Contacts of the helix formed by residues 110 - 124 (chain A) in PDB entry 2C56
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 PRO 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A TYR* 3.6 32.8 - - + +
95A GLN* 4.2 16.8 - - - +
103A VAL* 3.5 27.4 - - + -
107A VAL* 4.9 0.9 - - + -
108A PRO 3.6 6.7 - - - +
109A PRO* 1.3 84.5 - - + +
111A PRO* 1.3 78.6 - - + +
112A SER 3.4 2.0 - - - +
113A LEU* 3.1 12.6 + - + -
114A ARG* 2.9 18.2 + - - -
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Residues in contact with PRO 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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109A PRO 4.7 0.4 - - - +
110A PRO* 1.3 87.1 - - + +
112A SER* 1.3 57.4 + - - +
114A ARG* 3.3 29.4 + - + +
115A ASN* 2.9 35.6 + - - +
213A PRO* 3.6 33.0 - - + -
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Residues in contact with SER 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 4.8 9.2 - - - -
101A PHE* 4.7 11.9 - - - -
110A PRO* 3.2 1.8 + - - +
111A PRO* 1.3 76.1 - - - +
113A LEU* 1.3 56.6 + - - +
115A ASN* 3.2 5.5 + - - +
116A VAL* 3.0 31.6 + - - +
211A PRO* 3.5 22.1 - - - +
212A SER* 3.1 25.3 - - - -
213A PRO* 3.2 8.2 - - - +
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Residues in contact with LEU 113 (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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90A TYR* 3.8 14.0 + - - +
101A PHE* 3.5 29.8 - - + +
103A VAL* 3.5 23.8 - - + -
109A PRO* 3.8 13.5 - - + -
110A PRO* 3.1 11.5 + - + +
112A SER* 1.3 74.0 - - - +
114A ARG* 1.3 66.5 + - - +
116A VAL* 3.1 11.0 + - + +
117A LEU* 2.9 41.7 + - + +
133A GLY* 3.2 29.8 - - - +
135A LEU* 4.1 20.9 - - + -
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Residues in contact with ARG 114 (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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109A PRO* 4.0 16.7 - - + +
110A PRO 2.9 12.3 + - - +
111A PRO* 3.4 38.3 + - + +
113A LEU* 1.3 76.3 - - - +
115A ASN* 1.3 85.3 + - - +
117A LEU* 3.4 6.1 + - - +
118A ALA* 3.0 28.3 + - + +
213A PRO* 4.8 3.2 - - - +
1B GLC 3.4 32.9 + - - -
2B FRU 3.3 24.8 + - - +
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Residues in contact with ASN 115 (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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111A PRO 2.9 16.4 + - - -
112A SER 3.3 8.5 - - - +
114A ARG* 1.3 94.8 + - - +
116A VAL* 1.3 61.9 + - - +
118A ALA* 3.3 2.4 + - - +
119A ALA* 3.1 18.0 + - - +
211A PRO* 2.7 25.6 + - + +
212A SER 4.3 3.4 + - - -
213A PRO* 4.4 0.6 - - - +
219A PHE* 3.5 23.0 - - + +
220A GLY* 5.0 0.9 - - - +
1B GLC 2.9 38.8 + - - +
2B FRU 2.5 28.7 + - - -
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Residues in contact with VAL 116 (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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101A PHE* 4.5 10.3 - - + -
112A SER 3.0 21.0 + - - +
113A LEU* 3.1 14.8 + - + +
115A ASN* 1.3 74.2 - - - +
117A LEU* 1.3 65.7 + - + +
119A ALA* 3.3 4.3 + - - +
120A VAL* 3.1 21.1 + - - +
135A LEU* 5.9 0.9 - - + -
138A TRP* 3.9 29.6 - - + -
188A TRP* 3.7 28.0 - - + -
211A PRO* 3.7 16.2 - - + -
219A PHE* 3.7 8.7 - - + -
225A PHE* 4.2 13.8 - - + -
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Residues in contact with LEU 117 (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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109A PRO* 3.9 22.0 - - + -
113A LEU* 2.9 32.0 + - + +
