Contacts of the helix formed by residues 93 - 111 (chain p) in PDB entry 3J9X
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 GLY 93 (chain p).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92p SER* 1.3 76.8 - - - +
94p PRO* 1.3 69.0 - - - -
95p ALA 3.3 1.8 - - - -
96p LEU* 2.8 28.5 + - - +
97p VAL* 3.2 15.7 + - - +
133p VAL* 4.5 10.5 - - - -
64r THR* 4.5 0.7 - - - -
65r GLN* 5.3 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 94 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93p GLY* 1.3 83.9 - - - -
95p ALA* 1.3 64.2 + - - +
97p VAL* 3.0 6.1 + - - +
98p ASN* 2.9 26.3 + - - +
133p VAL* 3.8 25.9 - - + -
64r THR* 3.3 15.5 - - + +
65r GLN* 3.4 40.2 - - - +
67r GLY* 3.9 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90p ILE* 3.6 22.9 - - + -
93p GLY 3.1 0.4 + - - -
94p PRO* 1.3 79.3 - - - +
96p LEU* 1.3 57.0 + - - +
98p ASN* 3.3 1.8 + - - +
99p MET* 3.0 24.4 + - - +
64r THR* 3.2 17.7 + - + +
67r GLY* 3.5 16.4 - - - -
68r ILE 3.6 21.5 - - - +
69r THR* 3.4 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83p VAL* 4.5 3.8 - - + +
86p ALA* 3.8 33.0 - - + +
87p LEU* 3.6 39.7 - - + +
90p ILE* 4.0 5.6 - - + +
91p GLY 3.4 12.8 - - - +
92p SER* 3.8 11.7 - - - -
93p GLY 2.8 16.3 + - - +
95p ALA* 1.3 70.8 - - - +
97p VAL* 1.3 63.5 + - + +
99p MET* 3.1 5.2 + - + +
100p ILE* 2.8 50.7 + - + +
126p THR* 4.8 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93p GLY* 3.2 9.2 + - - +
94p PRO 3.0 8.2 + - - +
96p LEU* 1.3 79.6 - - + +
98p ASN* 1.3 65.8 - - - +
100p ILE* 3.2 5.6 + - + -
101p ASN* 2.9 27.9 + - - +
130p THR* 3.5 20.6 + - - +
131p GLY 3.7 26.2 - - - +
132p TYR* 4.2 6.7 - - - +
133p VAL* 3.8 33.7 - - + +
134p SER 5.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 98 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109o SER 3.5 22.2 - - - +
110o ALA* 3.6 4.4 - - - +
112o ASN* 5.1 9.7 + - - +
94p PRO* 2.9 13.4 + - - +
95p ALA* 3.4 8.3 - - - +
97p VAL* 1.3 81.5 - - - +
99p MET* 1.3 65.1 + - - +
101p ASN* 3.5 8.8 + - - +
102p GLY 3.3 13.5 + - - -
67r GLY* 3.1 35.0 + - - -
69r THR* 4.4 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 99 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957 A 4.1 13.5 - - - +
106o TYR* 4.6 12.6 - - - +
110o ALA* 3.9 20.9 + - - +
111o PHE* 3.7 31.4 - - + -
82p LYS* 5.9 2.5 - - - -
86p ALA* 3.8 24.0 - - + -
90p ILE* 3.8 22.7 - - + -
95p ALA 3.0 13.0 + - - +
96p LEU* 3.3 12.6 - - + +
98p ASN* 1.3 78.0 - - - +
100p ILE* 1.3 60.7 + - + +
102p GLY* 3.2 3.1 + - - -
103p LEU* 2.9 33.3 + - + +
69r THR* 4.7 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79p PHE* 5.1 1.1 - - + -
83p VAL* 4.3 22.4 - - + -
96p LEU* 2.8 47.7 + - + +
97p VAL* 4.7 3.4 - - + -
99p MET* 1.3 74.9 - - + +
101p ASN* 1.3 57.9 + - - +
103p LEU* 4.1 6.1 - - + -
104p LYS* 2.7 34.2 + - + +
122p VAL* 4.3 20.0 - - + -
126p THR* 4.1 23.8 - - + -
130p THR* 3.6 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109o SER* 4.2 7.6 + - - +
97p VAL* 2.9 22.4 + - - +
98p ASN* 3.7 10.1 + - - +
100p ILE* 1.3 76.3 - - - +
102p GLY* 1.3 59.8 + - - +
104p LYS* 3.8 3.0 - - - +
105p GLY* 3.2 19.2 + - - -
130p THR* 2.5 32.1 + - - +
131p GLY* 2.9 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105o GLY 4.2 2.1 - - - +
106o TYR* 3.7 12.2 + - - -
109o SER* 2.9 25.5 + - - -
110o ALA* 4.1 10.8 - - - -
