Contacts of the helix formed by residues 93 - 111 (chain X) 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 X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92X SER* 1.3 77.4 - - - +
94X PRO* 1.3 69.1 - - - -
95X ALA 3.3 1.8 - - - -
96X LEU* 2.8 28.0 + - - +
97X VAL* 3.2 16.7 + - - +
133X VAL* 4.5 10.3 - - - -
64Z THR* 4.5 0.7 - - - -
65Z GLN* 5.3 2.2 - - - -
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Residues in contact with PRO 94 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93X GLY* 1.3 83.7 - - - -
95X ALA* 1.3 63.1 + - - +
97X VAL* 3.0 6.8 + - - +
98X ASN* 2.9 25.9 + - - +
133X VAL* 3.8 26.1 - - + -
64Z THR* 3.3 15.7 - - + +
65Z GLN* 3.4 39.7 - - - +
66Z TYR 4.7 0.2 - - - -
67Z GLY* 3.9 11.0 - - - -
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Residues in contact with ALA 95 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90X ILE* 3.6 22.4 - - + -
93X GLY 3.3 0.4 - - - -
94X PRO* 1.3 78.5 - - - +
96X LEU* 1.3 57.2 + - - +
98X ASN* 3.3 1.8 + - - +
99X MET* 3.0 24.3 + - - +
64Z THR* 3.2 18.2 + - + +
67Z GLY* 3.5 15.9 - - - -
68Z ILE 3.6 22.0 - - - +
69Z THR* 3.4 13.2 - - + +
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Residues in contact with LEU 96 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83X VAL* 4.5 3.4 - - + +
86X ALA* 3.8 33.2 - - + +
87X LEU* 3.6 40.2 - - + +
90X ILE* 4.0 5.8 - - + +
91X GLY 3.4 12.6 - - - +
92X SER* 3.8 11.2 - - - -
93X GLY 2.8 16.7 + - - +
95X ALA* 1.3 71.3 - - - +
97X VAL* 1.3 63.7 + - + +
99X MET* 3.1 5.5 + - + +
100X ILE* 2.8 50.2 + - + +
126X THR* 4.8 10.3 - - + -
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Residues in contact with VAL 97 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93X GLY 3.2 9.4 + - - +
94X PRO 3.0 8.4 + - - +
96X LEU* 1.3 79.1 - - + +
98X ASN* 1.3 65.5 - - - +
100X ILE* 3.2 5.0 + - + -
101X ASN* 2.9 27.7 + - - +
130X THR* 3.5 20.8 + - - +
131X GLY 3.7 26.7 - - - +
132X TYR 4.2 6.5 - - - +
133X VAL* 3.8 33.9 - - + +
134X SER 5.2 0.7 - - - +
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Residues in contact with ASN 98 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109W SER 3.5 21.8 - - - +
110W ALA* 3.6 4.5 - - - +
112W ASN* 5.1 9.5 + - - +
94X PRO* 2.9 12.9 + - - +
95X ALA* 3.4 8.5 - - - +
97X VAL* 1.3 81.3 - - - +
99X MET* 1.3 65.5 + - - +
101X ASN* 3.5 9.0 + - - +
102X GLY 3.3 13.5 + - - -
67Z GLY* 3.1 35.0 + - - -
69Z THR* 4.4 7.2 - - + -
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Residues in contact with MET 99 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2037 A 4.1 13.5 - - - +
106W TYR* 4.6 12.6 - - - +
110W ALA* 3.9 21.1 + - - +
111W PHE* 3.7 31.2 - - + -
82X LYS* 5.9 2.5 - - - -
86X ALA* 3.8 24.0 - - + -
90X ILE* 3.8 23.6 - - + -
95X ALA 3.0 13.2 + - - +
96X LEU* 3.3 12.8 - - + +
98X ASN* 1.3 76.9 - - - +
100X ILE* 1.3 59.6 + - + +
102X GLY* 3.2 3.3 + - - -
103X LEU* 2.9 33.9 + - + +
69Z THR* 4.7 6.1 - - + -
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Residues in contact with ILE 100 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79X PHE* 5.1 1.3 - - + -
83X VAL* 4.3 22.2 - - + -
86X ALA* 6.0 0.2 - - + -
96X LEU* 2.8 47.9 + - + +
97X VAL* 4.7 3.4 - - + -
99X MET* 1.3 75.1 - - + +
101X ASN* 1.3 58.3 + - - +
103X LEU* 4.1 6.3 - - + -
104X LYS* 2.7 33.9 + - + +
122X VAL* 4.3 19.7 - - + -
126X THR* 4.1 24.2 - - + -
130X THR* 3.6 34.3 - - + +
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Residues in contact with ASN 101 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109W SER* 4.2 7.6 + - - +
97X VAL* 2.9 23.3 + - - +
98X ASN* 3.7 10.1 + - - +
100X ILE* 1.3 76.3 - - - +
102X GLY* 1.3 61.1 + - - +
104X LYS* 3.6 3.5 + - - +
105X GLY* 3.2 18.7 + - - -
130X THR* 2.5 31.6 + - - +
131X GLY* 2.9 33.1 + - - -
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Residues in contact with GLY 102 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105W GLY 4.2 2.8 - - - +
106W TYR* 3.7 11.8 + - - -
109W SER* 2.9 24.8 + - - -
110W ALA* 4.1 11.0 - - - -
