Contacts of the helix formed by residues 100 - 121 (chain C) in PDB entry 5Y3R
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 100 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C LEU* 6.3 1.1 - - + -
96C MET* 5.0 8.7 - - + +
97C GLY 4.4 4.0 - - - +
98C GLN* 2.8 11.6 - - + +
99C LYS* 1.3 78.0 - - - +
101C ALA* 1.3 55.7 + - + +
102C PRO* 3.3 2.5 - - - -
103C TYR* 2.5 22.8 + - + +
104C SER* 2.1 57.4 + - - +
107C ILE* 6.2 0.9 - - + -
141C SER* 3.4 37.7 - - - +
143C LEU* 3.4 28.9 - - + -
145C ASP* 6.3 0.7 - - + -
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Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LYS 3.4 1.3 - - - -
100C ILE* 1.3 77.7 - - - +
102C PRO* 1.3 72.4 - - + +
104C SER* 2.2 32.5 + - - +
105C VAL* 3.0 9.7 + - - +
146C GLU* 5.5 2.2 - - - +
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Residues in contact with PRO 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LYS 3.9 9.0 - - - +
100C ILE 3.2 3.4 - - - +
101C ALA* 1.3 92.3 - - + +
103C TYR* 1.3 93.1 + - + +
105C VAL* 4.2 1.2 - - - +
106C GLU* 2.9 32.3 + - - +
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Residues in contact with TYR 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C SER* 2.9 59.8 + - - -
61C ARG* 4.7 2.1 - - - +
63C PHE* 3.1 36.1 - + + -
64C GLY* 4.6 1.3 - - - -
99C LYS 4.5 8.1 - - - -
100C ILE* 2.5 19.2 + - + +
102C PRO* 1.3 90.2 - - + +
104C SER* 1.3 67.0 + - - +
106C GLU* 3.1 30.5 - - + -
107C ILE* 2.8 35.1 + - + +
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Residues in contact with SER 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C ILE* 2.1 52.5 + - - +
101C ALA* 2.2 35.2 + - - -
103C TYR* 1.3 74.5 - - - +
105C VAL* 1.3 66.3 + - - +
107C ILE* 3.6 1.0 - - - +
108C LYS* 2.7 40.1 + - - +
145C ASP* 6.6 0.2 - - - -
146C GLU* 3.7 12.3 + - - -
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ALA* 3.0 7.0 + - + +
102C PRO 4.4 0.9 - - - +
104C SER* 1.3 94.6 + - - +
106C GLU* 1.3 61.8 + - - +
108C LYS* 2.8 28.2 + - - +
109C ASN* 3.0 10.6 + - + +
146C GLU* 3.7 15.7 - - - +
149C ILE* 3.5 44.0 - - + -
153C PHE* 5.8 0.7 - - + -
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Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C PHE* 4.7 0.8 - - - -
64C GLY* 3.7 24.1 - - - -
67C VAL* 4.7 11.5 - - + +
68C PHE* 5.0 8.1 - - - -
102C PRO* 2.9 22.0 + - - +
103C TYR* 3.1 33.1 - - + -
105C VAL* 1.3 78.4 - - - +
107C ILE* 1.3 53.2 + - + +
109C ASN* 3.9 1.3 - - - +
110C THR* 2.2 44.3 + - - +
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Residues in contact with ILE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C PHE* 4.3 29.4 - - + -
67C VAL* 5.3 4.3 - - + -
89C LEU* 6.1 4.0 - - + -
93C LEU* 5.4 13.2 - - + -
100C ILE* 6.2 0.9 - - + -
103C TYR* 2.8 37.3 + - + +
104C SER 3.9 0.9 - - - +
106C GLU* 1.3 75.3 - - + +
108C LYS* 1.3 60.8 + - - +
110C THR* 3.4 9.6 - - + +
111C CYS* 2.8 51.6 + - + +
137C THR* 4.7 9.4 - - + -
141C SER* 5.7 2.9 - - - +
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Residues in contact with LYS 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C SER* 2.7 25.7 + - - +
105C VAL* 2.8 17.5 + - - +
107C ILE* 1.3 75.9 - - - +
109C ASN* 1.3 53.9 + - - +
111C CYS* 4.5 0.9 - - - +
112C THR* 2.4 37.4 + - - -
138C PHE* 6.1 2.8 - - - -
142C ARG* 5.7 7.7 - - - +
146C GLU* 3.8 20.6 - - + +
149C ILE* 3.3 22.7 - - + -
150C GLY* 3.1 42.6 - - - +
153C PHE* 3.2 13.1 - - + -
157C TYR* 4.0 0.7 + - - -
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Residues in contact with ASN 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C VAL* 3.0 9.5 + - + +
106C GLU 4.7 0.7 - - - +
108C LYS* 1.3 80.1 - - - +
110C THR* 1.3 58.1 + - - +
112C THR* 3.1 24.1 - - - +
113C SER* 2.9 33.6 + - - -
153C PHE* 3.3 22.5 - - + -
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Residues in contact with THR 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C VAL* 3.3 51.8 - - + +
106C GLU* 2.2 34.1 + - - +
107C ILE* 3.3 11.2 - - + +
108C LYS 3.1 0.4 - - - -
109C ASN* 1.3 75.1 - - - +
111C CYS* 1.3 62.9 + - - +
113C SER* 2.6 30.8 + - - -
114C VAL* 2.9 19.1 + - + +
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Residues in contact with CYS 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU* 4.9 4.5 - - - -
89C LEU* 5.2 6.1 - - - -
107C ILE* 2.8 38.5 + - + +
108C LYS 4.5 0.4 - - - +
110C THR* 1.3 77.0 - - - +
