Contacts of the helix formed by residues 98 - 112 (chain A) in PDB entry 1XO8
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 TYR 98 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.8 19.7 - - + -
36A ARG* 3.7 27.6 - - + -
37A ASP* 3.2 28.9 + - - +
38A SER* 3.6 1.4 - - - +
39A VAL* 4.0 14.4 - - + -
96A VAL 3.3 2.4 + - - -
97A PRO* 1.3 71.8 - - - +
99A SER* 1.3 57.0 + - - +
101A LEU* 3.5 2.0 + - + -
102A PHE* 2.8 51.0 + + + +
149A ASP 4.4 2.1 + - - -
150A PHE* 2.6 55.7 + + + +
151A PHE* 4.2 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP 4.7 1.6 + - - -
97A PRO* 3.1 5.3 + - - +
98A TYR* 1.3 81.1 - - - +
100A ILE* 1.3 61.7 + - - +
102A PHE* 3.1 18.6 - - - +
103A ASN* 2.7 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 4.6 1.6 - - + -
70A GLU* 3.0 64.6 - - + +
71A ILE* 3.7 16.8 - - - +
72A GLY* 5.5 0.4 - - - -
96A VAL* 4.8 0.2 - - + -
97A PRO* 2.9 31.3 + - + +
99A SER* 1.3 80.7 - - - +
101A LEU* 1.3 57.3 + - - +
102A PHE 2.9 3.8 - - - -
103A ASN* 2.8 30.1 + - - +
104A LEU* 3.1 15.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 4.6 4.3 - - + -
39A VAL* 3.4 45.1 - - + -
71A ILE* 4.0 5.4 - - + -
96A VAL* 3.6 19.2 - - + +
97A PRO 3.6 1.2 + - - -
98A TYR* 3.5 7.6 + - + +
100A ILE* 1.3 78.4 - - - +
102A PHE* 1.3 55.3 + - - +
104A LEU* 3.3 29.7 - - + +
105A ALA* 2.8 44.8 + - + +
116A TYR* 3.4 17.0 - - + +
145A PRO* 3.7 26.9 - - + -
151A PHE* 4.0 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TYR* 2.8 49.9 + + - +
99A SER* 3.1 16.8 - - - +
101A LEU* 1.3 79.8 - - - +
103A ASN* 1.3 55.8 + - - +
106A ARG* 2.8 63.6 + - + +
150A PHE 4.0 8.5 - - - -
151A PHE* 4.3 13.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 3.1 31.5 + - - +
70A GLU* 5.9 1.3 + - - +
99A SER* 2.7 28.5 + - - -
100A ILE* 2.8 12.1 + - + +
102A PHE* 1.3 76.2 - - - +
104A LEU* 1.3 65.7 + - - +
106A ARG* 2.9 46.4 + - - +
107A ASP* 3.2 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 3.1 37.7 - - - +
67A ALA* 3.5 24.5 - - + +
69A ARG* 3.5 15.0 - - + +
70A GLU 3.2 19.7 - - - +
71A ILE* 3.5 10.1 - - + -
100A ILE* 3.1 22.0 - - + +
101A LEU* 3.3 28.0 - - + -
103A ASN* 1.3 76.9 - - - +
105A ALA* 1.3 65.4 + - + +
107A ASP 3.0 2.3 + - - -
108A VAL* 2.7 39.5 + - - +
114A ILE* 4.4 4.5 - - + -
116A TYR* 4.1 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 2.8 35.0 + - + +
104A LEU* 1.3 74.6 - - + +
106A ARG* 1.3 61.1 + - - +
109A GLY* 2.8 34.8 - - - +
110A VAL 3.3 0.2 + - - -
114A ILE* 4.6 5.8 - - + -
144A LEU* 4.6 11.4 - - + -
151A PHE* 3.3 36.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 5.7 0.2 - - - -
102A PHE* 2.8 45.8 + - + +
103A ASN* 2.9 49.7 + - - +
105A ALA* 1.3 79.5 - - - +
107A ASP* 1.3 60.6 + - - +
110A VAL* 3.0 33.4 + - + +
151A PHE* 4.1 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 4.2 16.9 + - - +
103A ASN 3.2 7.8 + - - +
104A LEU 3.0 5.8 + - - +
106A ARG* 1.3 82.4 - - + +
108A VAL* 1.3 73.6 + - + +
110A VAL* 2.9 30.1 - - - +
111A ASP* 3.7 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ALA* 3.5 28.0 - - + -
104A LEU 2.7 19.5 + - - +
107A ASP* 1.3 82.6 - - + +
109A GLY* 1.3 51.8 + - - +
110A VAL 3.2 1.8 - - - -
111A ASP* 2.9 15.4 - - + +
112A TRP* 2.7 29.1 + - - -
113A ASP 3.1 28.0 - - - +
114A ILE* 3.3 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU 3.7 0.4 + - - -
105A ALA* 2.8 25.0 + - - +
108A VAL* 1.3 75.1 - - - +
110A VAL* 1.3 66.6 + - - +
111A ASP 3.0 10.9 - - - +
112A TRP* 3.5 6.5 + - - +
114A ILE* 3.9 1.2 - - - +
144A LEU* 3.4 27.9 - - - +
151A PHE* 4.7 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA 3.3 0.2 + - - -
106A ARG* 3.0 23.5 + - + +
107A ASP* 2.9 20.4 - - - +
109A GLY* 1.3 75.6 - - - +
111A ASP* 1.3 64.9 + - + +
151A PHE* 4.8 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ASP 4.8 0.4 - - - +
108A VAL* 2.9 16.5 + - + +
109A GLY 3.0 4.1 - - - +
110A VAL* 1.3 88.9 - - + +
112A TRP* 1.3 99.7 + - - +
113A ASP* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A VAL 2.7 11.9 + - - -
109A GLY* 3.7 9.0 - - - +
111A ASP* 1.3 114.8 + - - +
113A ASP* 1.3 88.3 + - + -
114A ILE* 3.1 17.3 - - - +
143A LYS* 3.6 37.5 - - + -
144A LEU* 3.3 24.8 + - + +
----------------------------------------------------------
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