Contacts of the helix formed by residues 93 - 111 (chain V) 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 V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92V SER* 1.3 77.4 - - - +
94V PRO* 1.3 67.4 - - - -
95V ALA 3.3 1.8 - - - -
96V LEU* 2.8 29.4 + - - +
97V VAL* 3.2 15.4 + - - +
133V VAL* 4.5 10.8 - - - -
64X THR* 4.5 1.1 - - - -
65X GLN* 5.3 2.0 - - - -
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Residues in contact with PRO 94 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93V GLY* 1.3 84.6 - - - -
95V ALA* 1.3 63.3 + - - +
97V VAL* 3.0 6.3 + - + +
98V ASN* 2.9 25.7 + - - +
133V VAL* 3.8 24.8 - - + -
64X THR* 3.3 15.7 - - + +
65X GLN* 3.4 39.3 - - - +
66X TYR 4.7 0.4 - - - -
67X GLY* 3.9 11.4 - - - +
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Residues in contact with ALA 95 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90V ILE* 3.6 22.6 - - + +
93V GLY 3.1 0.6 + - - -
94V PRO* 1.3 79.8 - - - +
96V LEU* 1.3 57.9 + - - +
98V ASN* 3.3 1.8 + - - +
99V MET* 3.0 24.6 + - - +
64X THR* 3.2 18.4 + - + +
67X GLY* 3.5 16.1 - - - -
68X ILE 3.6 22.4 - - - +
69X THR* 3.4 13.6 - - + +
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Residues in contact with LEU 96 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83V VAL* 4.5 4.0 - - + +
86V ALA* 3.8 20.0 - - + +
87V LEU* 3.6 53.4 - - + +
90V ILE* 4.0 6.0 - - + +
91V GLY 3.4 11.7 - - - +
92V SER* 3.8 12.1 - - - -
93V GLY 2.8 16.3 + - - +
95V ALA* 1.3 72.5 - - - +
97V VAL* 1.3 63.1 + - + +
99V MET* 3.1 5.7 + - + +
100V ILE* 2.8 49.2 + - + +
126V THR* 4.8 10.8 - - + -
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Residues in contact with VAL 97 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93V GLY* 3.2 9.2 + - - +
94V PRO 3.0 8.9 + - - +
96V LEU* 1.3 78.3 - - + +
98V ASN* 1.3 66.7 + - - +
100V ILE* 3.2 6.1 + - + +
101V ASN* 2.9 28.5 + - - +
130V THR* 3.5 20.7 + - - +
131V GLY 3.7 26.0 - - - +
132V TYR* 4.2 7.2 - - - +
133V VAL* 3.8 34.1 - - + +
134V SER 5.2 1.1 - - - +
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Residues in contact with ASN 98 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109U SER 3.5 22.9 - - - +
110U ALA* 3.6 3.7 - - - +
112U ASN* 5.1 9.6 - - - +
94V PRO* 2.9 13.5 + - - +
95V ALA* 3.4 8.5 - - - +
96V LEU 3.2 0.2 - - - -
97V VAL* 1.3 79.5 - - - +
99V MET* 1.3 63.9 + - - +
101V ASN* 3.5 8.7 + - - +
102V GLY 3.3 13.3 + - - -
67X GLY* 3.1 35.2 + - - -
69X THR* 4.4 7.4 - - + -
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Residues in contact with MET 99 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2157 A 4.1 13.0 - - - +
106U TYR* 4.6 13.7 - - - +
110U ALA* 3.9 20.8 + - - +
111U PHE* 3.7 30.7 - - + -
82V LYS* 5.9 2.0 - - - -
86V ALA* 3.8 24.7 - - + -
90V ILE* 3.8 22.9 - - + -
95V ALA 3.0 13.8 + - - +
96V LEU* 3.3 12.1 - - + +
98V ASN* 1.3 76.8 - - - +
100V ILE* 1.3 60.2 + - + +
102V GLY* 3.2 3.8 + - - -
103V LEU* 2.9 33.8 + - + +
69X THR* 4.7 5.4 - - + -
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Residues in contact with ILE 100 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79V PHE* 5.1 0.9 - - + -
83V VAL* 4.3 22.9 - - + -
96V LEU* 2.8 47.5 + - + +
97V VAL* 4.7 3.4 - - + -
99V MET* 1.3 74.3 - - + +
101V ASN* 1.3 57.9 + - - +
103V LEU* 4.1 6.3 - - + -
104V LYS* 2.7 33.8 + - + +
122V VAL* 4.3 20.0 - - + -
126V THR* 4.1 24.0 - - + -
130V THR* 3.6 34.5 - - + +
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Residues in contact with ASN 101 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109U SER* 4.2 8.0 + - - +
97V VAL* 2.9 22.0 + - - +
98V ASN* 3.7 10.8 + - - +
99V MET 3.2 0.2 - - - -
100V ILE* 1.3 75.8 - - - +
102V GLY* 1.3 61.9 + - - +
104V LYS* 3.8 3.4 - - - +
105V GLY* 3.2 19.2 + - - -
130V THR* 2.5 31.5 + - - +
131V GLY* 2.9 33.7 + - - -
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Residues in contact with GLY 102 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105U GLY 4.2 2.8 - - - +
106U TYR* 3.7 12.2 + - - -
109U SER* 2.9 25.2 + - - -
110U ALA* 4.1 11.0 - - - -