98p ASN 3.3 4.4 + - - -
99p MET 3.2 5.8 + - - -
101p ASN* 1.3 77.2 - - - +
103p LEU* 1.3 59.3 + - - +
105p GLY* 3.4 1.7 + - - -
106p TYR* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106o TYR* 4.0 11.1 - - + -
79p PHE* 3.7 10.8 - - + -
82p LYS* 3.5 50.9 - - + -
83p VAL* 3.7 34.1 - - + +
99p MET* 2.9 25.9 + - + +
100p ILE* 3.6 7.6 - - + +
102p GLY* 1.3 74.5 - - - +
104p LYS* 1.3 65.5 + - - +
106p TYR* 3.2 9.0 - - + +
107p TYR* 3.0 38.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79p PHE* 3.8 18.1 - - + -
100p ILE* 2.7 22.9 + - + +
101p ASN* 3.8 4.9 - - - +
103p LEU* 1.3 74.3 - - - +
105p GLY* 1.3 63.7 + - - +
107p TYR* 3.1 4.9 + - - +
108p ILE* 3.0 46.5 + - + +
115p PRO* 4.4 12.8 - - - +
118p LEU* 4.0 13.0 - - + +
119p ASP* 2.7 38.9 + - - +
122p VAL* 6.0 1.6 - - + -
130p THR* 4.3 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102o GLY 5.0 0.7 - - - -
105o GLY* 5.9 3.4 - - - -
106o TYR 5.7 0.2 - - - -
101p ASN 3.2 11.9 + - - -
102p GLY* 3.8 2.5 - - - -
104p LYS* 1.3 78.1 - - - +
106p TYR* 1.3 62.7 + - - +
108p ILE* 3.2 12.3 + - - +
109p SER* 3.0 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2448 T 4.2 0.2 + - - -
2458 A 3.3 15.6 + - - -
82o LYS* 2.7 34.8 + - - -
99o MET* 4.7 3.7 - - - -
102o GLY 3.5 27.5 + - - -
103o LEU* 4.1 13.9 - - + -
106o TYR* 3.7 26.6 - + + +
82p LYS* 5.0 6.7 - - - -
102p GLY 2.9 18.2 + - - +
103p LEU* 3.2 13.9 - - + +
105p GLY* 1.3 74.9 - - - +
107p TYR* 1.3 79.8 + + - +
110p ALA* 2.8 46.1 + - + +
111p PHE* 3.7 27.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2448 T 4.4 6.4 + - + +
2458 A 3.4 25.1 + - - -
71m PRO* 6.5 1.1 - - + -
75p ILE* 3.5 36.8 - - + -
78p GLY* 3.5 4.3 - - - -
79p PHE* 3.5 39.4 + + + -
82p LYS* 4.6 4.3 - - + -
103p LEU* 3.0 30.2 + - + +
104p LYS 3.8 6.1 - - - +
106p TYR* 1.3 96.1 - + - +
108p ILE* 1.3 66.0 + - - +
111p PHE* 3.0 47.0 + + - -
113p ALA* 3.1 22.7 + - + +
118p LEU* 4.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104p LYS* 3.0 46.5 + - + +
105p GLY* 3.2 11.0 + - - +
107p TYR* 1.3 74.8 - - - +
109p SER* 1.3 62.5 + - - +
112p ASN* 3.0 26.2 - - - +
113p ALA 3.5 16.6 - - - +
115p PRO* 3.9 24.0 - - + -
118p LEU* 3.3 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 109 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98o ASN* 3.5 18.4 - - - +
101o ASN* 4.2 6.5 + - - -
102o GLY* 3.0 28.2 - - - -
105p GLY 3.0 11.2 + - - -
108p ILE* 1.3 80.3 - - - +
110p ALA* 1.3 64.5 + - - +
111p PHE 3.4 0.2 - - - -
112p ASN* 4.0 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69m THR* 2.6 33.6 + - - +
98o ASN* 3.7 13.4 - - - +
99o MET* 4.2 15.2 - - - +
102o GLY* 4.1 11.4 - - - -
106p TYR* 2.8 36.4 + - + +
109p SER* 1.3 76.7 + - - +
111p PHE* 1.3 70.2 + - + +
112p ASN* 5.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 111 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2448 T 3.6 38.6 - - - -
69m THR* 3.4 17.5 - - - +
70m GLY* 3.6 19.5 - - - -
71m PRO* 4.6 3.1 - - + -
72m ASN* 3.2 18.6 + - - +
82o LYS* 6.1 0.2 - - - -
99o MET* 3.8 23.1 - - + -
75p ILE* 4.6 13.2 - - + +
106p TYR* 3.7 37.7 - + - -
107p TYR* 3.0 45.5 + + + +
110p ALA* 1.3 81.6 - - + +
112p ASN* 1.3 74.9 + - - +
113p ALA* 3.2 2.4 + - - +
----------------------------------------------------------
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