Contacts of the helix formed by residues 93 - 111 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F SER* 1.3 77.4 - - - +
94F PRO* 1.3 69.0 - - - -
95F ALA 3.3 1.6 - - - -
96F LEU* 2.8 28.4 + - - +
97F VAL* 3.2 16.3 + - - +
133F VAL* 4.5 10.8 - - - -
64H THR* 4.5 0.7 - - - -
65H GLN* 5.3 2.0 - - - -
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Residues in contact with PRO 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F SER 4.6 0.2 - - - +
93F GLY* 1.3 83.4 - - - -
95F ALA* 1.3 62.3 + - - +
97F VAL* 3.0 6.8 + - - +
98F ASN* 2.9 25.5 + - - +
133F VAL* 3.8 26.4 - - + -
64H THR* 3.3 15.7 - - + +
65H GLN* 3.4 39.9 - - - +
66H TYR 4.7 0.2 - - - -
67H GLY* 3.9 10.5 - - - -
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Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F ILE* 3.6 22.9 - - + -
93F GLY 3.1 0.6 + - - -
94F PRO* 1.3 78.5 - - - +
96F LEU* 1.3 57.3 + - - +
98F ASN* 3.3 1.8 + - - +
99F MET* 3.0 24.6 + - - +
64H THR* 3.2 18.2 + - + +
67H GLY* 3.5 15.9 - - - -
68H ILE 3.6 21.8 - - - +
69H THR* 3.4 14.1 - - + +
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Residues in contact with LEU 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F VAL* 4.5 3.4 - - + +
86F ALA* 3.8 32.3 - - + +
87F LEU* 3.6 39.7 - - + +
90F ILE* 4.0 6.0 - - + +
91F GLY 3.4 11.9 - - - +
92F SER* 3.8 11.9 - - - -
93F GLY 2.8 16.5 + - - +
95F ALA* 1.3 71.1 - - - +
97F VAL* 1.3 63.5 + - + +
99F MET* 3.1 5.4 + - + +
100F ILE* 2.8 50.6 + - + +
126F THR* 4.8 10.5 - - + -
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Residues in contact with VAL 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F GLY 3.2 9.6 + - - +
94F PRO 3.0 8.8 + - - +
96F LEU* 1.3 79.5 - - + +
98F ASN* 1.3 65.5 + - - +
100F ILE* 3.2 4.7 + - + +
101F ASN* 2.9 28.3 + - - +
130F THR* 3.5 21.3 + - - +
131F GLY 3.7 27.1 - - - +
132F TYR 4.2 6.3 - - - +
133F VAL* 3.8 33.4 - - + +
134F SER 5.2 0.9 - - - +
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Residues in contact with ASN 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E SER 3.5 21.8 - - - +
110E ALA* 3.6 4.4 - - - +
112E ASN* 5.1 9.7 + - - +
94F PRO* 2.9 13.0 + - - +
95F ALA* 3.4 8.3 - - - +
97F VAL* 1.3 80.5 - - - +
99F MET* 1.3 64.2 + - - +
101F ASN* 3.5 8.8 + - - +
102F GLY 3.3 13.5 + - - -
67H GLY* 3.1 35.4 + - - -
69H THR* 4.4 7.4 - - + -
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Residues in contact with MET 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3117 A 4.1 12.6 - - - +
106E TYR* 4.6 12.8 - - - +
110E ALA* 3.9 20.6 + - - +
111E PHE* 3.7 31.6 - - + -
82F LYS* 5.9 2.5 - - - -
86F ALA* 3.8 24.0 - - + -
90F ILE* 3.8 23.1 - - + -
95F ALA 3.0 12.7 + - - +
96F LEU* 3.3 12.3 - - + +
98F ASN* 1.3 76.7 - - - +
100F ILE* 1.3 60.0 + - + +
102F GLY* 3.2 3.5 + - - -
103F LEU* 2.9 33.7 + - + +
69H THR* 4.7 6.7 - - + -
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Residues in contact with ILE 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F PHE* 5.1 1.3 - - + -
83F VAL* 4.3 22.0 - - + -
86F ALA* 6.0 0.2 - - + -
96F LEU* 2.8 47.0 + - + +
97F VAL* 3.2 4.0 + - + -
99F MET* 1.3 75.6 - - + +
101F ASN* 1.3 57.7 + - - +
103F LEU* 4.1 6.3 - - + -
104F LYS* 2.7 33.9 + - + +
122F VAL* 4.3 20.0 - - + -
126F THR* 4.1 24.2 - - + -
130F THR* 3.6 35.0 - - + +
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Residues in contact with ASN 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E SER* 4.2 7.4 + - - +
97F VAL* 2.9 23.5 + - - +
98F ASN* 3.7 10.3 + - - +
100F ILE* 1.3 76.9 - - - +
102F GLY* 1.3 60.4 + - - +
104F LYS* 3.8 3.3 - - - +
105F GLY* 3.2 18.9 + - - -
130F THR* 2.5 31.4 + - - +
131F GLY* 2.9 33.3 + - - -
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Residues in contact with GLY 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E GLY 4.2 2.8 - - - +
106E TYR* 3.7 12.0 + - - -
109E SER* 2.9 25.5 + - - -
110E ALA* 4.1 10.8 - - - -
98F ASN 3.3 4.8 + - - -
99F MET 3.2 6.0 + - - -
