Contacts of the helix formed by residues 110 - 126 (chain C) in PDB entry 4A12
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 ARG 110 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ASP* 2.7 32.7 + - - +
101C SER* 3.0 16.9 + - - +
102C VAL 2.8 29.2 + - - -
103C PHE* 3.5 47.6 - - + +
104C HIS* 4.4 7.9 + - - -
109C ALA* 1.3 73.3 - - - +
111C GLY* 1.3 68.3 + - - +
112C HIS* 3.3 27.5 + - + -
113C VAL* 3.1 22.5 + - + +
114C LEU* 3.9 5.8 + - - +
75D GLU 4.7 0.2 + - - -
76D GLN 3.5 13.5 + - - -
77D GLU* 3.3 42.8 - - - +
119D ASN* 5.3 0.4 - - - +
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Residues in contact with GLY 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PHE* 5.0 3.8 - - - -
109C ALA 3.8 1.8 + - - -
110C ARG* 1.3 71.6 - - - +
112C HIS* 1.3 60.7 + - - +
113C VAL 3.3 1.0 + - - -
114C LEU* 3.5 6.3 + - - -
115C PHE* 3.5 5.0 + - - +
140C PHE* 3.3 41.6 - - - -
115D PHE* 4.3 2.9 - - - -
119D ASN* 3.7 19.0 - - - +
133D THR* 4.4 7.7 + - - -
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Residues in contact with HIS 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ARG* 3.6 25.2 + - + +
111C GLY* 1.3 71.7 - - - +
113C VAL* 1.4 69.0 + - + +
115C PHE* 3.9 2.1 - - - +
116C ALA* 3.0 31.2 + - - +
73D ILE* 3.6 20.9 + - + +
76D GLN 3.1 20.6 + - - -
77D GLU 3.7 12.1 - - - -
79D ILE* 3.3 24.0 - - + +
112D HIS* 5.2 1.3 - - - +
115D PHE* 3.8 16.4 - - + -
116D ALA* 3.6 28.0 + - + +
119D ASN* 3.6 18.3 + - - +
120D SER* 4.0 8.2 + - - -
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Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ILE* 4.3 1.2 - - - +
95C LEU* 3.9 19.0 - - + +
97C ILE* 4.1 9.9 - - + -
101C SER* 3.5 35.0 - - - +
109C ALA* 4.8 2.9 - - + -
110C ARG* 3.1 24.6 + - + +
112C HIS* 1.4 82.7 - - + +
114C LEU* 1.3 63.0 + - + +
116C ALA* 3.4 3.6 + - - +
117C GLN* 3.4 20.1 + - - +
74D GLU* 3.3 44.2 - - + +
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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
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95C LEU* 5.3 1.6 - - + -
97C ILE* 5.4 1.8 - - + -
109C ALA* 4.2 17.0 - - + +
110C ARG 4.3 7.4 - - - +
111C GLY* 3.5 5.6 + - - +
112C HIS 3.4 0.2 - - - -
113C VAL* 1.3 77.0 - - + +
115C PHE* 1.3 64.5 + - - +
117C GLN* 3.6 10.6 + - - +
118C ALA* 3.2 22.3 + - - +
140C PHE* 4.2 15.9 - - + -
144C VAL* 3.8 36.3 - - + +
150C VAL* 3.7 35.2 - - + -
170C SER* 4.8 2.6 + - - -
177C VAL* 4.6 0.7 - - + -
178C PHE* 4.1 35.3 - - + -
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Residues in contact with PHE 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 GLY 3.5 5.4 + - - +
112C HIS 3.5 3.1 + - - +
113C VAL 3.4 0.6 - - - -
114C LEU* 1.3 75.3 - - - +
116C ALA* 1.4 55.2 + - - +
118C ALA* 3.2 4.8 + - - +
119C ASN* 2.8 42.4 + - + +
133C THR* 5.2 0.2 - - + -
136C SER* 3.4 27.1 - - - -
138C ILE* 3.7 31.2 - - + -
178C PHE* 4.3 4.4 - - - -
182C PHE* 3.5 20.4 - + - -
111D GLY 4.2 2.2 - - - -
112D HIS* 3.7 29.4 - - + -
115D PHE* 3.6 44.4 - + + -
138D ILE* 3.6 21.3 - - + -
140D PHE* 4.7 3.8 - + - -
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Residues in contact with ALA 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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79C ILE* 3.7 24.3 - - + +
112C HIS 3.0 19.1 + - - +
113C VAL* 3.5 7.4 - - - +
114C LEU 3.3 0.2 - - - -
115C PHE* 1.4 77.1 - - - +
117C GLN* 1.3 56.7 + - - +
120C SER* 3.1 33.4 + - - -
73D ILE* 4.0 11.7 - - + -
74D GLU* 4.9 1.3 - - + -
112D HIS* 3.5 26.9 + - + -
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Residues in contact with GLN 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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79C ILE* 3.7 19.1 - - + +
80C GLY* 4.9 0.4 - - - -
93C SER* 3.2 35.1 + - - +
94C ILE 3.5 1.0 - - - -
95C LEU* 3.5 32.3 - - + +
113C VAL 3.4 9.3 + - - +
114C LEU* 3.8 10.5 - - - +
115C PHE 3.3 0.6 - - - -
116C ALA* 1.3 76.8 - - - +
118C ALA* 1.3 58.2 + - - +
120C SER* 3.5 3.1 + - - -
121C LEU* 3.1 28.3 + - - +
150C VAL* 3.1 47.1 + - - +
152C ALA* 3.5 13.5 - - + +
170C SER* 4.4 2.1 + - - -
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Residues in contact with ALA 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 LEU 3.2 12.1 + - - +
115C PHE 3.4 8.3 - - - +
117C GLN* 1.3 76.8 - - - +
119C ASN* 1.3 64.1 + - - +
121C LEU* 3.3 7.0 + - - +
122C CYS* 3.2 26.5 + - - -
152C ALA* 5.3 1.6 - - - -
168C VAL* 3.9 18.1 - - + +
