Contacts of the helix formed by residues 93 - 111 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92J SER* 1.3 76.5 - - - +
94J PRO* 1.3 68.2 - - - -
95J ALA 3.3 1.6 - - - -
96J LEU* 2.8 28.7 + - - +
97J VAL* 3.2 15.9 + - - +
133J VAL* 4.5 11.0 - - - -
64L THR* 4.5 0.9 - - - -
65L GLN* 5.3 2.2 - - - -
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Residues in contact with PRO 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J GLY* 1.3 83.8 - - - -
95J ALA* 1.3 63.6 + - - +
97J VAL* 3.0 6.6 + - - +
98J ASN* 2.9 26.5 + - - +
133J VAL* 3.8 26.2 - - + -
64L THR* 3.3 15.5 - - + +
65L GLN* 3.4 39.5 - - - +
66L TYR 4.7 0.4 - - - -
67L GLY* 3.9 11.4 - - - +
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Residues in contact with ALA 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J ILE* 3.6 22.4 - - + -
93J GLY 3.1 0.6 + - - -
94J PRO* 1.3 79.7 - - - +
96J LEU* 1.3 56.8 + - - +
98J ASN* 3.3 1.6 + - - +
99J MET* 3.0 24.3 + - - +
64L THR* 3.2 18.6 + - + +
67L GLY* 3.5 15.9 - - - -
68L ILE 3.6 21.5 - - - +
69L THR* 3.4 14.6 - - + +
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Residues in contact with LEU 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J VAL* 4.5 3.6 - - + +
86J ALA* 3.8 32.8 - - + +
87J LEU* 3.6 40.2 - - + +
90J ILE* 4.0 5.8 - - + +
91J GLY 3.4 12.8 - - - +
92J SER* 3.8 11.7 - - - -
93J GLY 2.8 16.0 + - - +
95J ALA* 1.3 71.1 - - - +
97J VAL* 1.3 63.0 + - + +
99J MET* 3.1 6.3 + - + +
100J ILE* 2.8 50.7 + - + +
126J THR* 4.8 10.5 - - + -
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Residues in contact with VAL 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J GLY* 3.2 9.2 + - - +
94J PRO 3.0 8.0 + - - +
96J LEU* 1.3 79.5 - - + +
98J ASN* 1.3 65.5 + - - +
100J ILE* 3.2 5.7 + - + -
101J ASN* 2.9 28.6 + - - +
130J THR* 3.5 20.8 + - - +
131J GLY 3.7 26.0 - - - +
132J TYR* 4.2 8.1 - - - +
133J VAL* 3.8 33.4 - - + +
134J SER 5.2 0.9 - - - +
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Residues in contact with ASN 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I SER 3.5 22.0 - - - +
110I ALA* 3.6 4.5 - - - +
112I ASN* 5.1 9.1 - - - +
94J PRO* 2.9 12.7 + - - +
95J ALA* 3.4 8.5 - - - +
97J VAL* 1.3 81.1 - - - +
99J MET* 1.3 64.5 + - - +
101J ASN* 3.5 8.6 + - - +
102J GLY 3.3 14.0 + - - -
67L GLY* 3.1 35.0 + - - -
69L THR* 4.4 7.0 - - + -
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Residues in contact with MET 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2877 A 4.1 13.2 - - - +
106I TYR* 4.6 13.0 - - - +
110I ALA* 3.9 20.1 + - - +
111I PHE* 3.7 30.7 - - + -
82J LYS* 5.9 2.0 - - - -
86J ALA* 3.8 24.7 - - + -
90J ILE* 3.8 22.9 - - + -
95J ALA 3.0 13.8 + - - +
96J LEU* 3.3 12.1 - - + +
98J ASN* 1.3 76.8 - - - +
100J ILE* 1.3 60.4 + - + +
102J GLY* 3.2 3.5 + - - -
103J LEU* 2.9 33.9 + - + +
69L THR* 4.7 5.4 - - + -
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Residues in contact with ILE 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J PHE* 5.1 0.9 - - + -
83J VAL* 4.3 21.8 - - + -
96J LEU* 2.8 48.1 + - + +
97J VAL* 4.7 2.9 - - + -
99J MET* 1.3 75.4 - - + +
101J ASN* 1.3 58.4 + - - +
103J LEU* 4.1 6.3 - - + -
104J LYS* 2.7 34.0 + - + +
122J VAL* 4.3 20.4 - - + -
126J THR* 4.1 23.8 - - + -
130J THR* 3.6 34.5 - - + +
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Residues in contact with ASN 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I SER* 4.2 8.0 + - - +
97J VAL* 2.9 23.4 + - - +
98J ASN* 3.7 10.3 + - - +
99J MET 3.2 0.2 - - - -
100J ILE* 1.3 75.8 - - - +
102J GLY* 1.3 61.3 + - - +
104J LYS* 3.8 3.3 - - - +
105J GLY* 3.2 19.2 + - - -
130J THR* 2.5 31.9 + - - +
131J GLY* 2.9 32.7 + - - -
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Residues in contact with GLY 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I GLY 4.2 3.0 - - - +
106I TYR* 3.7 11.6 + - - -
109I SER* 2.9 25.2 + - - -
110I ALA* 4.1 10.8 - - - -
98J ASN 3.3 4.6 + - - -
99J MET 3.2 6.0 + - - -
