Contacts of the helix formed by residues 93 - 111 (chain w) 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 w).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64u THR 4.6 0.2 - - - -
92w SER* 1.3 78.2 + - - +
94w PRO* 1.3 68.9 - - - -
95w ALA 3.3 1.8 - - - -
96w LEU* 2.7 29.6 + - - +
97w VAL* 3.1 14.2 + - - +
133w VAL* 4.3 17.9 - - - +
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Residues in contact with PRO 94 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64u THR* 3.3 17.5 - - + +
65u GLN* 3.4 27.8 - - + +
66u TYR 4.6 0.2 - - - -
67u GLY* 3.8 11.4 - - - +
92w SER 4.6 0.4 - - - +
93w GLY* 1.3 84.2 - - - -
95w ALA* 1.3 62.1 + - - +
97w VAL* 3.0 12.6 + - + +
98w ASN* 2.9 24.6 + - - +
133w VAL* 4.3 9.1 - - + -
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Residues in contact with ALA 95 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64u THR* 3.3 18.8 + - + +
67u GLY* 3.5 15.0 - - - -
68u ILE 3.7 21.1 - - - +
69u THR* 3.4 14.1 - - + +
90w ILE* 3.5 24.5 - - + -
93w GLY 3.1 0.8 + - - -
94w PRO* 1.3 79.8 - - - +
96w LEU* 1.3 62.3 + - - +
98w ASN* 3.3 1.7 + - - +
99w MET* 3.0 19.1 + - - +
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Residues in contact with LEU 96 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83w VAL* 4.3 6.1 - - + +
86w ALA* 3.9 29.2 - - + -
87w LEU* 3.8 36.3 - - + +
90w ILE* 4.2 5.1 - - + +
91w GLY 3.6 11.9 - - - +
92w SER* 3.9 11.4 - - - -
93w GLY 2.7 16.3 + - - +
95w ALA* 1.3 72.2 - - - +
97w VAL* 1.3 64.3 + - + +
99w MET* 3.1 5.1 + - + +
100w ILE* 2.8 52.1 + - + +
126w THR* 4.6 13.2 - - + -
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Residues in contact with VAL 97 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93w GLY 3.8 7.4 - - - +
94w PRO* 3.0 11.6 + - + +
96w LEU* 1.3 79.7 - - + +
98w ASN* 1.3 67.5 + - - +
100w ILE* 3.3 0.4 + - - -
101w ASN* 3.1 32.8 + - - +
130w THR* 3.4 25.7 + - - +
131w GLY* 3.6 29.2 - - - +
132w TYR 4.8 2.9 - - - +
133w VAL* 3.7 29.6 - - + -
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Residues in contact with ASN 98 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67u GLY* 3.1 36.1 + - - +
69u THR* 4.4 7.9 - - + -
94w PRO* 2.9 13.9 + - - +
95w ALA* 3.5 8.1 - - - +
97w VAL* 1.3 79.7 - - - +
99w MET* 1.3 63.0 + - - +
101w ASN* 3.5 9.6 + - - +
102w GLY 3.3 15.9 + - - -
109x SER 3.5 22.9 - - - +
110x ALA* 3.7 3.1 - - - +
112x ASN* 5.2 9.1 - - - +
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Residues in contact with MET 99 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2928 T 4.1 11.4 - - - +
69u THR* 4.6 5.6 - - + -
70u GLY 5.3 0.2 - - - +
82w LYS* 4.7 11.9 - - - -
83w VAL* 6.3 0.9 - - - -
86w ALA* 3.8 24.5 - - + -
90w ILE* 3.7 23.6 - - + -
95w ALA 3.0 13.2 + - - +
96w LEU* 3.1 13.9 + - + +
98w ASN* 1.3 78.0 - - - +
100w ILE* 1.3 60.3 + - + +
102w GLY* 3.2 3.5 + - - -
103w LEU* 2.8 31.5 + - + +
106x TYR* 4.7 10.3 - - - -
110x ALA* 4.2 20.0 + - - +
111x PHE* 3.8 29.4 - - + -
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Residues in contact with ILE 100 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79w PHE* 5.0 2.9 - - + -
83w VAL* 4.3 19.3 - - + -
96w LEU* 2.8 46.2 + - + +
97w VAL* 3.3 3.6 + - - +
99w MET* 1.3 73.4 - - + +
101w ASN* 1.3 57.9 + - - +
103w LEU* 3.2 6.4 + - + +
104w LYS* 2.8 43.2 + - + +
122w VAL* 4.2 16.2 - - + -
126w THR* 4.1 22.9 - - + -
130w THR* 3.5 36.3 - - + +
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Residues in contact with ASN 101 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97w VAL* 3.1 33.2 + - - +
98w ASN* 3.7 10.5 + - - +
100w ILE* 1.3 77.5 - - - +
102w GLY* 1.3 62.1 + - - +
104w LYS* 3.5 8.7 + - - +
105w GLY* 3.2 17.5 + - - -
130w THR* 3.3 20.4 - - - +
131w GLY* 4.3 7.8 + - - -
109x SER* 4.2 8.4 + - - +
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Residues in contact with GLY 102 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98w ASN 3.3 4.2 + - - -
99w MET 3.2 6.4 + - - -
101w ASN* 1.3 76.6 - - - +
103w LEU* 1.3 59.6 + - - +