170C SER* 5.3 0.9 - - - +
178C PHE* 3.7 26.0 - - + -
182C PHE* 3.7 15.0 - - + -
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Residues in contact with ASN 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 PHE* 2.8 32.1 + - + +
116C ALA 4.1 3.1 - - - +
118C ALA* 1.3 71.5 - - - +
120C SER* 1.4 63.7 + - - +
122C CYS* 3.1 14.2 + - - +
123C VAL* 3.2 24.6 + - - +
133C THR* 2.7 37.1 + - - +
182C PHE* 3.7 15.3 - - + -
184C MSE 4.8 0.3 - - - +
103D PHE* 5.5 1.4 - - - -
110D ARG* 5.2 0.8 - - - +
111D GLY* 3.7 11.7 - - - +
112D HIS* 3.5 34.5 + - - +
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Residues in contact with SER 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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77C GLU 4.3 1.6 + - - -
78C PHE* 3.3 26.5 - - - -
79C ILE* 3.1 32.4 + - - +
116C ALA 3.1 20.2 + - - -
117C GLN 3.7 4.7 - - - -
119C ASN* 1.4 76.4 - - - +
121C LEU* 1.3 61.9 + - - +
123C VAL* 3.4 10.5 + - - +
124C ALA* 3.2 17.5 + - - +
112D HIS* 3.9 13.8 - - - -
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Residues in contact with LEU 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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78C PHE* 3.9 5.8 - - - -
82C LEU* 3.7 18.4 - - + -
91C ALA* 3.8 11.0 - - + +
92C GLN 3.7 3.6 - - - -
93C SER* 3.7 28.5 - - - +
117C GLN 3.1 17.5 + - - +
118C ALA 3.5 6.3 - - - +
119C ASN 3.3 0.2 - - - -
120C SER* 1.3 74.5 - - - +
122C CYS* 1.3 57.8 + - - +
124C ALA* 3.4 2.9 + - - +
125C LEU* 2.9 29.3 + - - +
152C ALA* 3.4 39.9 - - + +
153C GLU 4.0 0.7 - - - +
154C ALA* 3.6 30.5 - - + +
168C VAL* 4.7 4.3 - - + -
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Residues in contact with CYS 122 (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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118C ALA 3.2 14.8 + - - -
119C ASN* 3.1 9.7 + - - +
121C LEU* 1.3 74.4 - - - +
123C VAL* 1.3 63.3 + - - +
125C LEU* 3.2 6.6 + - - +
126C ILE* 3.1 30.8 + - - +
154C ALA* 4.7 0.4 - - - -
166C VAL* 3.8 17.3 - - + -
168C VAL* 3.6 24.2 - - - -
182C PHE* 3.7 23.3 - - - -
184C MSE 3.8 25.1 - - + -
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Residues in contact with VAL 123 (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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119C ASN* 3.2 25.3 + - - +
120C SER* 3.4 8.0 + - - +
122C CYS* 1.3 74.0 - - - +
124C ALA* 1.4 60.6 + - - +
126C ILE* 3.2 18.4 - - - +
131C VAL* 4.3 26.4 - - + +
132C LEU* 6.3 0.2 - - - -
133C THR* 4.8 1.3 - - - +
184C MSE 3.8 15.7 - - + -
103D PHE* 4.1 35.7 - - + -
105D LYS* 5.9 5.6 - - - +
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Residues in contact with ALA 124 (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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78C PHE* 3.8 19.5 - - + -
82C LEU* 4.0 22.9 - - + -
85C VAL* 4.2 14.9 - - + +
120C SER 3.2 13.8 + - - +
121C LEU* 3.5 8.7 - - - +
122C CYS 3.3 0.2 - - - -
123C VAL* 1.4 76.1 - - - +
125C LEU* 1.3 63.2 + - - +
126C ILE 4.3 3.6 - - - +
127C LYS* 4.9 1.6 + - - +
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Residues in contact with LEU 125 (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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85C VAL* 5.0 2.7 - - + -
86C ASN 3.6 11.2 - - - +
87C PRO* 3.8 5.4 - - - +
88C ASN 2.9 25.1 + - - -
89C VAL 3.6 6.5 - - - +
90C LYS 3.5 36.6 - - - +
91C ALA* 3.8 10.3 - - + +
121C LEU 2.9 17.7 + - - +
122C CYS* 3.2 6.5 + - - +
124C ALA* 1.3 77.2 - - - +
126C ILE* 1.3 59.9 + - + +
127C LYS* 3.4 1.4 + - - +
154C ALA* 3.7 24.5 - - + +
155C ARG 4.2 0.7 - - - +
156C VAL* 3.8 24.5 - - + +
166C VAL* 3.8 25.1 - - + -
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Residues in contact with ILE 126 (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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88C ASN* 3.4 7.6 - - - +
122C CYS 3.1 23.9 + - - +
123C VAL 3.2 14.4 - - - +
124C ALA 3.5 2.5 - - - +
125C LEU* 1.3 77.9 - - + +
127C LYS* 1.3 58.1 + - - +
128C GLN* 3.3 30.9 + - + +
131C VAL* 3.7 25.7 - - + +
156C VAL* 4.8 1.1 - - + -
164C TYR* 3.8 34.8 - - + -
166C VAL* 3.8 17.3 - - + -
184C MSE 3.7 34.5 - - + -
186C TYR* 4.5 2.0 - - + -
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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
------------------------------------------------------------
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