Contacts of the helix formed by residues 93 - 111 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92N SER* 1.3 76.3 + - - +
94N PRO* 1.3 67.6 - - - -
95N ALA 3.3 1.6 - - - -
96N LEU* 2.8 30.2 + - - +
97N VAL* 3.2 16.4 + - - +
133N VAL* 4.5 9.9 - - - -
64P THR* 4.5 0.9 - - - -
65P GLN* 5.3 2.7 - - - -
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Residues in contact with PRO 94 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92N SER 4.6 0.2 - - - +
93N GLY* 1.3 82.1 - - - -
95N ALA* 1.3 63.0 + - - +
97N VAL* 3.0 6.2 + - - +
98N ASN* 2.9 26.7 + - - +
133N VAL* 3.8 26.8 - - + -
64P THR* 3.3 16.2 - - + +
65P GLN* 3.4 39.3 - - - +
66P TYR 4.7 0.4 - - - -
67P GLY* 3.9 11.2 - - - -
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Residues in contact with ALA 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90N ILE* 3.6 23.3 - - + +
93N GLY 3.1 0.6 + - - -
94N PRO* 1.3 77.7 - - - +
96N LEU* 1.3 57.1 + - - +
98N ASN* 3.3 2.2 + - - +
99N MET* 3.0 23.9 + - - +
64P THR* 3.2 19.2 + - + +
67P GLY* 3.5 15.5 - - - -
68P ILE 3.6 22.0 - - - +
69P THR* 3.4 14.5 - - + +
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Residues in contact with LEU 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83N VAL* 4.5 4.3 - - + +
86N ALA* 3.8 32.5 - - + +
87N LEU* 3.6 40.2 - - + +
90N ILE* 4.0 5.1 - - + +
91N GLY 3.4 12.3 - - - +
92N SER* 3.8 11.0 - - - -
93N GLY 2.8 16.3 + - - +
95N ALA* 1.3 72.1 - - - +
97N VAL* 1.3 62.3 + - + +
99N MET* 3.1 6.6 + - + +
100N ILE* 2.8 49.1 + - + +
126N THR* 4.8 11.0 - - + -
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Residues in contact with VAL 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93N GLY* 3.2 9.6 + - - +
94N PRO 3.0 8.4 + - - +
96N LEU* 1.3 80.1 - - + +
98N ASN* 1.3 66.3 + - - +
100N ILE* 3.2 5.7 + - + -
101N ASN* 2.9 28.6 + - - +
130N THR* 3.5 20.8 + - - +
131N GLY 3.7 26.2 - - - +
132N TYR 4.2 7.2 - - - +
133N VAL* 3.8 33.2 - - + +
134N SER 5.2 0.9 - - - +
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Residues in contact with ASN 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109M SER 3.5 22.2 - - - +
110M ALA* 3.6 3.6 - - - +
112M ASN* 5.1 9.3 - - - +
94N PRO* 2.9 13.3 + - - +
95N ALA* 3.4 8.3 - - - +
96N LEU 3.2 0.2 - - - -
97N VAL* 1.3 79.6 - - - +
99N MET* 1.3 63.9 + - - +
101N ASN* 3.5 8.8 + - - +
102N GLY 3.3 13.3 + - - -
67P GLY* 3.1 35.7 + - - +
69P THR* 4.4 7.4 - - + -
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Residues in contact with MET 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2637 A 4.1 13.7 - - - +
106M TYR* 4.6 12.6 - - - +
110M ALA* 3.9 20.2 + - - +
111M PHE* 3.7 31.0 - - + -
82N LYS* 5.9 2.0 - - - -
83N VAL* 6.5 0.2 - - - -
86N ALA* 3.8 24.0 - - + -
90N ILE* 3.8 22.2 - - + -
95N ALA 3.0 13.6 + - - +
96N LEU* 3.1 12.5 + - + +
98N ASN* 1.3 76.8 - - - +
100N ILE* 1.3 59.8 + - + +
102N GLY* 3.2 3.6 + - - -
103N LEU* 2.9 34.8 + - + +
69P THR* 4.7 5.6 - - + -
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Residues in contact with ILE 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79N PHE* 5.1 1.3 - - + -
83N VAL* 4.3 22.4 - - + -
96N LEU* 2.8 47.9 + - + +
97N VAL* 4.7 3.1 - - + -
99N MET* 1.3 74.3 - - + +
101N ASN* 1.3 57.4 + - - +
103N LEU* 3.6 7.4 - - + +
104N LYS* 2.7 34.3 + - + +
122N VAL* 4.3 20.6 - - + -
126N THR* 4.1 24.0 - - + -
130N THR* 3.6 34.1 - - + +
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Residues in contact with ASN 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109M SER* 4.2 8.0 + - - +
97N VAL* 2.9 23.2 + - - +
98N ASN* 3.7 10.1 + - - +
99N MET 3.2 0.2 - - - -
100N ILE* 1.3 75.8 - - - +
102N GLY* 1.3 61.3 + - - +
104N LYS* 3.8 3.4 - - - +
105N GLY* 3.2 19.4 + - - -
130N THR* 2.5 31.1 + - - +
131N GLY* 2.9 33.4 + - - -
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Residues in contact with GLY 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105M GLY 4.2 2.4 - - - +
106M TYR* 3.7 11.9 + - - -
109M SER* 2.9 25.4 + - - -
110M ALA* 4.1 11.2 - - - -
