Contacts of the helix formed by residues 96 - 116 (chain A) in PDB entry 5ON2
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 ALA 96 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ALA* 3.5 3.4 - - - +
95A THR* 1.3 80.4 - - - +
97A PRO* 1.4 74.9 - - + +
98A ALA 3.3 0.7 - - - +
99A PRO* 3.4 28.4 - - + +
100A TRP* 3.6 11.8 + - - +
456A GLU 4.1 13.9 - - - +
457A ASP* 5.9 0.2 - - - -
458A VAL* 3.7 24.0 - - + +
459A VAL* 6.0 0.2 - - - +
460A MET* 5.4 1.8 - - - -
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Residues in contact with PRO 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA* 3.8 16.1 - - + +
87A GLU* 4.2 3.4 - - + -
90A ALA* 3.8 12.6 - - + -
96A ALA* 1.4 87.8 - - + +
98A ALA* 1.3 55.8 + - - +
100A TRP* 3.8 2.6 + - + +
101A THR* 2.7 34.3 + - - -
427A TYR* 3.6 33.9 - - + +
428A TRP* 4.0 19.5 - - + -
458A VAL* 4.7 0.4 - - + -
460A MET* 3.6 34.8 - - + -
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA* 4.3 0.2 - - - +
97A PRO* 1.3 78.9 - - - +
99A PRO* 1.4 66.3 - - + +
101A THR* 3.1 6.1 + - - -
102A TYR* 3.0 34.0 + - + -
427A TYR* 4.9 0.8 + - - +
428A TRP* 3.7 25.9 - - + -
456A GLU* 3.7 43.7 - - + +
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Residues in contact with PRO 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A THR* 4.0 18.6 - - + -
96A ALA* 3.4 25.6 - - + +
98A ALA* 1.4 91.7 - - + +
100A TRP* 1.3 60.6 + - - +
102A TYR* 3.8 10.2 - - + +
103A ASP* 2.9 38.9 + - - +
456A GLU 5.0 1.3 - - - +
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Residues in contact with TRP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TYR* 3.8 12.8 - + - -
44A PRO 3.9 8.1 - - - -
45A SER* 3.5 16.6 - - - -
85A PRO* 4.3 6.3 - - + -
86A ALA* 3.6 34.5 - - + +
89A ALA* 3.4 36.6 - - + +
90A ALA* 4.9 4.7 - - + -
93A ASN* 4.4 20.2 - - + +
95A THR* 5.2 9.2 - - - +
96A ALA 3.7 14.6 - - - +
97A PRO* 3.8 4.9 - - + +
99A PRO* 1.3 80.6 - - - +
101A THR* 1.3 64.3 + - + +
103A ASP* 3.5 4.7 + - + +
104A ASN* 3.0 65.2 + - - +
622A LYS* 6.5 0.2 - - + -
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Residues in contact with THR 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TYR* 6.2 0.4 - - + -
44A PRO* 3.7 18.4 - - + +
81A ALA* 3.7 33.6 + - + +
86A ALA* 3.8 10.6 - - - +
97A PRO 2.7 17.2 + - - -
98A ALA 3.1 9.2 + - - -
100A TRP* 1.3 84.8 - - + +
102A TYR* 1.3 56.9 + - - +
104A ASN* 3.4 4.0 + - - +
105A ILE* 3.0 38.6 + - + +
128A CYS* 4.6 2.9 - - - -
428A TRP* 3.5 20.7 + - + -
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Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ALA* 3.0 31.8 + - + +
99A PRO* 3.4 8.3 + - + +
101A THR* 1.3 73.9 - - - +
103A ASP* 1.3 61.0 + - - +
105A ILE* 3.8 18.1 - - + +
106A ALA* 3.1 27.0 + - - +
126A ALA* 4.9 4.0 - - + -
128A CYS* 3.6 23.8 - - - -
129A THR* 3.5 27.2 - - + +
130A PRO* 5.8 0.2 - - - +
456A GLU* 2.8 40.0 + - - -
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Residues in contact with ASP 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PRO* 2.9 25.6 + - - +
100A TRP* 3.7 7.7 - - - +
101A THR 3.4 0.2 - - - -
102A TYR* 1.3 77.8 - - - +
104A ASN* 1.3 62.0 + - - +
106A ALA* 3.3 7.7 + - - +
107A TYR* 3.0 29.5 + - - +
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Residues in contact with ASN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PRO* 3.2 20.7 + - - +
45A SER 3.0 24.2 + - - -
46A GLY* 3.5 18.2 - - - +
47A ARG* 5.3 4.2 + - - -
100A TRP* 3.0 51.7 + - - +
101A THR 3.4 3.6 + - - +
103A ASP* 1.3 77.7 - - - +
105A ILE* 1.3 61.1 + - - +
107A TYR* 4.0 3.8 - - - +
108A MET* 3.1 35.9 + - - +
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PRO* 3.7 16.8 - - + -
79A TRP* 3.5 53.0 - - + +
81A ALA* 4.4 7.0 - - + -
101A THR* 3.0 38.9 + - + +
102A TYR* 3.8 23.1 - - + +
104A ASN* 1.3 76.4 - - - +
106A ALA* 1.3 58.6 + - - +
109A LYS* 2.9 31.6 + - + +
124A GLU* 4.5 4.5 - - - +
126A ALA* 4.6 8.3 - - + -
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Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR 3.1 19.0 + - - +
103A ASP* 3.5 8.5 - - - +
104A ASN 3.3 0.2 - - - -
105A ILE* 1.3 75.2 - - - +
107A TYR* 1.3 64.6 + - - +
109A LYS* 3.4 8.6 + - - +