101F ASN* 1.3 76.8 - - - +
103F LEU* 1.3 59.7 + - - +
105F GLY* 3.4 1.7 + - - -
106F TYR* 2.9 29.8 + - - +
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Residues in contact with LEU 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E TYR* 4.0 11.3 - - + -
79F PHE* 3.7 9.6 - - + -
82F LYS* 3.5 51.1 - - + +
83F VAL* 3.7 34.5 - - + +
99F MET* 2.9 25.3 + - + +
100F ILE* 3.6 7.2 - - + +
102F GLY* 1.3 74.3 - - - +
104F LYS* 1.3 66.7 + - - +
106F TYR* 3.2 8.7 - - + +
107F TYR* 3.0 37.6 + - + -
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Residues in contact with LYS 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F PHE* 3.8 17.7 - - + -
100F ILE* 2.7 22.6 + - + +
101F ASN* 3.8 5.8 - - - +
103F LEU* 1.3 74.1 - - - +
105F GLY* 1.3 63.9 + - - +
107F TYR* 3.1 5.2 + - - +
108F ILE* 3.0 45.6 + - + +
115F PRO* 4.4 12.6 - - - +
118F LEU* 4.0 12.9 - - + +
119F ASP* 2.7 39.7 + - - +
122F VAL* 6.0 1.8 - - + -
130F THR* 4.3 18.3 - - + +
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Residues in contact with GLY 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E GLY 5.0 0.7 - - - -
105E GLY* 5.9 4.0 - - - -
101F ASN 3.2 11.7 + - - -
102F GLY* 3.8 2.2 - - - -
104F LYS* 1.3 78.1 - - - +
106F TYR* 1.3 61.8 + - - +
108F ILE* 3.2 12.5 + - - +
109F SER* 3.0 29.4 + - - -
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Residues in contact with TYR 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288 T 4.2 0.2 + - - -
298 A 3.3 16.2 + - - -
82E LYS* 2.7 33.5 + - - -
99E MET* 4.7 3.7 - - - -
102E GLY 3.5 27.5 + - - -
103E LEU* 4.1 13.9 - - + -
106E TYR* 3.7 25.7 - + + +
82F LYS* 5.0 6.3 - - - -
102F GLY 2.9 18.9 + - - +
103F LEU* 3.2 13.5 - - + +
105F GLY* 1.3 74.2 - - - +
107F TYR* 1.3 79.6 + + - +
109F SER* 3.7 0.2 + - - -
110F ALA* 2.8 46.1 + - + +
111F PHE* 3.7 28.1 - + - -
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Residues in contact with TYR 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288 T 4.4 6.4 + - + +
298 A 3.4 25.1 + - - -
71C PRO* 6.5 0.9 - - + -
75F ILE* 3.5 38.6 - - + -
78F GLY* 3.5 4.7 - - - -
79F PHE* 3.5 40.4 + + + -
82F LYS* 4.6 4.7 - - + -
103F LEU* 3.0 29.6 + - + +
104F LYS 3.8 5.6 - - - +
106F TYR* 1.3 96.9 - + - +
108F ILE* 1.3 66.4 + - - +
111F PHE* 3.0 46.5 + + - -
113F ALA* 3.1 22.1 + - + +
118F LEU* 4.4 2.9 - - + -
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Residues in contact with ILE 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F LYS* 3.0 46.5 + - + +
105F GLY* 3.2 11.0 + - - +
107F TYR* 1.3 76.0 - - - +
109F SER* 1.3 63.3 + - - +
112F ASN* 3.0 26.2 - - - +
113F ALA 3.5 15.3 - - - +
115F PRO* 3.9 24.2 - - + -
118F LEU* 3.3 16.4 - - + -
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Residues in contact with SER 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E ASN* 3.5 18.2 - - - +
101E ASN* 4.2 6.1 + - - -
102E GLY* 3.0 28.8 - - - -
105F GLY 3.0 11.7 + - - -
108F ILE* 1.3 82.6 - - - +
110F ALA* 1.3 64.1 + - - +
111F PHE 3.4 0.2 - - - -
112F ASN* 4.0 10.2 - - - +
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Residues in contact with ALA 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C THR* 2.6 34.0 + - - +
98E ASN* 3.7 13.8 - - - +
99E MET* 4.2 14.6 - - - +
102E GLY* 4.1 11.7 - - - -
106F TYR* 2.8 36.0 + - + +
109F SER* 1.3 76.9 + - - +
111F PHE* 1.3 69.8 + - + +
112F ASN* 5.2 0.7 - - - +
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Residues in contact with PHE 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288 T 3.6 38.4 - - - -
69C THR* 3.4 16.6 - - - +
70C GLY* 3.6 19.3 - - - -
71C PRO* 4.6 3.1 - - + -
72C ASN* 3.2 19.1 + - - +
82E LYS* 6.1 0.4 - - - -
99E MET* 3.8 23.8 - - + -
75F ILE* 4.6 13.0 - - + +
106F TYR* 3.7 37.9 - + - -
107F TYR* 3.0 44.4 + + + +
110F ALA* 1.3 81.4 - - + +
112F ASN* 1.3 74.9 + - - +
113F ALA* 3.2 2.3 + - - +
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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