98X ASN 3.3 4.9 + - - -
99X MET 3.2 5.8 + - - -
101X ASN* 1.3 77.0 - - - +
103X LEU* 1.3 59.2 + - - +
105X GLY* 3.4 1.5 + - - -
106X TYR* 2.9 30.1 + - - +
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Residues in contact with LEU 103 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106W TYR* 4.0 11.1 - - + -
79X PHE* 3.7 9.2 - - + -
82X LYS* 3.5 52.0 - - + +
83X VAL* 3.7 34.1 - - + +
99X MET* 2.9 24.5 + - + +
100X ILE* 3.6 6.7 - - + +
102X GLY* 1.3 74.7 - - - +
104X LYS* 1.3 66.7 + - - +
106X TYR* 3.2 8.4 - - + +
107X TYR* 3.0 38.0 + - + -
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Residues in contact with LYS 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79X PHE* 3.8 18.1 - - + -
100X ILE* 2.7 22.7 + - + +
101X ASN* 3.8 5.4 - - - +
103X LEU* 1.3 74.1 - - - +
105X GLY* 1.3 63.6 + - - +
107X TYR* 3.1 5.4 + - - +
108X ILE* 3.0 45.9 + - + +
115X PRO* 4.4 13.3 - - - +
118X LEU* 4.0 13.0 - - + +
119X ASP* 2.7 38.9 + - - +
122X VAL* 6.0 1.6 - - + -
130X THR* 4.3 18.1 - - + +
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Residues in contact with GLY 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102W GLY 5.0 0.7 - - - -
105W GLY* 5.9 3.6 - - - -
106W TYR 5.7 0.2 - - - -
101X ASN 3.2 11.9 + - - -
102X GLY* 3.8 2.2 - - - -
104X LYS* 1.3 77.9 - - - +
106X TYR* 1.3 62.0 + - - +
108X ILE* 3.2 12.3 + - - +
109X SER* 3.0 29.4 + - - -
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Residues in contact with TYR 106 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1378 A 3.3 15.9 + - - -
82W LYS* 2.7 34.3 + - - -
99W MET* 4.7 3.7 - - - -
102W GLY 3.5 27.3 + - - -
103W LEU* 4.1 13.9 - - + -
106W TYR* 3.7 25.3 - + + +
82X LYS* 5.0 6.5 - - - -
102X GLY 2.9 18.4 + - - +
103X LEU* 3.2 14.1 - - + +
105X GLY* 1.3 74.8 - - - +
107X TYR* 1.3 80.5 + + - +
110X ALA* 2.8 46.1 + - + +
111X PHE* 3.7 27.9 - + - -
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Residues in contact with TYR 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1368 T 4.4 6.8 + - + +
1378 A 3.4 25.1 + - - -
71U PRO* 6.5 1.3 - - + -
75X ILE* 3.5 37.7 - - + -
78X GLY* 3.5 4.5 - - - -
79X PHE* 3.5 40.5 + + + -
82X LYS* 4.6 4.7 - - + -
103X LEU* 3.0 29.6 + - + +
104X LYS 3.8 6.1 - - - +
106X TYR* 1.3 97.2 - + - +
108X ILE* 1.3 65.8 + - - +
111X PHE* 3.0 46.5 + + - -
113X ALA* 3.1 22.3 + - + +
118X LEU* 4.4 2.7 - - + -
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Residues in contact with ILE 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104X LYS* 3.0 45.9 + - + +
105X GLY* 3.2 11.2 + - - +
107X TYR* 1.3 75.4 - - - +
109X SER* 1.3 62.1 + - - +
112X ASN* 3.0 26.3 - - - +
113X ALA 3.5 16.2 - - - +
115X PRO* 3.9 24.0 - - + -
118X LEU* 3.3 17.3 - - + -
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Residues in contact with SER 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98W ASN* 3.5 18.4 - - - +
101W ASN* 4.2 6.3 + - - -
102W GLY* 3.0 28.5 - - - -
105X GLY 3.0 11.3 + - - -
108X ILE* 1.3 82.1 - - - +
110X ALA* 1.3 64.1 + - - +
111X PHE 3.4 0.2 - - - -
112X ASN* 4.0 10.2 - - - +
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Residues in contact with ALA 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69U THR* 2.6 34.0 + - - +
98W ASN* 3.7 13.2 - - - +
99W MET* 4.2 15.2 - - - +
102W GLY* 4.1 11.7 - - - -
106X TYR* 2.8 35.6 + - + +
109X SER* 1.3 77.2 + - - +
111X PHE* 1.3 70.2 + - + +
112X ASN* 5.2 0.6 - - - -
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Residues in contact with PHE 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1368 T 3.6 38.8 - - - -
69U THR* 3.4 17.7 - - - +
70U GLY* 3.6 19.7 - - - -
71U PRO* 4.6 3.4 - - + -
72U ASN* 3.2 19.0 + - - +
82W LYS* 6.1 0.4 - - - -
99W MET* 3.8 23.1 - - + -
75X ILE* 4.6 13.2 - - + +
106X TYR* 3.7 37.5 - + - -
107X TYR* 3.0 45.5 + + + +
110X ALA* 1.3 81.8 - - + +
112X ASN* 1.3 75.1 + - - +
113X 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
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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