110A ASN* 3.3 19.8 + - - +
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Residues in contact with TYR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY 3.5 21.1 - - - +
47A ARG* 3.2 39.3 - - - +
103A ASP 3.0 16.9 + - - +
104A ASN* 4.0 2.5 - - - +
106A ALA* 1.3 75.7 - - - +
108A MET* 1.3 61.2 + - - +
110A ASN* 3.3 9.7 + - - +
111A GLN* 3.3 45.1 + - + +
629A ASP* 4.4 1.7 + - - -
631A GLN* 5.3 5.8 - - + +
579D GLU* 3.5 26.6 + - - -
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Residues in contact with MET 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PRO* 4.4 9.2 - - + -
43A TYR 4.1 13.7 - - - +
44A PRO* 3.7 20.9 - - - -
45A SER* 3.8 0.7 - - - +
46A GLY 3.3 32.3 - - - +
47A ARG* 4.0 14.4 - - - +
48A LEU* 3.6 28.4 - - + +
52A HIS* 4.6 5.4 - - + -
79A TRP* 3.5 26.9 - - + -
104A ASN 3.1 21.5 + - - +
107A TYR* 1.3 72.8 - - - +
109A LYS* 1.3 65.4 + - - +
110A ASN 3.2 0.2 - - - -
111A GLN* 3.4 8.2 + - - +
112A LEU* 3.1 28.2 + - - +
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Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TRP* 3.8 10.7 - - + -
105A ILE* 2.9 22.5 + - + +
106A ALA* 3.6 8.5 - - - +
107A TYR 3.3 0.2 - - - -
108A MET* 1.3 76.4 - - - +
110A ASN* 1.3 60.4 + - - +
112A LEU* 3.8 2.3 + - - +
113A LYS* 3.2 41.8 + - + +
121A TRP* 3.8 28.5 + - + +
124A GLU* 2.9 38.4 + - - +
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Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ALA 3.3 8.6 + - - +
107A TYR* 3.3 11.8 + - - +
108A MET 3.2 0.2 - - - -
109A LYS* 1.3 76.1 - - - +
111A GLN* 1.3 62.9 + - + +
113A LYS* 3.2 11.0 + - - +
114A MET* 2.9 52.2 + - - +
631A GLN* 5.2 1.2 + - - -
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Residues in contact with GLN 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 3.8 2.8 - - - -
48A LEU* 2.9 47.6 + - + +
107A TYR* 3.3 34.6 + - + +
108A MET* 3.4 6.6 + - - +
110A ASN* 1.3 80.8 - - + +
112A LEU* 1.3 61.7 + - - +
114A MET* 3.5 4.1 + - - +
115A LEU* 3.2 27.8 + - + +
629A ASP* 2.7 35.3 + - - -
630A PRO* 5.2 2.9 - - + -
631A GLN* 3.6 33.9 + - - +
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PRO* 5.4 2.2 - - + -
48A LEU* 3.8 23.1 - - + -
56A TYR* 4.0 20.4 - - + -
77A ILE* 4.2 22.2 - - + -
79A TRP* 3.6 28.7 - - + -
108A MET 3.1 21.9 + - - +
109A LYS 4.0 3.1 - - - +
111A GLN* 1.3 74.6 - - - +
113A LYS* 1.3 63.4 + - - +
115A LEU* 3.2 5.5 + - - +
116A GLY 3.2 15.8 + - - -
117A PHE* 3.7 41.2 + - + +
119A TYR* 4.6 4.9 - - + -
121A TRP* 4.4 12.6 - - + -
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLN* 3.2 24.0 - - - +
19A ASP* 3.0 31.9 + - - +
109A LYS* 3.2 37.3 + - + +
110A ASN* 3.2 11.7 + - - +
112A LEU* 1.3 78.2 - - - +
114A MET* 1.3 58.9 + - + +
116A GLY* 3.2 11.9 + - - +
117A PHE 5.4 2.0 - - - +
121A TRP* 3.5 51.6 - - + +
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Residues in contact with MET 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLU* 4.7 1.4 - - - +
15A GLN* 2.7 29.1 + - - +
110A ASN* 2.9 41.9 + - - +
111A GLN 3.9 5.2 - - - +
113A LYS* 1.3 75.2 - - + +
115A LEU* 1.3 59.1 + - - +
116A GLY 3.2 0.7 - - - -
631A GLN* 3.1 35.2 - - - +
634A VAL* 4.6 16.4 - - + +
635A GLU* 5.1 7.6 - - + +
639A ALA* 3.5 12.2 - - - +
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 4.2 14.4 - - + -
53A VAL* 4.1 32.8 - - + -
111A GLN* 3.2 16.4 + - + +
112A LEU 3.2 8.0 + - - +
114A MET* 1.3 75.8 - - - +
116A GLY* 1.3 52.3 + - - +
117A PHE* 3.5 30.5 - - + -
630A PRO* 4.7 6.3 - - + -
631A GLN* 6.1 0.4 - - - +
634A VAL* 3.8 28.9 - - + -
639A ALA* 3.9 12.5 - - + +
642A VAL* 4.8 5.8 - - + -
643A ARG* 2.8 44.5 + - + -
767A HIS* 3.6 5.8 - - - -
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Residues in contact with GLY 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLN* 4.1 1.3 - - - -
18A TRP* 3.9 9.9 - - - -
64A ARG* 2.9 25.5 + - - -
112A LEU 3.2 5.9 + - - -
113A LYS* 3.2 14.4 + - - -
114A MET 3.2 0.6 - - - -
115A LEU* 1.3 78.8 - - - +
117A PHE* 1.3 62.3 + - - +
643A ARG* 3.2 9.0 + - - -
766A PRO* 4.3 1.2 - - - +
767A HIS* 3.6 18.4 - - - -
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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