98V ASN 3.3 4.4 + - - -
99V MET 3.2 6.5 + - - -
101V ASN* 1.3 76.0 - - - +
103V LEU* 1.3 59.4 + - - +
105V GLY* 3.4 1.3 + - - -
106V TYR* 2.9 30.1 + - - +
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Residues in contact with LEU 103 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106U TYR* 4.0 11.9 - - + -
79V PHE* 3.7 11.2 - - + -
82V LYS* 3.5 50.9 - - + +
83V VAL* 3.7 33.7 - - + +
99V MET* 2.9 24.1 + - + +
100V ILE* 3.6 8.1 - - + +
102V GLY* 1.3 74.5 - - - +
104V LYS* 1.3 66.5 + - - +
106V TYR* 3.2 9.5 - - + +
107V TYR* 3.0 37.9 + - + -
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Residues in contact with LYS 104 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79V PHE* 3.8 18.1 - - + -
100V ILE* 2.7 22.7 + - + +
101V ASN* 3.8 4.7 - - - +
103V LEU* 1.3 73.7 - - - +
105V GLY* 1.3 64.5 + - - +
107V TYR* 3.1 4.5 + - - +
108V ILE* 3.0 48.0 + - + +
115V PRO* 4.4 12.8 - - - +
118V LEU* 4.0 13.8 - - + +
119V ASP* 2.7 39.3 + - - +
122V VAL* 6.0 1.1 - - + -
130V THR* 4.3 19.8 - - + +
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Residues in contact with GLY 105 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102U GLY* 5.0 1.1 - - - -
105U GLY* 5.9 3.6 - - - -
101V ASN 3.2 12.8 + - - -
102V GLY* 3.8 2.9 - - - -
104V LYS* 1.3 78.3 - - - +
106V TYR* 1.3 62.9 + - - +
108V ILE* 3.2 13.1 + - - +
109V SER* 3.0 28.2 + - - -
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Residues in contact with TYR 106 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248 T 4.2 0.2 + - - -
1258 A 3.3 15.9 + - - -
82U LYS* 2.7 34.4 + - - -
99U MET* 4.7 4.1 - - - -
102U GLY 3.5 26.4 + - - -
103U LEU* 4.1 14.4 - - + -
106U TYR* 3.7 25.2 - + + +
82V LYS* 5.0 6.1 - - - -
102V GLY 2.9 19.1 + - - +
103V LEU* 3.2 14.1 - - + +
105V GLY* 1.3 74.9 - - - +
107V TYR* 1.3 79.9 + + - +
110V ALA* 2.8 45.6 + - + +
111V PHE* 3.7 28.5 - + - -
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Residues in contact with TYR 107 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248 T 4.4 6.3 - - + +
1258 A 3.4 25.4 + - - -
71S PRO* 6.5 0.9 - - + -
75V ILE* 3.5 37.7 - - + -
78V GLY* 3.5 4.7 - - - -
79V PHE* 3.5 40.2 + + + -
82V LYS* 4.6 4.7 - - + -
103V LEU* 3.0 29.4 + - + +
104V LYS 3.8 6.3 - - - +
106V TYR* 1.3 96.9 - + - +
108V ILE* 1.3 65.4 + - - +
111V PHE* 3.0 46.8 + + - +
113V ALA* 3.1 22.0 + - + +
118V LEU* 4.4 2.9 - - + -
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Residues in contact with ILE 108 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104V LYS* 3.0 46.6 + - + +
105V GLY* 3.2 11.2 + - - +
107V TYR* 1.3 76.6 - - - +
109V SER* 1.3 63.1 + - - +
112V ASN* 3.0 25.5 - - - +
113V ALA* 3.4 15.6 + - - +
115V PRO* 3.9 24.9 - - + -
118V LEU* 3.3 16.6 - - + -
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Residues in contact with SER 109 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98U ASN* 3.5 18.7 - - - +
101U ASN* 4.2 7.0 + - - +
102U GLY* 3.0 27.9 - - - -
105V GLY 3.0 10.8 + - - -
108V ILE* 1.3 82.1 - - - +
110V ALA* 1.3 63.5 + - - +
111V PHE 3.4 0.4 - - - -
112V ASN* 4.0 11.2 - - - +
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Residues in contact with ALA 110 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69S THR* 2.6 33.4 + - - +
98U ASN* 3.7 13.9 - - - +
99U MET* 4.2 15.1 - - - +
102U GLY* 4.1 11.4 - - - -
106V TYR* 2.8 35.1 + - + +
109V SER* 1.3 76.3 + - - +
111V PHE* 1.3 68.6 + - + +
112V ASN* 5.2 1.1 - - - -
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Residues in contact with PHE 111 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248 T 3.6 39.0 - - - -
69S THR* 3.4 17.7 - - - +
70S GLY* 3.6 17.9 - - - -
71S PRO* 4.6 3.6 - - + -
72S ASN* 3.2 18.5 + - - +
82U LYS* 6.1 0.2 - - - -
99U MET* 3.8 24.2 - - + -
75V ILE* 4.6 13.5 - - + +
106V TYR* 3.7 37.2 - + - -
107V TYR* 3.0 45.5 + + + +
110V ALA* 1.3 80.5 - - + +
112V ASN* 1.3 74.5 + - - +
113V ALA* 3.3 1.9 + - - +
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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