Contacts of the helix formed by residues 107 - 123 (chain C) 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 CYS 107 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C LEU* 6.4 0.2 - - - -
72C MET* 3.6 35.9 - - + +
73C ALA 5.8 0.2 - - - -
105C ILE 3.5 1.8 + - - -
106C PRO* 1.3 70.4 - - - +
108C GLU* 1.3 64.8 + - - +
110C LEU* 3.1 21.9 + - - +
111C VAL* 3.2 18.3 + - - +
136C TYR* 4.4 17.7 - - - -
137C ILE 4.1 4.7 - - - -
138C GLY* 3.9 16.2 - - - -
140C ASP* 3.4 13.0 - - + +
146C GLN* 3.6 19.5 - - + +
148C TYR* 5.4 2.9 - - - -
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Residues in contact with GLU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C PRO 3.2 0.6 - - - -
107C CYS* 1.3 77.5 - - - +
109C GLN* 1.3 61.1 + - - +
111C VAL* 3.4 7.7 + - - +
112C THR* 3.1 38.3 + - - +
140C ASP* 4.5 6.3 - - - +
143C TYR* 5.3 7.9 - - + -
146C GLN* 3.5 15.4 - - - +
148C TYR* 3.2 33.4 - - + +
156C TYR* 3.5 23.7 - - - -
70K ARG 5.7 1.2 - - - +
71K ASN* 5.3 7.6 - - - +
73K TYR* 4.8 9.3 + - + +
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Residues in contact with GLN 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C TYR* 3.2 27.9 - - - -
105C ILE* 4.0 7.2 - - + +
106C PRO* 3.4 21.1 - - - +
107C CYS 3.2 0.2 - - - -
108C GLU* 1.3 77.4 - - - +
110C LEU* 1.3 63.4 + - - +
112C THR* 3.0 25.8 + - - +
113C ALA* 3.1 11.4 + - - +
67K TYR* 3.6 17.6 + - - -
71K ASN* 3.4 39.4 + - + +
73K TYR* 3.3 28.4 + - - +
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 3.7 25.8 - - + -
69C ASN* 3.7 21.5 - - - +
72C MET* 4.6 9.2 - - + -
90C LEU* 3.3 40.1 - - + +
93C ILE* 4.1 17.9 - - + -
94C ALA* 4.1 5.4 - - + +
105C ILE* 3.8 25.1 - - + +
106C PRO 3.4 1.9 + - - +
107C CYS* 3.1 12.9 + - - +
109C GLN* 1.3 77.3 - - - +
111C VAL* 1.4 62.3 + - + +
113C ALA* 3.4 4.0 + - - +
114C LEU* 3.2 20.6 + - - +
136C TYR* 5.3 2.5 - - + -
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Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C CYS* 3.2 15.2 + - - +
108C GLU* 3.5 9.0 - - - +
110C LEU* 1.4 75.2 - - + +
112C THR* 1.4 64.2 + - - +
114C LEU* 3.3 1.9 + - - +
115C CYS* 3.1 25.7 + - - -
136C TYR* 2.9 63.7 - - + +
148C TYR* 4.2 11.4 - - + -
156C TYR* 3.5 33.4 - - + -
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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 GLU* 3.1 37.7 + - - +
109C GLN* 3.0 18.3 + - - +
111C VAL* 1.4 75.2 - - - +
113C ALA* 1.3 53.8 + - - +
115C CYS 3.5 0.3 + - - -
116C ASP* 2.8 39.8 + - - +
156C TYR* 3.5 31.4 - - + +
81D ARG* 3.8 6.4 + - - -
70K ARG 6.1 0.7 - - - +
71K ASN* 5.7 1.2 + - - -
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Residues in contact with ALA 113 (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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93C ILE* 3.7 35.2 - - + -
105C ILE* 5.8 0.2 - - + -
109C GLN 3.1 10.5 + - - +
110C LEU 3.6 8.7 - - - +
111C VAL 3.2 0.2 - - - -
112C THR* 1.3 74.5 + - - +
114C LEU* 1.3 65.4 + - - +
116C ASP* 3.2 20.4 + - - +
117C ILE* 3.2 16.2 + - + +
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Residues in contact with LEU 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU* 3.7 41.3 - - + +
89C GLU* 4.1 17.0 - - + -
90C LEU* 3.7 28.3 - - + +
93C ILE* 4.1 2.8 - - + +
110C LEU 3.2 5.0 + - - +
111C VAL 3.3 2.2 + - - +
113C ALA* 1.3 78.3 - - - +
115C CYS* 1.3 57.4 + - - +
117C ILE* 3.1 15.9 + - + +
118C LYS* 2.9 33.5 + - - +
134C LEU* 3.4 24.5 - - + -
136C TYR* 3.3 23.8 - - - +
150C SER* 5.4 0.9 - - - +
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Residues in contact with CYS 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C VAL* 3.1 26.1 + - - +
112C THR 4.0 1.1 - - - +
114C LEU* 1.3 75.0 - - - +
116C ASP* 1.3 58.8 + - - +
118C LYS* 3.7 9.5 - - - +
119C GLN* 3.0 25.3 + - - +
136C TYR* 4.4 2.9 - - - -
150C SER* 3.1 32.8 - - - -
154C GLY* 4.2 5.9 - - - -
155C ASN 3.4 20.4 - - - +
156C TYR* 4.3 2.0 - - + -
