Contacts of the helix formed by residues 93 - 111 (chain Z) 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 Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Z SER* 1.3 76.8 + - - +
94Z PRO* 1.3 67.5 - - - -
95Z ALA 3.3 1.8 - - - -
96Z LEU* 2.8 29.1 + - - +
97Z VAL* 3.2 16.5 + - - +
133Z VAL* 4.5 10.5 - - - -
64b THR* 4.5 0.7 - - - -
65b GLN* 5.3 2.2 - - - -
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Residues in contact with PRO 94 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93Z GLY* 1.3 82.9 - - - -
95Z ALA* 1.3 63.4 + - - +
97Z VAL* 3.0 5.5 + - - +
98Z ASN* 2.9 26.3 + - - +
133Z VAL* 3.8 25.7 - - + -
64b THR* 3.3 15.5 - - + +
65b GLN* 3.4 39.0 - - - +
66b TYR 4.7 0.4 - - - -
67b GLY* 3.9 10.8 - - - -
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Residues in contact with ALA 95 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90Z ILE* 3.6 22.2 - - + -
93Z GLY 3.1 0.4 + - - -
94Z PRO* 1.3 80.2 - - - +
96Z LEU* 1.3 57.4 + - - +
98Z ASN* 3.3 1.6 + - - +
99Z MET* 3.0 24.6 + - - +
64b THR* 3.2 19.6 + - + +
67b GLY* 3.5 15.9 - - - -
68b ILE 3.6 22.0 - - - +
69b THR* 3.4 13.2 - - + +
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Residues in contact with LEU 96 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83Z VAL* 4.5 3.8 - - + +
86Z ALA* 3.8 31.9 - - + +
87Z LEU* 3.6 40.2 - - + +
90Z ILE* 4.0 6.4 - - + +
91Z GLY 3.4 11.4 - - - +
92Z SER* 3.8 11.7 - - - -
93Z GLY 2.8 16.0 + - - +
95Z ALA* 1.3 71.2 - - - +
97Z VAL* 1.3 62.8 + - + +
99Z MET* 3.1 5.4 + - + +
100Z ILE* 2.8 50.0 + - + +
126Z THR* 4.8 10.8 - - + -
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Residues in contact with VAL 97 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93Z GLY* 3.9 9.0 - - - +
94Z PRO 3.0 8.2 + - - +
96Z LEU* 1.3 79.3 - - + +
98Z ASN* 1.3 65.2 + - - +
100Z ILE* 3.2 4.9 + - + -
101Z ASN* 2.9 27.9 + - - +
130Z THR* 3.5 21.5 + - - +
131Z GLY 3.7 26.5 - - - +
132Z TYR 4.2 7.2 - - - +
133Z VAL* 3.8 34.3 - - + +
134Z SER 5.2 0.7 - - - +
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Residues in contact with ASN 98 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109Y SER 3.5 22.7 - - - +
110Y ALA* 3.6 3.6 - - - +
112Y ASN* 5.1 9.5 - - - +
94Z PRO* 2.9 14.1 + - - +
95Z ALA* 3.4 7.9 - - - +
96Z LEU 3.2 0.2 - - - -
97Z VAL* 1.3 79.1 - - - +
99Z MET* 1.3 64.7 + - - +
101Z ASN* 3.5 9.2 + - - +
102Z GLY 3.3 13.7 + - - -
67b GLY* 3.1 34.8 + - - -
69b THR* 4.4 8.1 - - + -
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Residues in contact with MET 99 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1917 A 4.1 12.3 - - - +
106Y TYR* 4.6 13.2 - - - +
110Y ALA* 3.9 21.2 + - - +
111Y PHE* 3.7 31.4 - - + -
82Z LYS* 5.9 2.0 - - - -
86Z ALA* 3.8 24.7 - - + -
90Z ILE* 3.8 23.1 - - + -
95Z ALA 3.0 13.0 + - - +
96Z LEU* 3.1 12.1 + - + +
98Z ASN* 1.3 76.8 - - - +
100Z ILE* 1.3 60.8 + - + +
102Z GLY* 3.2 3.3 + - - -
103Z LEU* 2.9 34.5 + - + +
69b THR* 4.7 4.9 - - + -
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Residues in contact with ILE 100 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Z PHE* 5.1 1.3 - - + -
83Z VAL* 4.3 22.4 - - + -
86Z ALA* 6.0 0.2 - - + -
96Z LEU* 2.8 47.3 + - + +
97Z VAL* 3.2 3.8 + - + -
99Z MET* 1.3 74.0 - - + +
101Z ASN* 1.3 58.0 + - - +
103Z LEU* 3.6 7.1 - - + +
104Z LYS* 2.7 34.0 + - + +
122Z VAL* 4.3 19.7 - - + -
126Z THR* 4.1 23.8 - - + -
130Z THR* 3.6 35.2 - - + +
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Residues in contact with ASN 101 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109Y SER* 4.2 8.2 + - - +
97Z VAL* 2.9 22.7 + - - +
98Z ASN* 3.7 10.6 + - - +
99Z MET 3.2 0.2 - - - -
100Z ILE* 1.3 76.1 - - - +
102Z GLY* 1.3 61.5 + - - +
104Z LYS* 3.8 3.5 - - - +
105Z GLY* 3.2 19.2 + - - -
130Z THR* 2.5 30.8 + - - +
131Z GLY* 2.9 34.0 + - - -
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Residues in contact with GLY 102 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105Y GLY 4.2 3.0 - - - +
106Y TYR* 3.7 12.2 + - - -
109Y SER* 2.9 25.0 + - - -
