 16.6 + - + +
115B LYS* 1.3 83.8 - - + +
117B THR* 1.3 67.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 3.0 27.6 + - - +
114B ALA* 2.8 24.5 - - - +
115B LYS 4.8 0.3 - - - +
116B GLU* 1.3 82.2 - - + +
----------------------------------------------------------
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