Contacts of the helix formed by residues 93 - 111 (chain q) 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 q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64o THR* 4.6 0.7 - - - -
92q SER* 1.3 76.9 - - - +
94q PRO* 1.3 68.1 - - - -
95q ALA 3.3 1.8 - - - -
96q LEU* 2.7 29.0 + - - +
97q VAL* 3.1 14.9 + - - +
133q VAL* 4.3 19.3 - - - +
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Residues in contact with PRO 94 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64o THR 3.3 17.3 - - - +
65o GLN* 3.4 27.1 - - + +
67o GLY* 3.8 11.2 - - - +
92q SER 4.6 0.2 - - - +
93q GLY* 1.3 84.1 - - - -
95q ALA* 1.3 63.1 + - - +
97q VAL* 3.0 13.2 + - + +
98q ASN* 2.9 25.4 + - - +
133q VAL* 4.3 8.7 - - + -
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Residues in contact with ALA 95 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64o THR* 3.3 18.8 + - + +
67o GLY* 3.6 15.7 - - - -
68o ILE 3.7 20.6 - - - +
69o THR* 3.4 13.6 - - + +
90q ILE* 3.5 24.2 - - + -
93q GLY 3.3 0.4 - - - -
94q PRO* 1.3 79.3 - - - +
96q LEU* 1.3 62.8 + - - +
98q ASN* 3.3 1.4 + - - +
99q MET* 3.0 19.8 + - - +
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Residues in contact with LEU 96 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83q VAL* 4.3 6.1 - - + +
86q ALA* 3.9 28.3 - - + -
87q LEU* 3.8 38.1 - - + +
90q ILE* 4.2 4.9 - - + +
91q GLY 3.6 12.7 + - - +
92q SER* 3.9 10.8 - - - -
93q GLY 2.7 16.3 + - - +
95q ALA* 1.3 71.9 - - - +
97q VAL* 1.3 61.8 + - + +
99q MET* 3.1 5.5 + - + +
100q ILE* 2.8 52.7 + - + +
126q THR* 4.6 12.8 - - + -
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Residues in contact with VAL 97 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93q GLY* 3.1 8.3 + - - +
94q PRO* 3.0 10.4 + - + +
96q LEU* 1.3 79.1 - - + +
98q ASN* 1.3 66.5 + - - +
100q ILE* 3.3 0.8 + - + -
101q ASN* 3.1 33.1 + - - +
130q THR* 3.4 25.3 + - - +
131q GLY* 3.6 29.4 - - - +
132q TYR 4.8 2.9 - - - +
133q VAL* 3.7 30.3 - - + -
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Residues in contact with ASN 98 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67o GLY* 3.1 35.2 + - - -
69o THR* 4.4 7.6 - - + -
94q PRO* 2.9 13.1 + - - +
95q ALA* 3.5 7.9 - - - +
97q VAL* 1.3 82.0 - - - +
99q MET* 1.3 63.5 + - - +
101q ASN* 3.5 8.8 + - - +
102q GLY 3.3 16.1 + - - -
109r SER 3.5 21.9 - - - +
110r ALA* 3.7 4.0 - - - +
112r ASN* 5.2 9.3 + - - +
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Residues in contact with MET 99 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2568 T 4.1 11.4 - - - +
69o THR* 4.6 5.6 - - + -
82q LYS* 4.7 12.6 - - - -
83q VAL* 6.3 0.7 - - - -
86q ALA* 3.8 23.3 - - + -
90q ILE* 3.7 23.6 - - + -
95q ALA 3.0 12.6 + - - +
96q LEU* 3.1 13.7 + - + +
98q ASN* 1.3 77.4 - - - +
100q ILE* 1.3 58.5 + - + +
102q GLY* 3.2 3.3 + - - -
103q LEU* 2.8 32.5 + - + +
106r TYR* 4.7 9.9 - - - -
110r ALA* 4.2 20.2 + - - +
111r PHE* 3.8 29.8 - - + -
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Residues in contact with ILE 100 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79q PHE* 5.0 2.9 - - + -
83q VAL* 4.3 18.8 - - + -
96q LEU* 2.8 45.9 + - + +
97q VAL* 3.9 3.4 - - + +
99q MET* 1.3 74.7 - - + +
101q ASN* 1.3 57.5 + - - +
103q LEU* 3.5 6.2 - - + +
104q LYS* 2.8 43.8 + - + +
122q VAL* 4.2 15.9 - - + -
126q THR* 4.1 22.7 - - + -
130q THR* 3.5 34.5 - - + +
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Residues in contact with ASN 101 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97q VAL* 3.1 34.5 + - - +
98q ASN* 3.7 10.5 + - - +
100q ILE* 1.3 77.3 - - - +
102q GLY* 1.3 61.6 + - - +
104q LYS* 3.5 8.4 + - - +
105q GLY* 3.2 17.3 + - - -
130q THR* 3.3 20.8 - - - +
131q GLY* 4.3 7.1 + - - -
109r SER* 4.2 8.5 + - - +
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Residues in contact with GLY 102 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98q ASN 3.3 4.6 + - - -
99q MET 3.2 6.7 + - - -
101q ASN* 1.3 75.3 - - - +
103q LEU* 1.3 59.1 + - - +
105q GLY* 3.1 4.3 + - - -
106q TYR 2.9 23.6 + - - -
105r GLY 5.3 0.2 - - - -