101J ASN* 1.3 77.0 - - - +
103J LEU* 1.3 60.5 + - - +
105J GLY* 3.4 1.7 + - - -
106J TYR* 2.9 30.0 + - - +
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Residues in contact with LEU 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I TYR* 4.0 11.7 - - + -
79J PHE* 3.7 10.8 - - + -
82J LYS* 3.5 50.5 - - + +
83J VAL* 3.7 34.5 - - + +
99J MET* 2.9 24.7 + - + +
100J ILE* 3.6 7.2 - - + +
102J GLY* 1.3 74.9 - - - +
104J LYS* 1.3 65.6 + - - +
106J TYR* 3.2 9.2 - - + +
107J TYR* 3.0 38.4 + - + -
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Residues in contact with LYS 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J PHE* 3.8 17.7 - - + -
100J ILE* 2.7 24.2 + - + +
101J ASN* 3.8 4.0 - - - +
103J LEU* 1.3 73.7 - - - +
105J GLY* 1.3 63.8 + - - +
107J TYR* 3.1 4.9 + - - +
108J ILE* 3.0 46.3 + - + +
115J PRO* 4.4 12.8 - - - +
118J LEU* 4.0 13.4 - - + +
119J ASP* 2.7 39.5 + - - +
122J VAL* 6.0 1.8 - - + -
130J THR* 4.3 19.1 - - + +
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Residues in contact with GLY 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I GLY 5.0 0.7 - - - -
105I GLY* 5.9 3.6 - - - -
106I TYR 5.7 0.2 - - - -
101J ASN 3.2 11.7 + - - -
102J GLY* 3.8 2.7 - - - -
104J LYS* 1.3 78.4 - - - +
106J TYR* 1.3 61.8 + - - +
108J ILE* 3.2 12.7 + - - +
109J SER* 3.0 29.2 + - - -
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Residues in contact with TYR 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528 T 4.2 0.2 + - - -
538 A 3.3 15.9 + - - -
82I LYS* 2.7 35.1 + - - -
99I MET* 4.7 4.1 - - - -
102I GLY 3.5 27.3 + - - -
103I LEU* 4.1 13.7 - - + -
106I TYR* 3.7 26.1 - + + +
82J LYS* 5.0 7.0 - - + -
102J GLY 2.9 18.0 + - - +
103J LEU* 3.2 13.7 - - + +
105J GLY* 1.3 74.9 - - - +
107J TYR* 1.3 81.2 + + - +
109J SER* 3.7 0.2 + - - -
110J ALA* 2.8 45.3 + - + +
111J PHE* 3.7 28.5 - + - -
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Residues in contact with TYR 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528 T 4.4 7.1 + - + +
538 A 3.4 25.3 + - - -
71G PRO* 6.5 1.3 - - + -
75J ILE* 3.5 37.0 - - + -
78J GLY* 3.5 5.0 - - - -
79J PHE* 3.5 39.4 + + + -
82J LYS* 4.6 4.5 - - + -
103J LEU* 3.0 30.0 + - + +
104J LYS 3.8 5.4 - - - +
106J TYR* 1.3 95.8 - + - +
108J ILE* 1.3 67.1 + - - +
111J PHE* 3.0 44.2 + + - -
113J ALA* 3.1 22.9 + - + +
118J LEU* 4.4 2.2 - - + -
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Residues in contact with ILE 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104J LYS* 3.0 45.9 + - + +
105J GLY* 3.2 10.7 + - - +
107J TYR* 1.3 76.0 - - - +
109J SER* 1.3 62.7 + - - +
112J ASN* 3.0 26.3 - - - +
113J ALA 3.5 16.3 - - - +
115J PRO* 3.9 24.2 - - + -
118J LEU* 3.3 16.4 - - + -
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Residues in contact with SER 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98I ASN* 3.5 18.1 - - - +
101I ASN* 4.2 6.6 + - - -
102I GLY* 3.0 28.9 - - - -
105J GLY 3.0 11.7 + - - -
108J ILE* 1.3 81.2 - - - +
110J ALA* 1.3 63.7 + - - +
111J PHE 3.4 0.2 - - - -
112J ASN* 4.0 10.4 - - - +
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Residues in contact with ALA 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G THR* 2.6 33.8 + - - +
98I ASN* 3.7 14.4 - - - +
99I MET* 4.2 15.4 - - - +
102I GLY* 4.1 10.8 - - - -
106J TYR* 2.8 36.2 + - + +
109J SER* 1.3 76.6 + - - +
111J PHE* 1.3 68.8 + - + +
112J ASN* 3.6 1.1 - - - -
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Residues in contact with PHE 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528 T 3.6 38.8 - - - -
69G THR* 3.4 16.8 - - - +
70G GLY* 3.6 19.1 - - - -
71G PRO* 4.6 3.8 - - + -
72G ASN* 3.2 18.9 + - - +
82I LYS* 6.1 0.2 - - - -
99I MET* 3.8 23.6 - - + -
75J ILE* 4.6 13.3 - - + +
106J TYR* 3.7 37.0 - + - -
107J TYR* 3.0 44.8 + + + +
110J ALA* 1.3 81.1 - - + +
112J ASN* 1.3 74.6 + - - +
113J ALA* 3.2 2.0 + - - +
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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