Contacts of the helix formed by residues 96 - 106 (chain A) in PDB entry 6JOD
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 96 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU 4.0 4.5 - - - +
93A LEU* 2.5 21.2 + - - -
95A ALA* 1.3 79.0 - - + +
97A LEU* 1.3 62.7 + - - +
98A PRO* 3.3 2.0 - - - -
99A LEU* 3.1 24.4 + - + +
100A TRP* 3.1 26.2 + - - -
120A PHE* 4.3 26.0 - - + +
123A PHE* 3.8 28.9 - - + -
124A LEU* 3.1 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 3.9 25.7 - - + +
54A ILE* 3.8 13.2 - - + -
55A PHE* 3.7 35.7 - - + +
93A LEU 4.9 0.7 - - - +
94A LEU* 3.0 40.2 + - + +
96A THR* 1.3 78.3 + - - +
98A PRO* 1.3 66.4 - - + +
100A TRP* 3.2 10.3 + - + +
101A ALA* 2.9 23.4 + - - +
305A LEU* 5.2 1.1 - - + -
308A PHE* 3.7 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 4.1 28.9 - - + +
55A PHE* 3.5 41.7 - - + -
95A ALA 3.3 17.9 - - - +
96A THR 3.5 0.7 - - - -
97A LEU* 1.3 88.7 - - + +
99A LEU* 1.3 59.5 + - + +
101A ALA* 3.3 1.6 + - - +
102A THR* 2.9 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ALA 5.1 2.2 - - - +
96A THR* 3.1 23.9 + - + +
98A PRO* 1.3 79.5 - - + +
100A TRP* 1.3 63.9 + - + +
102A THR* 3.4 6.8 + - - -
103A TYR* 2.9 27.2 + - - +
110A TRP* 4.6 7.2 - - + -
112A PHE* 3.9 38.0 - - + -
120A PHE* 3.5 52.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 3.5 21.8 - + + -
96A THR* 3.1 27.7 + - - -
97A LEU* 3.2 17.8 + - + +
99A LEU* 1.3 76.0 - - + +
101A ALA* 1.3 61.3 + - - +
103A TYR* 3.2 11.8 + + + +
104A TYR* 2.9 38.8 + - + -
110A TRP* 3.7 30.5 - + - -
120A PHE* 3.5 45.1 - - + -
121A GLY* 4.0 8.1 - - - -
124A LEU* 3.3 39.3 - - + +
182A ARG* 5.9 0.4 - - - -
195A CYS* 4.7 10.8 - - - -
308A PHE* 4.6 1.8 - + - -
7B PRO* 3.5 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO* 3.2 26.1 - - + +
51A TYR* 3.6 10.5 - - + -
52A TYR* 3.4 36.1 - - + -
97A LEU 2.9 16.1 + - - +
98A PRO 3.6 0.4 - - - +
99A LEU 3.3 0.2 - - - -
100A TRP* 1.3 74.9 - - - +
102A THR* 1.3 55.4 + - - +
104A TYR* 3.5 1.0 + - - -
105A SER* 2.4 38.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 4.6 8.5 + - - -
98A PRO 2.9 18.2 + - - -
99A LEU* 3.6 5.4 - - - -
101A ALA* 1.3 75.0 - - - +
103A TYR* 1.3 65.2 + - - +
105A SER* 3.1 7.7 + - - -
106A TYR* 3.0 49.2 + - + -
111A LEU* 4.4 3.6 - - + -
112A PHE* 4.0 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU 2.9 17.9 + - - +
100A TRP* 3.2 17.0 + + + +
102A THR* 1.3 79.0 - - - +
104A TYR* 1.3 75.9 + + - +
106A TYR* 3.7 1.6 + - - -
107A ARG 3.4 3.6 + - - -
108A TYR* 3.0 69.4 + + - -
109A ASP 4.4 4.7 + - - -
110A TRP* 3.4 38.6 - + + -
112A PHE* 5.5 1.8 - - + -
194A ALA* 3.8 1.7 - - - +
195A CYS* 3.4 28.2 + - + -
5B ILE* 2.9 45.7 + - - +
6B HIS 5.5 0.2 - - - -
7B PRO* 5.0 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 4.1 26.2 - - + +
47A ILE* 3.6 35.7 - - + -
48A PRO* 4.5 4.7 - - + -
51A TYR* 3.8 18.1 + + - -
100A TRP* 2.9 29.9 + - + +
101A ALA* 4.1 3.8 - - - +
103A TYR* 1.3 83.1 - + - +
105A SER* 1.3 65.0 + - - +
107A ARG* 3.4 16.7 + - - +
108A TYR* 3.9 24.7 - + - +
301A PRO* 3.4 34.7 - - + +
304A ILE* 4.1 0.9 - - - +
6B HIS* 3.1 23.1 + - - +
7B PRO* 3.3 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU 5.5 0.4 - - - -
48A PRO* 3.1 21.3 - - - +
101A ALA 2.4 27.8 + - - -
102A THR* 3.1 10.2 + - - -
104A TYR* 1.3 77.1 - - - +
106A TYR* 1.3 62.6 + - - +
107A ARG* 3.1 13.4 + - - +
28H THR* 5.5 3.3 - - - +
30H SER 3.3 13.1 - - - +
31H GLY* 4.0 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A THR* 3.0 30.7 + - + +
103A TYR 3.7 0.6 + - - +
105A SER* 1.3 76.4 - - - +
107A ARG* 1.3 70.8 + - - +
108A TYR 3.4 1.3 - - - -
109A ASP* 3.3 21.0 + - + +
111A LEU* 3.4 43.5 - - + +
30H SER* 3.0 43.0 - - - -
31H GLY* 4.4 0.9 - - - -
53H SER* 2.8 31.4 + - - +
54H GLY* 4.7 3.4 - - - -
74H ASN* 4.4 17.9 + - - +
----------------------------------------------------------
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