Contacts of the helix formed by residues 92 - 111 (chain A) in PDB entry 1JUO
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 PHE 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ASP* 3.9 14.4 - - + -
35A LEU* 3.8 9.9 - - + -
36A TYR* 3.4 57.7 - + + -
39A PHE* 3.3 43.0 - + + -
47A GLY 4.1 2.2 + - - +
91A GLY* 1.3 70.8 - - - -
93A ASN* 1.3 67.0 + - - +
95A PHE* 3.0 8.0 + + - +
96A LYS* 2.8 68.5 + - + +
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Residues in contact with ASN 93 (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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91A GLY 3.3 0.8 - - - -
92A PHE* 1.3 86.7 - - - +
94A GLU* 1.3 71.8 + - - +
96A LYS* 3.3 18.6 + - - +
97A GLU* 3.1 27.3 + - - +
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Residues in contact with GLU 94 (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 GLN* 3.8 5.0 - - - +
82A LEU* 3.7 27.8 - - + +
84A ARG* 4.1 14.8 - - + +
89A THR 5.1 0.5 - - - +
90A MET* 3.3 23.2 - - + -
91A GLY* 2.6 32.0 + - - +
93A ASN* 1.3 85.7 + - - +
95A PHE* 1.3 66.7 + - - +
97A GLU* 3.1 15.2 + - - +
98A LEU* 3.0 21.3 + - - +
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Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 4.0 34.1 - - + -
38A TYR* 4.8 3.6 - - + -
39A PHE* 3.9 29.4 - + + -
49A ILE* 4.5 3.6 - - + -
54A LEU* 3.8 17.9 - - + -
57A CYS* 3.5 36.3 - - - -
58A LEU* 3.6 28.7 - - + -
61A SER* 5.0 5.4 - - - -
90A MET* 3.9 9.3 - - - +
91A GLY 2.9 12.1 + - - +
92A PHE* 3.0 18.8 + + - +
94A GLU* 1.3 76.3 - - - +
96A LYS* 1.3 63.8 + - - +
98A LEU* 3.1 8.1 + - + +
99A TRP* 2.9 26.4 + + + +
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Residues in contact with LYS 96 (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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33A ASP* 2.6 32.1 + - - +
35A LEU* 4.5 16.1 - - + +
92A PHE* 2.8 48.7 + - + +
93A ASN* 3.4 18.6 - - - +
95A PHE* 1.3 76.3 - - - +
97A GLU* 1.3 62.1 + - + +
99A TRP* 3.3 5.5 + - - +
100A ALA* 3.1 20.8 + - - +
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Residues in contact with GLU 97 (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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82A LEU* 3.9 12.9 - - + +
84A ARG* 2.8 44.7 + - - -
93A ASN* 3.1 11.7 + - - +
94A GLU* 3.3 20.4 + - - +
96A LYS* 1.3 79.3 - - - +
98A LEU* 1.3 62.8 + - - +
100A ALA* 3.1 10.2 + - - +
101A VAL* 2.9 28.6 + - + +
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Residues in contact with LEU 98 (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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54A LEU* 4.1 17.9 - - + -
58A LEU* 4.1 16.2 - - + -
78A MET* 3.9 24.2 - - + -
81A MET* 4.3 18.6 - - + -
82A LEU* 3.8 16.7 - - + +
90A MET* 4.8 3.1 - - + -
94A GLU 3.0 12.1 + - - +
95A PHE* 3.3 13.5 - - + +
97A GLU* 1.3 75.8 - - - +
99A TRP* 1.3 55.0 + - - +
101A VAL* 3.0 6.7 + - + -
102A LEU* 2.7 72.3 + - + +
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Residues in contact with TRP 99 (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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35A LEU* 3.4 46.0 - - + +
38A TYR* 5.6 1.6 - + - -
58A LEU* 4.9 9.2 - - + -
61A SER* 3.3 47.1 - - - -
63A ILE* 3.6 24.9 - - + -
95A PHE* 2.9 16.3 + + + +
96A LYS 3.5 8.5 - - - +
98A LEU* 1.3 76.2 - - - +
100A ALA* 1.3 67.5 + - + +
102A LEU* 4.1 6.1 - - + +
103A ASN* 3.0 49.5 + - - +
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Residues in contact with ALA 100 (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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96A LYS 3.1 9.6 + - - +
97A GLU* 3.1 12.6 + - - +
99A TRP* 1.3 85.4 - - + +
101A VAL* 1.3 62.6 + - + +
103A ASN* 3.5 4.5 + - - +
104A GLY* 3.2 17.3 + - - -
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Residues in contact with VAL 101 (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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81A MET* 4.7 7.6 - - + -
82A LEU* 6.3 1.3 - - + -
97A GLU* 2.9 22.2 + - + +
98A LEU* 3.5 10.3 - - + +
100A ALA* 1.3 76.8 - - + +
102A LEU* 1.3 66.0 + - + +
104A GLY* 3.0 12.1 + - - -
105A TRP* 3.1 56.5 + - + +
167A ARG* 3.9 25.4 - - - +
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Residues in contact with LEU 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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58A LEU* 4.1 11.9 - - + -
