Contacts of the helix formed by residues 82 - 103 (chain S) in PDB entry 5A0Q
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 ILE 82 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152R THR* 4.8 21.5 - - + +
154R HIS* 5.6 6.3 - - + +
33S LEU 5.7 2.5 - - - +
34S GLY* 5.9 1.6 - - - -
35S SER 6.2 0.9 - - - +
53S ARG* 5.8 5.8 - - + -
65S GLU 5.1 8.7 - - - +
66S LYS* 4.9 20.6 - - - +
78S MET* 4.0 22.8 - - + +
79S SER* 5.8 3.4 - - - -
80S GLY 3.5 16.8 - - - +
81S LEU* 1.4 70.9 - - - +
83S ALA* 1.4 61.9 + - - +
85S ALA* 3.4 18.8 + - - +
86S LYS* 3.9 19.3 - - - +
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Residues in contact with ALA 83 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116R GLN* 4.2 11.1 - - + +
150R SER* 3.6 16.8 - - - +
151R GLY* 3.3 37.1 - - - +
152R THR* 3.8 12.6 + - - +
81S LEU* 3.3 1.7 - - + -
82S ILE* 1.4 76.6 - - - +
84S ASP* 1.3 67.2 + - - +
85S ALA 3.3 0.5 + - - -
86S LYS* 3.6 19.2 + - - +
87S THR* 4.4 4.0 + - - +
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Residues in contact with ASP 84 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116R GLN* 3.3 28.7 + - - +
150R SER 4.8 1.9 - - - +
81S LEU* 3.2 32.0 + - + +
83S ALA* 1.3 78.0 - - - +
85S ALA* 1.4 60.3 + - - +
87S THR* 2.8 25.3 + - - -
88S LEU* 4.1 1.7 + - - +
135S ARG* 3.2 36.9 + - - -
137S PHE* 4.0 16.6 - - + -
138S GLY 4.1 4.4 + - - +
139S VAL* 3.7 12.6 - - + +
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Residues in contact with ALA 85 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78S MET* 3.8 24.7 - - + -
81S LEU 3.3 5.5 + - - +
82S ILE* 3.4 12.8 - - - +
83S ALA 3.2 0.6 - - - -
84S ASP* 1.4 79.0 - - - +
86S LYS* 1.3 57.7 + - - +
88S LEU* 3.2 9.5 + - - +
89S ILE* 3.0 35.0 + - + +
139S VAL* 3.6 31.9 - - + -
141S LEU* 4.7 0.7 - - + +
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Residues in contact with LYS 86 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109R ARG* 6.5 0.4 - - - -
153R TYR* 3.3 44.4 + - + -
65S GLU* 5.9 5.5 + - - +
68S VAL* 6.0 3.8 - - + -
78S MET* 5.0 10.1 - - + -
82S ILE* 3.9 27.6 - - - +
83S ALA* 4.0 10.1 - - - +
84S ASP 3.3 1.0 - - - -
85S ALA* 1.3 75.9 - - + +
87S THR* 1.3 60.3 + - + +
89S ILE* 3.8 15.0 - - + +
90S ASP* 2.9 41.8 + - - +
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Residues in contact with THR 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113R SER* 5.9 7.6 - - - +
116R GLN* 3.8 28.8 + - + +
83S ALA 4.8 3.8 - - - +
84S ASP* 2.8 20.3 + - - +
86S LYS* 1.3 78.1 - - + +
88S LEU* 1.4 59.3 + - - +
90S ASP* 3.3 5.0 + - - +
91S LYS* 3.0 35.5 + - - +
137S PHE* 3.6 19.9 - - - -
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Residues in contact with LEU 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84S ASP 4.7 0.7 - - - +
85S ALA* 3.2 8.5 + - - +
87S THR* 1.4 78.4 + - - +
89S ILE* 1.3 59.6 + - - +
91S LYS* 3.7 5.0 + - + +
92S ALA* 3.0 26.3 + - - +
116S VAL* 4.2 33.7 - - + +
119S LEU* 4.1 30.2 - - + +
120S ALA* 5.5 1.8 - - + -
137S PHE* 3.8 57.7 - - + -
139S VAL* 5.0 9.9 - - + +
141S LEU* 4.5 14.8 - - + -
143S PHE* 6.5 0.2 - - - -