105w GLY* 3.1 3.8 + - - -
106w TYR 2.9 24.1 + - - -
105x GLY 5.0 0.2 - - - -
106x TYR* 3.5 20.0 - - - -
109x SER* 3.0 23.9 + - - -
110x ALA* 4.0 10.3 - - - -
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Residues in contact with LEU 103 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79w PHE* 3.6 16.6 - - + -
82w LYS* 3.5 48.0 - - + +
83w VAL* 3.6 31.4 - - + +
99w MET* 2.8 22.4 + - + +
100w ILE* 3.2 9.6 + - - +
102w GLY* 1.3 73.2 - - - +
104w LYS* 1.3 65.9 + - - +
106w TYR* 3.1 10.9 + - + +
107w TYR* 3.0 40.5 + - + -
106x TYR* 3.9 10.4 - - + -
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Residues in contact with LYS 104 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79w PHE* 3.8 29.2 - - + -
100w ILE* 2.8 35.4 + - + +
101w ASN* 3.7 7.5 + - - +
103w LEU* 1.3 71.1 - - - +
105w GLY* 1.3 58.9 + - - +
107w TYR* 3.2 1.6 + - - +
108w ILE* 2.8 54.3 + - + +
115w PRO* 5.0 6.0 - - - +
118w LEU* 4.8 6.1 - - + -
119w ASP* 2.7 37.9 + - - +
122w VAL* 5.0 1.8 - - + -
129w PRO* 6.1 0.2 - - - +
130w THR* 4.6 12.2 - - + +
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Residues in contact with GLY 105 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101w ASN 3.2 8.7 + - - -
102w GLY* 3.1 8.1 + - - -
104w LYS* 1.3 77.7 - - - +
106w TYR* 1.3 57.9 + - - +
108w ILE* 4.5 6.7 - - - +
109w SER* 2.6 37.3 + - - -
102x GLY 4.4 3.4 - - - -
105x GLY* 5.9 2.2 - - - -
106x TYR 5.3 2.0 - - - -
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Residues in contact with TYR 106 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477 A 3.8 5.7 + - - -
487 T 2.9 18.1 + - - -
82w LYS* 5.6 4.0 - - - -
102w GLY 2.9 12.1 + - - +
103w LEU* 3.2 15.7 - - + +
105w GLY* 1.3 75.4 - - - +
107w TYR* 1.3 84.9 + + - +
110w ALA* 2.8 40.9 + - + +
111w PHE* 3.7 27.0 - + - -
82x LYS* 2.8 41.1 + - - -
99x MET* 4.6 7.2 - - - +
102x GLY 3.7 15.3 + - - -
103x LEU* 4.0 13.2 - - + -
106x TYR* 3.7 31.0 - + + -
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Residues in contact with TYR 107 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477 A 4.5 5.3 - - + +
487 T 3.3 34.4 + - - -
75w ILE* 3.5 38.1 - - + -
78w GLY* 3.5 9.6 - - - -
79w PHE* 3.7 31.2 - + + -
82w LYS* 5.2 0.9 - - + -
103w LEU* 3.0 25.2 + - + +
104w LYS 4.0 1.8 - - - +
106w TYR* 1.3 97.8 - + - +
108w ILE* 1.3 66.5 + - - +
111w PHE* 3.1 41.5 + + - -
113w ALA* 3.0 26.0 + - + +
118w LEU* 4.4 7.9 - - + -
71z PRO* 6.5 0.7 - - + -
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Residues in contact with ILE 108 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104w LYS* 2.8 43.9 + - + +
105w GLY* 4.1 5.4 - - - +
107w TYR* 1.3 72.7 - - - +
109w SER* 1.3 62.4 + - - +
112w ASN* 3.1 25.3 - - - +
113w ALA 3.6 16.2 + - - +
115w PRO* 3.9 31.6 - - + -
118w LEU* 3.3 21.5 - - + -
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Residues in contact with SER 109 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105w GLY* 2.6 21.1 + - - -
108w ILE* 1.3 86.1 - - - +
110w ALA* 1.3 61.7 + - - +
112w ASN* 4.0 10.2 - - - +
98x ASN* 3.5 17.2 - - - +
101x ASN* 4.2 6.0 + - - +
102x GLY* 2.9 21.9 - - - -
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Residues in contact with ALA 110 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106w TYR* 2.8 25.4 + - + +
109w SER* 1.3 79.3 + - - +
111w PHE* 1.3 62.7 + - + +
112w ASN* 5.1 1.5 + - - -
98x ASN* 3.6 12.4 - - - +
99x MET* 3.9 35.0 + - - +
102x GLY* 4.1 4.9 - - - -
69z THR* 2.6 34.1 + - - +
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Residues in contact with PHE 111 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477 A 3.8 24.9 - - - -
75w ILE* 4.8 13.3 - - + +
106w TYR* 3.7 34.8 - + - -
107w TYR* 3.1 48.0 + + + +
110w ALA* 1.3 78.8 - - + +
112w ASN* 1.3 75.0 + - - +
113w ALA* 3.2 1.8 + - - +
99x MET* 3.7 28.0 - - + -
69z THR* 3.4 16.8 - - - +
70z GLY* 3.5 31.2 - - - -
71z PRO* 4.6 4.5 - - + -
72z ASN* 3.3 19.8 + - - +
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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