Contacts of the helix formed by residues 93 - 111 (chain b) 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 b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92b SER* 1.3 77.8 - - - +
94b PRO* 1.3 67.5 - - - -
95b ALA 3.3 1.8 - - - -
96b LEU* 2.8 28.9 + - - +
97b VAL* 3.2 15.8 + - - +
133b VAL* 4.5 10.8 - - - -
64d THR* 4.5 0.9 - - - -
65d GLN* 5.3 2.5 - - - -
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Residues in contact with PRO 94 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93b GLY* 1.3 83.3 - - - -
95b ALA* 1.3 63.4 + - - +
97b VAL* 3.0 6.6 + - - +
98b ASN* 2.9 26.4 + - - +
133b VAL* 3.8 26.2 - - + -
64d THR* 3.3 15.5 - - + +
65d GLN* 3.4 39.5 - - - +
66d TYR 4.7 0.4 - - - -
67d GLY* 3.9 11.7 - - - -
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Residues in contact with ALA 95 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90b ILE* 3.6 22.8 - - + +
93b GLY 3.1 0.6 + - - -
94b PRO* 1.3 80.0 - - - +
96b LEU* 1.3 56.7 + - - +
98b ASN* 3.3 1.8 + - - +
99b MET* 3.0 24.1 + - - +
64d THR* 3.2 18.6 + - + +
67d GLY* 3.5 16.6 - - - -
68d ILE 3.6 21.8 - - - +
69d THR* 3.4 14.0 - - + +
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Residues in contact with LEU 96 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83b VAL* 4.5 3.6 - - + +
86b ALA* 3.8 32.8 - - + +
87b LEU* 3.6 40.2 - - + +
90b ILE* 4.0 5.3 - - + +
91b GLY 3.4 13.0 - - - +
92b SER* 3.8 11.2 - - - -
93b GLY 2.8 16.0 + - - +
95b ALA* 1.3 72.2 - - - +
97b VAL* 1.3 62.4 + - + +
99b MET* 3.1 6.3 + - + +
100b ILE* 2.8 50.6 + - + +
126b THR* 4.8 10.8 - - + -
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Residues in contact with VAL 97 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93b GLY 3.2 9.4 + - - +
94b PRO 3.0 7.8 + - - +
96b LEU* 1.3 79.9 - - + +
98b ASN* 1.3 66.2 + - - +
100b ILE* 3.2 5.9 + - + +
101b ASN* 2.9 28.6 + - - +
130b THR* 3.5 21.5 + - - +
131b GLY 3.7 26.2 - - - +
132b TYR* 4.2 7.6 - - - +
133b VAL* 3.8 33.0 - - + +
134b SER 5.2 0.7 - - - +
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Residues in contact with ASN 98 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109a SER 3.5 22.7 - - - +
110a ALA* 3.6 3.8 - - - +
112a ASN* 5.1 9.5 - - - +
94b PRO* 2.9 12.9 + - - +
95b ALA* 3.4 9.0 - - - +
96b LEU 3.2 0.2 - - - -
97b VAL* 1.3 80.3 - - - +
99b MET* 1.3 64.2 + - - +
101b ASN* 3.5 8.9 + - - +
102b GLY 3.3 13.7 + - - -
67d GLY* 3.1 35.0 + - - -
69d THR* 4.4 7.0 - - + -
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Residues in contact with MET 99 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1797 A 4.1 13.0 - - - +
106a TYR* 4.6 13.0 - - - +
110a ALA* 3.9 19.8 + - - +
111a PHE* 3.7 31.2 - - + -
82b LYS* 5.9 2.0 - - - -
86b ALA* 3.8 24.7 - - + -
90b ILE* 3.8 22.7 - - + -
95b ALA 3.0 13.6 + - - +
96b LEU* 3.3 12.1 - - + +
98b ASN* 1.3 76.6 - - - +
100b ILE* 1.3 60.4 + - + +
102b GLY* 3.2 3.8 + - - -
103b LEU* 2.9 33.7 + - + +
69d THR* 4.7 5.2 - - + -
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Residues in contact with ILE 100 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79b PHE* 5.1 0.9 - - + -
83b VAL* 4.3 21.5 - - + -
96b LEU* 2.8 48.8 + - + +
97b VAL* 4.7 2.9 - - + -
99b MET* 1.3 75.8 - - + +
101b ASN* 1.3 57.5 + - - +
103b LEU* 4.1 7.0 - - + -
104b LYS* 2.7 34.0 + - + +
122b VAL* 4.3 20.6 - - + -
126b THR* 4.1 23.8 - - + -
130b THR* 3.6 34.5 - - + +
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Residues in contact with ASN 101 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109a SER* 4.2 8.4 + - - +
97b VAL* 2.9 23.3 + - - +
98b ASN* 3.7 10.7 + - - +
99b MET 3.2 0.2 - - - -
100b ILE* 1.3 75.8 - - - +
102b GLY* 1.3 61.7 + - - +
104b LYS* 3.8 3.4 - - - +
105b GLY* 3.2 18.9 + - - -
130b THR* 2.5 31.6 + - - +
131b GLY* 2.9 33.3 + - - -
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Residues in contact with GLY 102 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105a GLY 4.2 2.8 - - - -
106a TYR* 3.7 12.0 + - - -
109a SER* 2.9 25.0 + - - -