63A ILE* 4.0 17.6 - - + +
70A PHE* 4.0 14.8 - - + -
78A MET* 3.8 17.0 - - + -
98A LEU* 2.7 56.2 + - + +
99A TRP* 4.1 4.0 - - - +
101A VAL* 1.3 72.5 - - - +
103A ASN* 1.3 62.2 + - - +
105A TRP* 3.3 19.0 + - + +
106A ARG* 2.9 25.6 + - - +
156A PHE* 5.6 0.3 - - - -
160A ILE* 3.7 34.0 - - + +
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Residues in contact with ASN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 3.5 13.6 - - - +
99A TRP* 3.0 57.0 + - + +
100A ALA* 3.7 6.3 - - - +
102A LEU* 1.3 77.0 - - - +
104A GLY* 1.3 56.5 + - - +
106A ARG* 3.9 23.1 + - - +
107A GLN* 2.9 34.5 + - - +
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Residues in contact with GLY 104 (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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100A ALA 3.2 8.1 + - - -
101A VAL 3.0 8.0 + - - -
103A ASN* 1.3 80.0 - - - +
105A TRP* 1.3 60.0 + - - +
107A GLN* 3.4 7.3 - - - +
108A HIS* 3.0 34.3 + - - -
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Residues in contact with TRP 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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81A MET* 4.2 13.2 - - + -
101A VAL* 3.1 36.5 + - + +
102A LEU* 3.9 25.4 - - + +
103A ASN 3.3 0.2 - - - -
104A GLY* 1.3 77.7 - - - +
106A ARG* 1.3 59.9 + - - +
108A HIS* 3.2 6.0 + - - -
109A PHE* 2.7 26.9 + - - +
132A MET* 4.0 28.9 - - + +
134A PHE* 5.2 3.5 - + - -
159A TYR* 3.0 17.7 + - + +
160A ILE* 3.8 17.7 - - + -
163A CYS* 3.6 25.1 - - + -
164A VAL* 3.7 43.5 - - + -
167A ARG* 3.8 25.9 - - + +
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A GLY 4.3 3.4 + - - -
63A ILE* 3.2 34.1 + - + +
65A GLY* 3.9 19.3 - - - +
67A TYR* 4.6 9.9 - - + -
102A LEU 2.9 17.6 + - - +
103A ASN* 3.9 24.0 - - - +
105A TRP* 1.3 73.8 - - - +
107A GLN* 1.3 66.5 + - - +
109A PHE* 3.0 1.3 + - - +
110A ILE* 2.7 61.6 + - + +
156A PHE* 3.7 33.0 - - + -
160A ILE* 4.6 0.6 - - - +
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Residues in contact with GLN 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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103A ASN* 2.9 22.7 + - - +
104A GLY* 3.4 8.1 - - - +
106A ARG* 1.3 86.6 - - - +
108A HIS* 1.3 65.1 + - + +
110A ILE* 3.3 26.9 + - - +
111A SER* 3.3 12.6 + - - -
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Residues in contact with HIS 108 (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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104A GLY* 3.0 22.1 + - - +
105A TRP* 3.5 10.0 - + - +
107A GLN* 1.3 75.9 - - + +
109A PHE* 1.3 64.3 + - - +
111A SER* 2.7 26.9 + - - -
112A PHE* 3.0 16.1 - + + -
128A ALA* 5.6 2.5 - - + +
131A THR* 4.1 21.0 + - - +
132A MET* 3.8 37.7 - - + +
159A TYR* 3.9 9.6 - - - +
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Residues in contact with PHE 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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67A TYR* 3.6 33.7 - + - -
105A TRP 2.7 20.4 + - - +
106A ARG* 3.4 8.1 - - - +
108A HIS* 1.3 72.4 - - - +
110A ILE* 1.3 64.4 + - - +
112A PHE* 3.0 17.6 + - - +
113A ASP* 3.1 24.7 + - + -
118A GLY 4.0 3.8 - - - -
119A THR* 3.9 26.9 - - - -
120A VAL* 3.9 22.7 - - + -
128A ALA* 6.0 0.9 - - - -
154A ILE 4.4 0.4 - - - -
155A THR 4.3 2.2 - - - -
156A PHE* 3.9 23.6 - + + -
159A TYR* 3.4 51.8 + + + -
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Residues in contact with ILE 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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67A TYR* 4.4 15.3 - - + +
106A ARG* 2.7 52.2 + - + +
107A GLN* 3.3 23.8 - - - +
109A PHE* 1.3 71.5 - - - +
111A SER* 1.3 57.2 + - - +
112A PHE 2.8 11.8 + - - -
113A ASP* 3.3 17.8 + - - +
114A THR* 4.5 1.6 + - - -
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Residues in contact with SER 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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107A GLN 3.3 7.2 + - - -
108A HIS* 2.7 26.9 + - - -
110A ILE* 1.3 77.8 - - - +
112A PHE* 1.3 78.3 + - - +
114A THR* 5.1 6.4 - - - +
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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
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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