156S MET* 5.1 6.1 - - + -
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Residues in contact with ILE 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68S VAL* 3.7 23.1 - - + -
70S ILE* 4.5 4.8 - - + +
76S CYS* 4.0 21.5 - - - -
78S MET* 3.5 35.4 - - + -
85S ALA* 3.0 32.6 + - + +
86S LYS* 3.8 11.0 - - + +
88S LEU* 1.3 73.5 - - - +
90S ASP* 1.3 66.8 + - - +
92S ALA* 3.1 16.1 + - - +
93S ARG* 3.1 37.4 + - - +
141S LEU* 4.5 6.3 - - + -
143S PHE* 6.4 0.7 - - + -
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Residues in contact with ASP 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86S LYS* 2.9 29.6 + - - +
87S THR* 3.9 4.2 - - - +
89S ILE* 1.3 75.7 - - - +
91S LYS* 1.3 65.4 + - + +
93S ARG* 3.2 31.0 + - - +
94S VAL* 3.1 27.1 + - + +
69Z ARG* 3.5 29.4 - - - +
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Residues in contact with LYS 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87S THR* 3.0 22.5 + - - +
88S LEU* 4.0 5.4 - - + +
90S ASP* 1.3 79.4 - - + +
92S ALA* 1.3 55.6 + - - +
94S VAL* 3.4 26.3 + - + +
95S GLU* 3.1 35.7 + - + +
116S VAL* 5.7 0.2 - - - -
119S LEU* 4.2 26.2 - - + -
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Residues in contact with ALA 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70S ILE* 3.9 16.8 - - + -
88S LEU 3.0 16.2 + - - +
89S ILE* 3.1 12.3 + - - +
91S LYS* 1.3 73.3 - - - +
93S ARG* 1.3 57.9 + - - +
95S GLU* 3.3 7.4 + - - +
96S THR* 3.0 32.6 + - - +
112S VAL* 4.9 4.2 - - + +
116S VAL* 3.8 22.6 - - + +
143S PHE* 4.5 11.4 - - + -
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Residues in contact with ARG 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68S VAL* 4.1 14.1 - - - +
69S GLU* 2.9 36.1 + - - +
70S ILE* 3.7 23.1 - - + +
89S ILE* 3.1 30.5 + - - +
90S ASP* 3.2 31.3 + - - +
92S ALA* 1.3 71.4 - - - +
94S VAL* 1.3 65.2 + - + +
96S THR* 2.9 21.1 + - - -
97S GLN* 3.1 18.6 + - - +
65Z ILE* 5.1 8.5 - - + -
68Z LEU* 3.0 46.3 + - + +
69Z ARG* 4.1 13.6 + - + +
71Z LYS* 5.2 4.4 - - - +
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Residues in contact with VAL 94 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90S ASP* 3.1 16.8 + - + +
91S LYS* 3.6 33.7 - - + +
92S ALA 3.3 0.2 - - - -
93S ARG* 1.3 73.1 - - - +
95S GLU* 1.3 62.5 + - - +
97S GLN* 4.2 1.0 - - - +
98S ASN* 3.0 30.6 + - + +
61Z ARG* 5.4 0.5 - - - -
65Z ILE* 4.3 25.5 - - + +
69Z ARG* 4.8 14.8 - - - +
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Residues in contact with GLU 95 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91S LYS* 3.1 21.0 + - + +
92S ALA* 3.5 11.2 - - - +
93S ARG 3.3 0.2 - - - -
94S VAL* 1.3 79.5 - - + +
96S THR* 1.3 59.7 + - + +
98S ASN* 3.3 17.2 + - - +
99S HIS* 3.0 26.5 + - - +
107S MET* 4.4 15.9 - - - +
112S VAL* 6.3 0.7 - - - -
115S ALA* 4.1 29.4 - - + +
116S VAL* 6.4 0.2 - - + -
119S LEU* 6.1 3.8 - - + -
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Residues in contact with THR 96 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70S ILE* 4.0 5.9 + - + -
71S ASP* 3.1 38.0 + - - +
92S ALA 3.0 15.5 + - - +
93S ARG* 2.9 20.4 + - - -