110Y ALA* 4.1 10.5 - - - -
98Z ASN 3.3 4.6 + - - -
99Z MET 3.2 6.4 + - - -
101Z ASN* 1.3 76.0 - - - +
103Z LEU* 1.3 60.1 + - - +
105Z GLY* 3.4 1.3 + - - -
106Z TYR* 2.9 29.6 + - - +
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Residues in contact with LEU 103 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106Y TYR* 4.0 12.2 - - + -
79Z PHE* 3.7 10.3 - - + -
82Z LYS* 3.5 52.3 - - + +
83Z VAL* 3.7 35.2 - - + +
99Z MET* 2.9 23.6 + - + +
100Z ILE* 3.6 7.6 - - - +
102Z GLY* 1.3 74.1 - - - +
104Z LYS* 1.3 67.0 + - - +
106Z TYR* 3.2 8.8 - - + +
107Z TYR* 3.0 37.5 + - + -
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Residues in contact with LYS 104 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Z PHE* 3.8 17.9 - - + -
100Z ILE* 2.7 23.7 + - + +
101Z ASN* 3.8 4.3 - - - +
103Z LEU* 1.3 74.1 - - - +
105Z GLY* 1.3 62.9 + - - +
107Z TYR* 3.1 5.0 + - - +
108Z ILE* 3.0 46.8 + - + +
115Z PRO* 4.4 12.8 - - - +
118Z LEU* 4.0 12.7 - - + +
119Z ASP* 2.7 40.0 + - - +
122Z VAL* 6.0 1.6 - - + -
130Z THR* 4.3 18.7 - - + +
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Residues in contact with GLY 105 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Y GLY 5.0 0.9 - - - -
105Y GLY* 5.9 3.4 - - - -
106Y TYR 5.7 0.2 - - - -
101Z ASN 3.2 12.7 + - - -
102Z GLY* 3.8 2.0 - - - -
104Z LYS* 1.3 77.9 - - - +
106Z TYR* 1.3 62.8 + - - +
108Z ILE* 3.2 12.6 + - - +
109Z SER* 3.0 28.0 + - - -
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Residues in contact with TYR 106 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1498 A 3.3 15.9 + - - -
82Y LYS* 2.7 34.4 + - - -
99Y MET* 4.7 3.7 - - - -
102Y GLY 3.5 26.8 + - - -
103Y LEU* 4.1 14.8 - - + -
106Y TYR* 3.7 25.5 - + + +
82Z LYS* 5.0 5.4 - - - -
102Z GLY 2.9 19.0 + - - +
103Z LEU* 3.2 13.9 - - + +
105Z GLY* 1.3 74.5 - - - +
107Z TYR* 1.3 80.5 + + - +
109Z SER* 3.7 0.3 + - - -
110Z ALA* 2.8 44.7 + - + +
111Z PHE* 3.7 29.0 - + - -
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Residues in contact with TYR 107 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1488 T 4.4 6.1 - - + +
1498 A 3.4 25.4 + - - -
71W PRO* 6.5 0.9 - - + -
75Z ILE* 3.5 37.7 - - + -
78Z GLY* 3.5 5.0 - - - -
79Z PHE* 3.5 40.4 + + + -
82Z LYS* 4.6 4.9 - - + -
103Z LEU* 3.0 28.8 + - + +
104Z LYS 3.1 6.3 + - - +
106Z TYR* 1.3 95.8 - + - +
108Z ILE* 1.3 66.7 + - - +
111Z PHE* 3.0 44.5 + + - -
113Z ALA* 3.1 22.5 + - + +
118Z LEU* 4.4 2.9 - - + -
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Residues in contact with ILE 108 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Z LYS* 3.0 47.3 + - + +
105Z GLY* 3.2 11.2 + - - +
107Z TYR* 1.3 76.0 - - - +
109Z SER* 1.3 61.4 + - - +
112Z ASN* 3.0 26.2 - - - +
113Z ALA 3.4 15.9 + - - +
115Z PRO* 3.9 24.9 - - + -
118Z LEU* 3.3 16.2 - - + -
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Residues in contact with SER 109 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98Y ASN* 3.5 18.4 - - - +
101Y ASN* 4.2 6.8 + - - -
102Y GLY* 3.0 28.2 + - - -
105Z GLY 3.0 11.1 + - - -
108Z ILE* 1.3 82.6 - - - +
110Z ALA* 1.3 64.1 + - - +
111Z PHE 3.4 0.2 - - - -
112Z ASN* 4.0 11.0 - - - +
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Residues in contact with ALA 110 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69W THR* 2.6 33.3 + - - +
98Y ASN* 3.7 14.6 - - - +
99Y MET* 4.2 15.2 - - - +
102Y GLY* 4.1 11.7 - - - -
106Z TYR* 2.8 36.8 + - + +
109Z SER* 1.3 76.3 + - - +
111Z PHE* 1.3 68.8 + - + +
112Z ASN* 3.6 1.3 - - - +
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Residues in contact with PHE 111 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1488 T 3.6 38.1 - - - -
69W THR* 3.4 17.5 - - - +
70W GLY* 3.6 19.1 - - - -
71W PRO* 4.6 3.1 - - + -
72W ASN* 3.2 18.3 + - - +
99Y MET* 3.8 24.2 - - + -
75Z ILE* 4.6 13.9 - - + +
106Z TYR* 3.7 37.7 - + - -
107Z TYR* 3.0 44.2 + + + +
110Z ALA* 1.3 80.7 - - + +
112Z ASN* 1.3 74.7 + - - +
113Z ALA* 3.2 2.4 + - - +
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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