Contacts of the helix formed by residues 110 - 122 (chain A) in PDB entry 3ZS4
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 ASN 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ARG 5.6 4.2 + - - +
106A ALA* 2.9 19.3 + - + +
109A GLU* 1.3 81.9 - - + +
111A PRO* 1.4 63.1 - - - +
112A GLN* 3.7 9.9 + - - +
113A TRP* 3.2 38.2 + - + +
114A CYS 3.0 17.8 + - - -
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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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106A ALA 3.9 0.4 - - - -
107A ALA 4.1 4.9 - - - +
108A LEU 4.2 9.2 - - - +
109A GLU 3.6 8.1 - - - +
110A ASN* 1.4 89.2 - - - +
112A GLN* 1.3 60.9 + - + +
114A CYS* 3.7 4.2 - - + +
115A ALA* 2.9 31.0 + - - +
158A ARG* 3.6 40.4 - - - +
162A GLU* 4.3 4.7 - - - +
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Residues in contact with GLN 112 (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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110A ASN* 3.2 8.8 - - - +
111A PRO* 1.3 79.0 - - + +
113A TRP* 1.3 65.5 + - - +
115A ALA* 3.5 5.5 + - - +
116A ARG* 3.2 22.2 + - - +
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Residues in contact with TRP 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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84A ILE 4.2 5.4 - - - -
85A ARG* 3.6 14.8 - - - -
86A ASP* 3.3 38.6 - - - -
87A ASP* 2.8 26.7 + - - +
90A LEU* 4.2 11.2 - - + -
103A VAL* 4.4 14.8 - - + -
106A ALA* 3.5 33.2 - - + -
110A ASN* 3.2 31.8 + - + +
112A GLN* 1.3 77.7 - - - +
114A CYS* 1.3 72.5 + - - +
116A ARG* 3.1 30.9 + - - +
117A VAL* 2.9 48.7 + - + +
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Residues in contact with CYS 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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103A VAL* 3.9 22.0 - - - -
106A ALA 4.1 2.9 - - - +
107A ALA* 3.8 33.9 - - - +
110A ASN 3.0 16.8 + - - +
111A PRO* 3.7 5.8 - - + +
113A TRP* 1.3 85.7 - - + +
115A ALA* 1.3 55.9 + - - +
117A VAL* 3.3 4.6 + - - +
118A ILE* 2.8 42.9 + - - +
125A VAL* 5.9 0.4 - - - -
127A VAL* 4.0 12.1 - - - -
159A LEU* 4.1 6.5 - - + -
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Residues in contact with ALA 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 18.1 + - - +
112A GLN* 3.8 6.7 - - - +
113A TRP 3.3 0.2 - - - -
114A CYS* 1.3 75.2 - - - +
116A ARG* 1.3 57.5 + - - +
118A ILE* 3.4 6.8 + - - +
119A GLY* 2.9 24.8 + - - -
162A GLU* 3.5 39.2 + - + +
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Residues in contact with ARG 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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87A ASP* 2.7 43.6 + - - -
112A GLN 3.2 9.6 + - - +
113A TRP* 3.1 31.3 + - - +
115A ALA* 1.3 75.6 - - - +
117A VAL* 1.3 69.0 + - - +
119A GLY* 3.3 2.0 + - - +
120A GLU* 3.0 52.1 + - + +
121A HIS* 5.5 4.9 + - - -
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Residues in contact with VAL 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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90A LEU* 3.6 27.8 - - + -
103A VAL* 5.2 3.4 - - + -
113A TRP* 2.9 57.8 + - + +
114A CYS* 3.5 10.3 - - - +
116A ARG* 1.3 82.4 - - - +
118A ILE* 1.3 61.0 + - - +
121A HIS* 2.8 43.3 + - + +
125A VAL* 3.7 27.8 - - + -
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Residues in contact with ILE 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 CYS* 2.8 26.8 + - - +
115A ALA* 3.5 7.0 - - - +
117A VAL* 1.3 76.3 - - - +
119A GLY* 1.3 57.7 + - - +
122A GLY* 3.0 32.7 + - - +
125A VAL* 4.9 15.3 - - + +
127A VAL* 4.5 3.1 - - + -
159A LEU* 3.8 28.7 - - + -
162A GLU* 3.4 36.1 - - + +
163A GLY 3.5 21.0 - - - +
164A CYS* 3.6 26.0 - - + +
165A SER 4.9 1.3 - - - +
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Residues in contact with GLY 119 (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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115A ALA 2.9 15.2 + - - -
116A ARG* 3.3 4.9 + - - -
117A VAL 3.2 0.2 - - - -
118A ILE* 1.3 79.4 - - - +
120A GLU* 1.3 61.7 + - - +
122A GLY* 4.9 1.0 + - - -
162A GLU 5.3 2.9 - - - -
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Residues in contact with GLU 120 (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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116A ARG* 3.0 41.7 + - + +
119A GLY* 1.3 80.0 - - - +
121A HIS* 1.3 76.1 + - + +
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Residues in contact with HIS 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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90A LEU* 3.5 25.0 - - + +
91A ALA* 6.3 1.1 - - - -
94A LEU* 3.5 29.4 - - + +
116A ARG* 5.5 4.5 + - - -
117A VAL* 2.8 30.5 + - + +
120A GLU* 1.3 91.1 + - + +
122A GLY* 1.3 66.4 + - - +
123A ASP 3.2 0.7 + - - -
124A GLN* 3.1 23.4 + - + +
125A VAL* 3.5 22.7 - - + -
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Residues in contact with GLY 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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117A VAL 4.1 0.2 + - - -
118A ILE* 3.0 22.7 + - - +
119A GLY 4.7 1.1 - - - -
120A GLU 3.7 1.4 - - - -
121A HIS* 1.3 74.2 - - - +
123A ASP* 1.3 58.5 + - - -
124A GLN 3.0 6.1 + - - -
125A VAL* 3.0 24.9 + - - +
163A GLY 5.8 2.2 - - - -
165A SER* 3.4 10.3 + - - -
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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