114A ARG* 3.9 4.9 - - - +
116A VAL* 1.3 78.3 - - + +
118A ALA* 1.3 57.3 + - - +
120A VAL* 3.4 5.2 + - - +
121A LYS* 2.9 28.1 + - - +
129A MET* 4.0 14.5 - - + +
131A GLY* 5.4 2.7 - - - +
132A HIS 3.8 20.6 - - - +
133A GLY* 4.2 1.3 - - - -
135A LEU* 4.5 11.4 - - + -
138A TRP* 4.6 9.9 - - + -
244A VAL* 3.6 29.8 - - + -
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Residues in contact with ALA 118 (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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114A ARG* 3.0 18.9 + - + +
115A ASN 3.6 2.7 - - - +
116A VAL 3.2 0.2 - - - -
117A LEU* 1.3 77.0 - - - +
119A ALA* 1.3 57.7 + - - +
121A LYS* 3.1 8.3 + - - +
122A ASN* 2.8 35.0 + - - +
2B FRU 3.5 39.5 - - - +
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Residues in contact with ALA 119 (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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115A ASN 3.1 7.6 + - - +
116A VAL 3.7 7.0 - - - +
118A ALA* 1.3 75.5 - - - +
120A VAL* 1.3 62.7 - - - +
122A ASN* 3.0 2.8 + - - +
123A CYS* 2.8 27.0 + - - -
219A PHE* 3.6 39.0 - - + +
220A GLY* 3.7 14.8 + - - +
222A CYS* 3.8 15.3 - - + +
225A PHE* 4.0 7.6 - - + -
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Residues in contact with VAL 120 (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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116A VAL 3.1 19.8 + - - +
117A LEU* 3.5 11.0 - - - +
119A ALA* 1.3 76.5 - - - +
121A LYS* 1.3 56.5 + - - +
123A CYS* 3.1 3.0 + - - -
124A TYR* 2.9 34.7 + - + +
127A ALA* 5.3 0.4 - - + -
129A MET* 3.9 15.9 - - + -
138A TRP* 3.7 30.3 - - + -
225A PHE* 3.8 27.6 - - + -
242A TRP* 3.6 34.5 - - + +
243A SER* 5.1 0.2 - - - -
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Residues in contact with LYS 121 (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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117A LEU 2.9 14.0 + - - +
118A ALA* 3.1 10.5 + - - +
120A VAL* 1.3 77.5 - - - +
122A ASN* 1.3 65.0 + - - +
124A TYR 3.1 24.6 + - - +
125A PRO* 3.2 31.0 + - + +
127A ALA 4.2 10.3 + - - +
129A MET* 3.8 29.8 - - + -
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Residues in contact with ASN 122 (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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118A ALA* 2.8 18.8 + - - +
119A ALA 3.0 7.2 + - - +
121A LYS* 1.3 81.3 - - - +
123A CYS* 1.3 62.4 + - - +
125A PRO* 3.9 12.4 - - - +
220A GLY* 3.0 33.3 + - - +
2B FRU 4.5 8.7 + - - -
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Residues in contact with CYS 123 (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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119A ALA 2.8 11.2 + - - -
120A VAL* 3.1 8.7 + - - +
122A ASN* 1.3 78.6 - - - +
124A TYR* 1.3 82.0 + - + +
125A PRO* 3.4 7.7 - - - +
222A CYS 3.3 26.0 - - - -
223A GLN* 3.7 18.4 - - - -
225A PHE* 3.9 13.7 - - - -
226A LEU* 3.8 32.7 - - + +
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Residues in contact with TYR 124 (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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120A VAL* 2.9 20.0 + - + +
121A LYS* 3.1 12.1 - - - +
123A CYS* 1.3 90.9 - - + +
125A PRO* 1.3 67.4 - - - +
126A GLU* 2.9 4.8 + - + +
127A ALA* 3.0 30.1 + - + +
225A PHE* 3.4 29.9 + - + -
226A LEU* 3.6 25.6 - - + +
229A ASN* 3.5 15.8 + - - +
242A TRP* 3.5 33.6 - + + -
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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