110a ALA* 4.1 11.2 - - - -
98b ASN 3.3 4.8 + - - -
99b MET 3.2 5.8 + - - -
101b ASN* 1.3 76.8 - - - +
103b LEU* 1.3 59.5 + - - +
105b GLY* 3.4 1.0 + - - -
106b TYR* 2.9 30.0 + - - +
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Residues in contact with LEU 103 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106a TYR* 4.0 11.5 - - + -
79b PHE* 3.7 11.0 - - + -
82b LYS* 3.5 50.5 - - + +
83b VAL* 3.7 34.5 - - + +
99b MET* 2.9 24.4 + - + +
100b ILE* 3.6 7.6 - - + +
102b GLY* 1.3 74.9 - - - +
104b LYS* 1.3 64.7 + - - +
106b TYR* 3.2 9.3 - - + +
107b TYR* 3.0 38.6 + - + -
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Residues in contact with LYS 104 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79b PHE* 3.8 17.7 - - + -
100b ILE* 2.7 23.7 + - + +
101b ASN* 3.8 4.0 - - - +
103b LEU* 1.3 73.6 - - - +
105b GLY* 1.3 63.8 + - - +
107b TYR* 3.1 4.9 + - - +
108b ILE* 3.0 46.5 + - + +
115b PRO* 4.4 13.2 - - - +
118b LEU* 4.0 12.7 - - + +
119b ASP* 2.7 39.1 + - - +
122b VAL* 6.0 1.6 - - + -
130b THR* 4.3 19.1 - - + +
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Residues in contact with GLY 105 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102a GLY 5.0 0.9 - - - -
105a GLY* 5.9 3.8 - - - -
106a TYR 5.7 0.2 - - - -
101b ASN 3.2 11.7 + - - -
102b GLY 3.8 2.7 - - - -
104b LYS* 1.3 78.7 - - - +
106b TYR* 1.3 62.3 + - - +
108b ILE* 3.2 12.1 + - - +
109b SER* 3.1 29.0 + - - -
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Residues in contact with TYR 106 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1608 T 4.2 0.2 + - - -
1618 A 3.3 15.7 + - - -
82a LYS* 2.7 34.4 + - - -
99a MET* 4.7 3.9 - - - -
102a GLY 3.5 27.7 + - - -
103a LEU* 4.1 14.4 - - + -
106a TYR* 3.7 25.7 - + + +
82b LYS* 5.0 6.7 - - + -
102b GLY 2.9 18.0 + - - +
103b LEU* 3.2 13.9 - - + +
105b GLY* 1.3 75.3 - - - +
107b TYR* 1.3 80.7 - + - +
110b ALA* 2.8 45.9 + - + +
111b PHE* 3.7 27.6 - + - -
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Residues in contact with TYR 107 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1608 T 4.4 7.1 + - + +
1618 A 3.4 24.8 + - - -
71Y PRO* 6.5 1.3 - - + -
75b ILE* 3.5 37.2 - - + -
78b GLY* 3.5 4.7 - - - -
79b PHE* 3.5 39.0 + + + -
82b LYS* 4.6 4.7 - - + -
103b LEU* 3.0 30.2 + - + +
104b LYS 3.8 5.8 - - - +
106b TYR* 1.3 96.7 - + - +
108b ILE* 1.3 65.9 + - - +
111b PHE* 3.0 44.9 + + - -
113b ALA* 3.1 22.4 + - + +
118b LEU* 4.4 2.5 - - + -
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Residues in contact with ILE 108 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104b LYS* 3.0 47.2 + - + +
105b GLY* 3.2 11.2 + - - +
107b TYR* 1.3 76.4 - - - +
109b SER* 1.3 62.4 + - - +
112b ASN* 3.0 26.3 - - - +
113b ALA 3.5 16.1 - - - +
115b PRO* 3.9 24.2 - - + -
118b LEU* 3.3 16.6 - - + -
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Residues in contact with SER 109 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98a ASN* 3.5 18.9 - - - +
101a ASN* 4.2 6.6 + - - -
102a GLY* 3.0 29.2 + - - -
105b GLY 3.1 12.1 + - - -
108b ILE* 1.3 81.2 - - - +
110b ALA* 1.3 63.1 + - - +
111b PHE 3.4 0.4 - - - -
112b ASN* 4.0 9.8 - - - +
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Residues in contact with ALA 110 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69Y THR* 2.6 34.0 + - - +
98a ASN* 3.7 13.8 - - - +
99a MET* 4.2 15.8 - - - +
102a GLY* 4.1 10.5 - - - -
106b TYR* 2.8 36.2 + - + +
109b SER* 1.3 76.9 + - - +
111b PHE* 1.3 69.4 + - + +
112b ASN* 3.6 1.1 - - - -
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Residues in contact with PHE 111 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1608 T 3.6 38.4 - - - -
69Y THR* 3.4 17.5 - - - +
70Y GLY* 3.6 19.3 - - - -
71Y PRO* 4.6 4.0 - - + -
72Y ASN* 3.2 18.5 + - - +
82a LYS* 6.1 0.2 - - - -
99a MET* 3.8 23.8 - - + -
75b ILE* 4.6 13.5 - - + +
106b TYR* 3.7 37.2 - + - -
107b TYR* 3.0 45.2 + + + +
110b ALA* 1.3 80.3 - - + +
112b ASN* 1.3 74.6 + - - +
113b 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