95S GLU* 1.3 74.2 - - + +
97S GLN* 1.4 61.9 + - - +
99S HIS* 3.2 9.9 + - - +
100S TRP* 3.0 25.1 + - - +
106S THR* 5.7 0.2 - - - -
107S MET* 4.2 9.1 + - + +
112S VAL* 3.5 35.0 - - + -
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Residues in contact with GLN 97 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71S ASP* 3.0 27.1 + - - -
93S ARG 3.1 14.6 + - - +
94S VAL 4.2 0.4 - - - +
96S THR* 1.4 80.5 + - - +
98S ASN* 1.3 59.9 + - - +
100S TRP* 3.3 16.6 + - - +
101S PHE* 2.9 28.1 + - - +
61Z ARG* 3.7 28.8 - - + +
64Z ARG* 3.2 49.9 + - + +
65Z ILE* 3.6 23.1 - - + -
68Z LEU* 4.3 8.0 - - + +
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Residues in contact with ASN 98 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94S VAL* 3.0 23.3 + - + +
95S GLU* 3.4 20.6 + - - +
97S GLN* 1.3 75.3 - - - +
99S HIS* 1.3 63.6 + - - +
101S PHE* 3.4 2.4 + - - +
102S THR* 3.0 36.9 + - - -
103S TYR* 6.1 1.4 - - - -
61Z ARG* 3.6 24.5 + - - +
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Residues in contact with HIS 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95S GLU 3.0 14.4 + - - +
96S THR 3.2 9.6 + - - +
98S ASN* 1.3 77.9 - - - +
100S TRP* 1.3 58.9 + - - +
102S THR* 3.3 0.4 + - - -
103S TYR* 2.8 57.8 + + - +
104S ASN 3.7 0.2 + - - -
105S GLU* 3.0 55.4 + - - +
106S THR 3.7 4.4 + - - -
107S MET* 3.2 46.7 - - + +
75a TYR* 3.9 15.5 - + - -
79a ASN* 4.3 10.3 + - - -
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Residues in contact with TRP 100 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96S THR 3.0 12.9 + - - +
97S GLN* 3.3 22.0 + - - +
99S HIS* 1.3 77.5 - - - +
101S PHE* 1.3 64.6 + + + +
104S ASN* 2.8 45.9 + - - -
105S GLU 3.7 10.1 + - - +
106S THR* 4.2 25.5 - - + +
57Z ARG* 3.1 51.8 + - + -
60Z ALA* 5.0 13.9 - - + -
61Z ARG* 6.0 4.3 - - + -
64Z ARG* 4.5 16.9 - - - +
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Residues in contact with PHE 101 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97S GLN 2.9 17.4 + - - +
98S ASN 3.6 2.0 - - - +
100S TRP* 1.3 86.3 - + + +
102S THR* 1.3 67.8 + - - +
54Z PHE* 3.6 30.1 - + - -
57Z ARG* 3.0 61.3 + - + +
58Z LEU* 3.6 26.0 - - + -
61Z ARG* 3.5 39.9 - - + +
94a THR* 3.9 22.1 - - + +
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Residues in contact with THR 102 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98S ASN* 3.0 25.7 + - - -
101S PHE* 1.3 86.5 - - - +
103S TYR* 1.3 80.8 + - + +
104S ASN 3.9 0.2 - - - -
71a ARG* 3.4 29.2 - - - +
90a ALA 3.2 5.4 - - - +
91a MET* 3.1 26.6 - - + +
94a THR* 4.1 11.8 + - - +
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Residues in contact with TYR 103 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98S ASN* 6.1 1.1 - - - -
99S HIS* 2.8 41.6 + + - +
102S THR* 1.3 100.1 - - + +
104S ASN* 1.3 61.0 + - - +
105S GLU* 2.7 36.4 + - + +
71a ARG* 3.6 22.0 + - - -
75a TYR* 4.3 20.4 - + - +
83a MET* 4.1 12.6 - - + -
86a GLY 4.2 0.3 - - - +
87a ALA* 3.5 32.6 + - + -
90a ALA* 3.8 2.7 - - - -
91a MET* 3.7 31.2 - - + -
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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