98N ASN 3.3 4.9 + - - -
99N MET 3.2 5.8 + - - -
101N ASN* 1.3 76.2 - - - +
103N LEU* 1.3 59.9 + - - +
105N GLY* 3.4 1.6 + - - -
106N TYR* 2.9 29.8 + - - +
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Residues in contact with LEU 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106M TYR* 4.0 12.2 - - + -
79N PHE* 3.7 10.8 - - + -
82N LYS* 3.5 51.4 - - + +
83N VAL* 3.7 34.3 - - + +
99N MET* 2.9 24.2 + - + +
100N ILE* 3.6 8.3 - - + +
102N GLY* 1.3 74.0 - - - +
104N LYS* 1.3 65.7 + - - +
106N TYR* 3.2 9.3 - - + +
107N TYR* 3.0 37.2 + - + -
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Residues in contact with LYS 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79N PHE* 3.8 17.2 - - + -
100N ILE* 2.7 23.1 + - + +
101N ASN* 3.8 4.0 - - - +
103N LEU* 1.3 72.8 - - - +
105N GLY* 1.3 64.5 + - - +
107N TYR* 3.1 4.9 + - - +
108N ILE* 3.0 46.5 + - + +
115N PRO* 4.4 13.4 - - - +
118N LEU* 4.0 13.4 - - + +
119N ASP* 2.7 39.1 + - - +
122N VAL* 6.0 1.6 - - + -
130N THR* 4.3 19.3 - - + +
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Residues in contact with GLY 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102M GLY 5.0 0.9 - - - -
105M GLY* 5.9 3.6 - - - -
106M TYR 5.7 0.2 - - - -
101N ASN 3.2 12.1 + - - -
102N GLY* 3.8 2.9 - - - -
104N LYS* 1.3 78.0 - - - +
106N TYR* 1.3 63.0 + - - +
108N ILE* 3.2 12.3 + - - +
109N SER* 3.0 29.5 + - - -
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Residues in contact with TYR 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768 T 4.2 0.2 + - - -
778 A 3.3 15.5 + - - -
82M LYS* 2.7 35.3 + - - -
99M MET* 4.7 3.4 - - - -
102M GLY 3.5 26.9 + - - -
103M LEU* 4.1 14.1 - - + -
106M TYR* 3.7 25.7 - + + +
82N LYS* 5.0 5.8 - - + -
102N GLY 2.9 18.6 + - - +
103N LEU* 3.2 13.5 - - + +
105N GLY* 1.3 75.1 - - - +
107N TYR* 1.3 80.7 + + - +
110N ALA* 2.8 45.7 + - + +
111N PHE* 3.7 28.2 - + - -
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Residues in contact with TYR 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768 T 4.4 6.1 + - + +
778 A 3.4 24.8 + - - -
71K PRO* 6.5 1.1 - - + -
75N ILE* 3.5 38.1 - - + -
78N GLY* 3.5 4.9 - - - -
79N PHE* 3.5 37.3 + + + -
82N LYS* 4.6 4.0 - - + -
103N LEU* 3.0 30.8 + - + +
104N LYS 3.8 5.4 - - - +
106N TYR* 1.3 95.6 - + - +
108N ILE* 1.3 66.3 + - - +
111N PHE* 3.0 44.8 + + - -
113N ALA* 3.1 21.5 + - + +
118N LEU* 4.4 2.9 - - + -
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Residues in contact with ILE 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104N LYS* 3.0 46.1 + - + +
105N GLY* 3.6 11.7 - - - +
107N TYR* 1.3 76.4 - - - +
109N SER* 1.3 63.2 + - - +
112N ASN* 3.0 25.6 - - - +
113N ALA 3.4 16.3 + - - +
115N PRO* 3.9 24.5 - - + -
118N LEU* 3.3 16.2 - - + -
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Residues in contact with SER 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98M ASN* 3.5 18.7 - - - +
101M ASN* 4.2 7.1 - - - +
102M GLY* 3.0 28.3 + - - -
105N GLY 3.0 11.0 + - - -
108N ILE* 1.3 82.3 - - - +
110N ALA* 1.3 64.2 + - - +
111N PHE 3.4 0.4 - - - -
112N ASN* 4.0 10.0 - - - +
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Residues in contact with ALA 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69K THR* 2.6 34.5 + - - +
98M ASN* 3.7 13.6 - - - +
99M MET* 4.2 15.1 - - - +
102M GLY* 4.1 11.0 - - - -
106N TYR* 2.8 36.4 + - + +
109N SER* 1.3 77.2 + - - +
111N PHE* 1.3 69.4 + - + +
112N ASN* 3.6 1.1 - - - -
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Residues in contact with PHE 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768 T 3.6 39.5 - - - -
69K THR* 3.4 17.9 - - - +
70K GLY* 3.6 19.1 - - - -
71K PRO* 4.6 4.0 - - + -
72K ASN* 3.2 18.1 + - - +
99M MET* 3.8 23.3 - - + -
75N ILE* 4.6 13.4 - - + +
106N TYR* 3.7 38.8 - + - -
107N TYR* 3.0 44.4 + + + +
110N ALA* 1.3 80.1 - - + +
112N ASN* 1.3 74.8 + - - +
113N ALA* 3.2 2.2 + - - +
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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