81D ARG* 2.8 30.9 + - - +
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Residues in contact with ASP 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C THR* 2.8 28.5 + - - +
113C ALA* 3.2 12.5 + - - +
115C CYS* 1.3 74.4 - - - +
117C ILE* 1.4 64.9 + - + +
119C GLN* 3.4 2.4 + - - +
120C ALA* 3.3 22.3 + - - +
81D ARG* 2.9 19.2 + - - -
82D ILE* 3.0 20.2 - - + +
85D ASN* 4.1 12.2 - - - +
70K ARG* 5.5 3.1 + - - -
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Residues in contact with ILE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU* 6.2 1.1 - - + -
89C GLU* 3.9 32.8 - - + +
93C ILE* 3.8 29.8 - - + -
96C ARG* 6.2 0.4 - - - +
113C ALA* 3.4 9.0 - - + +
114C LEU* 3.1 14.9 + - + +
116C ASP* 1.4 77.8 - - + +
118C LYS* 1.3 62.9 + - - +
120C ALA* 3.6 10.8 + - + +
121C TYR* 3.4 22.1 - - + -
130C PHE* 4.7 15.5 - - + -
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Residues in contact with LYS 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU* 4.2 23.1 - - + -
114C LEU* 2.9 22.2 + - - +
115C CYS* 3.7 9.0 - - - +
116C ASP 3.3 0.2 - - - -
117C ILE* 1.3 75.6 - - - +
119C GLN* 1.3 64.6 + - - +
121C TYR* 3.1 20.8 + - - +
122C THR* 3.7 7.2 + - - +
129C PRO* 5.1 2.1 - - + +
130C PHE* 4.0 35.8 + - + +
132C VAL 2.7 29.8 + - - -
134C LEU* 4.5 4.6 - - - +
150C SER* 3.1 28.2 + - - +
151C ASP 3.5 18.0 + - - +
152C PRO* 4.1 9.1 - - + +
153C SER* 4.5 6.0 - - - +
154C GLY 4.9 6.1 - - - +
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Residues in contact with GLN 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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115C CYS 3.0 18.8 + - - +
116C ASP 3.4 4.7 + - - +
118C LYS* 1.3 76.4 - - - +
120C ALA* 1.3 61.8 + - - +
122C THR* 2.8 40.2 + - - -
123C GLN* 3.0 24.2 + - + +
153C SER* 4.3 5.7 - - - +
154C GLY* 3.2 25.7 - - - +
78D ALA* 3.5 31.9 + - - +
79D ASP* 3.4 8.0 + - - +
81D ARG* 4.9 0.2 - - - +
82D ILE* 3.8 20.9 - - + -
125D ARG* 3.1 19.9 + - - -
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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
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116C ASP 3.3 12.1 + - - +
117C ILE* 3.7 12.8 - - + +
118C LYS 3.2 0.4 - - - -
119C GLN* 1.3 76.6 - - - +
121C TYR* 1.4 62.9 + - + +
123C GLN* 4.4 2.5 - - - -
124C PHE* 3.1 58.7 + - + +
82D ILE* 6.6 0.2 - - - -
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Residues in contact with TYR 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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122B GLN* 3.8 19.2 + - + +
9C THR 4.7 2.4 - - - +
10C THR* 5.4 0.5 - - - -
117C ILE* 3.4 22.9 - - + -
118C LYS 3.1 9.8 + - - +
120C ALA* 1.4 79.3 - - + +
122C THR* 1.3 63.7 + - - +
124C PHE 3.7 10.5 - - - +
126C GLY 5.3 0.3 + - - -
127C LYS* 3.3 49.5 + - + +
128C ARG 3.4 17.9 - - - -
129C PRO* 3.9 18.1 - - + -
130C PHE* 3.5 30.7 - + + -
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Residues in contact with THR 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C THR 5.1 3.8 - - - -
10C THR* 3.1 27.5 + - - -
18C LEU* 4.3 11.1 - - + +
20C GLN* 5.8 0.9 - - + -
21C VAL* 3.9 24.5 - - + -
118C LYS 3.7 5.6 + - - +
119C GLN* 2.8 43.1 + - - +
121C TYR* 1.3 78.7 - - - +
123C GLN* 1.4 55.8 + - - +
124C PHE 3.5 0.2 + - - -
129C PRO* 3.9 26.0 - - + -
153C SER* 5.1 8.3 - - - -
125D ARG* 3.7 14.2 + - - -
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Residues in contact with GLN 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C THR* 3.3 8.9 + - - -
119C GLN* 3.0 35.5 + - + +
120C ALA* 4.4 1.6 - - - -
121C TYR 3.5 0.2 - - - -
122C THR* 1.4 77.0 + - - +
124C PHE* 1.3 75.1 + - + +
79D ASP* 3.1 39.2 + - - +
82D ILE* 5.5 3.3 - - + +
118D TYR* 4.1 7.0 - - + -
124D ARG* 3.6 1.6 - - - +
125D ARG* 3.4 51.2 + - - +
127D PHE* 3.3 35.8 - - + -
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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