112C THR* 1.3 65.9 + - - +
114C VAL* 3.2 12.8 - - - +
115C TYR* 2.8 31.2 + - + -
134C LEU* 3.6 28.2 - - + +
137C THR* 3.7 17.5 - - + -
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Residues in contact with THR 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C LYS 2.4 24.2 + - - -
109C ASN* 3.1 30.9 - - - +
111C CYS* 1.3 72.7 - - - +
113C SER* 1.3 58.8 + - - +
115C TYR* 3.0 31.5 + - - +
116C THR* 3.0 8.5 + - - +
153C PHE* 3.5 13.7 - - + -
157C TYR* 2.3 44.1 + - + +
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Residues in contact with SER 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ASP* 5.7 1.0 + - - -
71C LYS* 5.3 19.7 + - - -
109C ASN* 2.9 20.7 + - - -
110C THR* 2.6 16.9 + - - -
112C THR* 1.3 72.0 - - - +
114C VAL* 1.3 57.6 + - - -
116C THR* 3.0 22.5 + - - +
117C LYS* 2.8 26.7 + - - +
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Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C LYS* 6.5 0.9 - - - -
82C ARG* 3.1 28.0 - - - +
86C LEU* 4.2 16.8 - - + -
110C THR* 3.4 22.2 - - + +
111C CYS* 2.9 19.1 + - + +
113C SER* 1.3 76.9 - - - +
115C TYR* 1.3 61.8 + - - +
116C THR 3.0 0.7 - - - -
117C LYS* 2.8 19.1 + - + +
118C ASP* 2.9 12.6 + - - +
130C LEU* 5.1 2.7 - - + +
134C LEU* 3.4 30.4 - - + +
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Residues in contact with TYR 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C CYS* 2.8 31.0 + - + -
112C THR* 3.0 10.8 - - - +
114C VAL* 1.3 73.6 - - - +
116C THR* 1.3 57.6 + - - +
118C ASP* 3.2 8.1 + - - +
119C ARG* 2.8 25.4 + - - +
131C LEU* 3.4 31.0 - - + +
134C LEU* 3.3 13.7 + - + +
135C LEU* 3.4 28.1 - - + +
138C PHE* 4.0 10.3 - + - +
157C TYR* 3.8 26.5 - + + -
160C LEU* 3.9 40.2 - - + -
173C LYS* 5.5 3.8 - - + -
176C GLU* 6.4 0.2 - - + -
177C LEU* 3.2 31.7 - - + +
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Residues in contact with THR 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ASP* 5.0 1.6 - - - -
301B ASP* 3.4 22.1 + - + +
302B GLU* 2.8 36.0 - - - +
112C THR* 3.0 6.3 + - - +
113C SER* 3.0 29.6 + - - +
114C VAL 3.0 0.8 - - - -
115C TYR* 1.3 80.4 - - - +
117C LYS* 1.3 58.4 + - + -
119C ARG* 2.8 49.3 + - - +
120C ALA 2.9 4.9 + - - -
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Residues in contact with LYS 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ASP* 3.5 9.8 + - - +
300B ASP* 2.9 29.2 + - - +
70C ARG 3.8 1.6 - - - +
71C LYS* 3.3 19.4 + - + +
73C LEU 2.5 25.9 + - - -
74C ASN* 3.1 14.7 + - - +
79C ARG* 2.9 23.9 + - - +
82C ARG* 3.0 54.3 - - - +
113C SER 2.8 19.1 + - - +
114C VAL* 2.8 15.4 + - + +
116C THR* 1.3 73.9 - - + +
118C ASP* 1.3 62.8 + - - +
120C ALA* 3.3 10.4 + - - +
130C LEU* 4.4 1.6 - - - -
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Residues in contact with ASP 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C VAL 2.9 6.0 + - - +
115C TYR 3.3 9.0 - - - +
117C LYS* 1.3 77.2 - - - +
119C ARG* 1.3 56.9 + - - +
121C ALA 2.8 30.0 - - - -
122C LYS* 2.2 53.6 + - - +
123C CYS 3.9 0.5 + - - -
127C ALA* 3.0 34.0 - - - +
130C LEU* 4.0 12.7 - - + +
131C LEU* 3.0 30.5 - - + +
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Residues in contact with ARG 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A LYS* 2.6 32.2 + - - +
299A LYS* 4.1 19.2 - - - +
301B ASP* 2.3 54.1 + - - +
302B GLU* 2.3 27.4 + - + +
303B THR* 5.9 0.2 - - - -
115C TYR 2.8 13.5 + - - +
116C THR* 2.8 37.0 + - - +
118C ASP* 1.3 76.4 - - - +
120C ALA* 1.3 55.8 + - - +
122C LYS* 4.6 3.8 - - - -
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Residues in contact with ALA 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LYS* 2.7 27.4 + - - +
298B ASN* 3.9 16.3 - - - +
299B ASP* 3.5 31.6 - - - +
302B GLU* 3.6 10.2 + - - +
74C ASN 5.5 1.6 - - - +
79C ARG* 4.3 2.9 - - - +
116C THR 2.9 7.7 + - - +
117C LYS* 3.5 15.0 - - + +
118C ASP 3.2 0.4 - - - -
119C ARG* 1.3 75.5 - - - +
121C ALA* 1.3 57.2 + - + +
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Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A LYS* 3.5 2.9 - - - +
75C SER* 5.3 4.3 - - - +
79C ARG* 2.6 48.3 + - - +
118C ASP 2.8 8.2 - - - +
120C ALA* 1.3 79.9 - - + +
122C LYS* 1.3 60.0 + - - +
124C LYS* 3.9 12.3 - - - +
127C ALA* 3.4 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
------------------------------------------------------------
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