106r TYR* 3.5 19.9 - - - -
109r SER* 3.0 24.1 + - - -
110r ALA* 4.0 9.9 - - - -
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Residues in contact with LEU 103 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79q PHE* 3.6 17.5 - - + -
82q LYS* 3.5 47.1 - - + +
83q VAL* 3.6 31.2 - - + +
99q MET* 2.8 22.5 + - + +
100q ILE* 3.5 8.5 - - + +
102q GLY* 1.3 73.6 - - - +
104q LYS* 1.3 65.5 + - - +
106q TYR* 3.1 11.5 + - + +
107q TYR* 3.0 41.0 + - + -
106r TYR* 3.9 10.6 - - + -
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Residues in contact with LYS 104 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79q PHE* 3.8 28.5 - - + -
100q ILE* 2.8 35.4 + - + +
101q ASN* 3.7 7.3 + - - +
103q LEU* 1.3 72.5 - - - +
105q GLY* 1.3 58.6 + - - +
107q TYR* 3.2 1.6 + - - +
108q ILE* 2.8 53.9 + - + +
115q PRO* 5.0 5.1 - - - +
118q LEU* 4.8 5.4 - - + -
119q ASP* 2.7 37.3 + - - +
122q VAL* 5.0 2.0 - - + -
129q PRO* 6.1 0.6 - - - +
130q THR* 4.6 12.0 - - + +
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Residues in contact with GLY 105 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101q ASN 3.2 8.7 + - - -
102q GLY* 3.1 7.8 + - - -
104q LYS* 1.3 77.3 - - - +
106q TYR* 1.3 57.6 + - - +
108q ILE* 4.6 6.7 - - - -
109q SER* 2.6 36.6 + - - -
102r GLY* 4.4 3.8 - - - -
105r GLY* 5.9 2.7 - - - -
106r TYR 5.3 2.0 - - - -
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Residues in contact with TYR 106 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837 A 3.8 5.5 + - - -
847 T 2.9 17.9 + - - -
82q LYS* 5.6 3.8 - - - -
102q GLY 2.9 11.9 + - - +
103q LEU* 3.2 15.3 - - + +
105q GLY* 1.3 76.3 - - - +
107q TYR* 1.3 85.4 + + - +
110q ALA* 2.8 41.6 + - + +
111q PHE* 3.7 25.6 - + - -
82r LYS* 2.8 39.0 + - - -
99r MET* 4.6 7.4 - - - +
102r GLY 3.7 15.3 + - - -
103r LEU* 4.0 13.5 - - + -
106r TYR* 3.7 32.1 - + + -
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Residues in contact with TYR 107 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837 A 4.5 5.1 - - + +
847 T 3.3 35.1 + - - -
75q ILE* 3.5 37.9 - - + -
78q GLY* 3.5 9.5 - - - -
79q PHE* 3.7 30.7 - + + -
82q LYS* 5.2 0.9 - - + -
103q LEU* 3.0 26.2 + - + +
104q LYS 4.0 1.6 - - - +
106q TYR* 1.3 98.5 - + - +
108q ILE* 1.3 66.5 + - - +
111q PHE* 3.1 40.5 + + + -
113q ALA* 3.0 25.8 + - + +
118q LEU* 4.4 8.3 - - + -
71t PRO* 6.5 1.1 - - + -
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Residues in contact with ILE 108 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104q LYS* 2.8 44.8 + - + +
105q GLY* 4.1 5.2 - - - +
107q TYR* 1.3 72.1 - - - +
109q SER* 1.3 61.7 + - - +
112q ASN* 3.1 25.1 - - - +
113q ALA 3.6 16.1 - - - +
115q PRO* 3.9 30.5 - - + -
118q LEU* 3.3 22.2 - - + -
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Residues in contact with SER 109 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105q GLY* 2.6 21.8 + - - -
108q ILE* 1.3 84.9 - - - +
110q ALA* 1.3 60.7 + - - +
112q ASN* 4.0 10.1 - - - +
98r ASN* 3.5 16.7 - - - +
101r ASN* 4.2 5.8 + - - +
102r GLY* 2.9 22.6 - - - -
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Residues in contact with ALA 110 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106q TYR* 2.8 25.8 + - + +
109q SER* 1.3 80.2 + - - +
111q PHE* 1.3 63.7 + - + +
112q ASN* 5.1 1.8 + - - -
98r ASN* 3.6 12.4 - - - +
99r MET* 3.9 34.4 - - - +
102r GLY* 4.1 4.5 - - - -
69t THR* 2.6 34.5 + - - +
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Residues in contact with PHE 111 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837 A 3.8 24.2 - - - -
75q ILE* 4.8 12.6 - - + +
106q TYR* 3.7 34.3 - + - -
107q TYR* 3.1 46.9 + + + +
110q ALA* 1.3 80.2 - - + +
112q ASN* 1.3 75.2 + - - +
113q ALA* 3.2 2.4 + - - +
99r MET* 3.7 27.8 - - + -
69t THR* 3.4 17.3 - - - +
70t GLY* 3.5 31.6 - - - -
71t PRO* 4.6 3.4 - - + -
72t ASN* 3.3 19.6 + - - +
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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) + - + + + + + -
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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