Contacts of the helix formed by residues 109 - 122 (chain A) in PDB entry 1ZIA
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 LYS 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A ASN 3.6 4.0 + - - -
108A PRO* 1.3 71.7 - - - +
110A LYS* 1.3 62.4 + - + +
112A GLN* 3.1 16.6 + - + +
113A GLU* 3.0 49.8 + - + +
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Residues in contact with LYS 110 (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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83A GLY 3.9 20.2 + - - +
84A MET* 4.2 7.5 + - - -
85A GLY* 3.9 11.4 - - - +
108A PRO* 3.4 1.8 - - - +
109A LYS* 1.3 76.3 - - + +
111A ALA* 1.3 65.7 + - - +
113A GLU* 2.7 34.4 + - - +
114A ARG* 3.4 35.0 + - - +
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Residues in contact with ALA 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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82A TYR* 3.7 30.9 + - + +
85A GLY* 3.7 10.3 - - - +
87A VAL* 3.6 27.9 - - + +
107A ASN* 4.1 3.1 - - + -
108A PRO* 3.0 12.6 + - + +
110A LYS* 1.3 76.2 - - - +
112A GLN* 1.3 62.5 + - - +
114A ARG 3.2 2.3 + - - -
115A LEU* 2.8 34.4 + - + +
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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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102A VAL 5.7 1.0 - - - +
103A LYS* 4.7 7.8 - - - +
105A ALA 3.2 14.9 + - - +
106A LYS* 4.5 0.4 - - - +
107A ASN* 3.0 45.7 + - - +
108A PRO 2.8 13.0 + - - +
109A LYS* 3.1 21.3 + - + +
111A ALA* 1.3 78.4 - - - +
113A GLU* 1.4 61.3 + - + +
115A LEU* 4.2 8.0 - - - +
116A ASP* 2.9 61.1 + - - +
119A LEU* 5.6 1.9 - - - +
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Residues in contact with GLU 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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109A LYS* 3.0 34.6 + - + +
110A LYS* 2.7 44.1 + - - +
111A ALA 3.3 0.4 - - - -
112A GLN* 1.4 74.6 - - + +
114A ARG* 1.4 64.1 + - + +
116A ASP* 3.7 7.0 + - - +
117A ALA* 3.3 21.5 + - - +
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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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13A ASP* 3.0 45.7 + - - +
14A GLY* 3.6 2.0 - - - -
15A ALA 2.9 27.5 + - - +
16A MET 2.8 28.1 + - - -
17A VAL* 3.7 11.7 - - - +
21A ALA* 5.9 2.8 - - + +
84A MET 3.7 6.9 + - - -
85A GLY* 2.9 25.7 + - - -
87A VAL* 3.8 15.3 - - + +
110A LYS* 3.4 19.7 + - - +
111A ALA 3.2 7.6 + - - +
113A GLU* 1.4 80.2 - - + +
115A LEU* 1.3 58.5 + - - +
117A ALA* 3.4 7.0 + - - +
118A ALA* 2.9 28.4 + - - +
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Residues in contact with LEU 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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45A ILE* 4.2 9.2 - - + -
48A MET* 4.0 21.3 - - + -
75A GLY* 5.0 0.2 - - - -
87A VAL* 3.7 21.5 - - + -
88A GLY* 3.9 10.5 - - - +
89A VAL* 3.6 25.6 - - + -
107A ASN* 3.3 41.5 - - + +
111A ALA 2.8 26.0 + - - +
112A GLN* 3.8 9.6 - - - +
114A ARG* 1.3 71.7 - - - +
116A ASP* 1.3 54.3 + - - +
118A ALA* 3.1 3.9 + - - +
119A LEU* 2.7 44.0 + - + +
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Residues in contact with ASP 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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103A LYS* 5.2 4.2 - - - +
112A GLN* 2.9 48.8 + - - +
113A GLU* 3.8 6.9 + - - +
115A LEU* 1.3 75.1 - - - +
117A ALA* 1.3 60.8 + - - +
119A LEU* 3.8 12.9 - - - +
120A ALA* 3.0 25.3 + - - +
124A ASN* 5.6 0.2 - - - +
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Residues in contact with ALA 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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13A ASP* 6.0 1.6 - - - +
113A GLU 3.3 11.7 + - - +
114A ARG* 3.7 9.9 - - - +
115A LEU 3.3 0.4 - - - -
116A ASP* 1.3 76.1 - - - +
118A ALA* 1.3 62.7 + - - +
120A ALA* 3.3 7.2 + - - +
121A ALA* 3.0 23.1 + - - +
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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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21A ALA* 3.6 20.9 - - + +
22A SER* 3.1 28.8 + - - +
88A GLY* 5.2 1.3 - - - -
89A VAL* 4.1 15.5 - - + +
114A ARG 2.9 18.2 + - - +
115A LEU* 3.1 5.6 + - - +
117A ALA* 1.3 76.8 - - - +
119A LEU* 1.3 61.8 + - - +
121A ALA* 3.2 11.7 + - - +
122A LEU* 3.6 14.0 + - - +
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Residues in contact with LEU 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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48A MET* 4.9 2.9 - - + -
73A VAL* 4.2 1.6 - - + -
89A VAL* 4.0 24.9 - - + -
99A LEU* 3.9 26.0 - - + -
102A VAL* 3.9 24.0 - - + +
103A LYS* 3.9 28.7 - - + -
112A GLN* 5.6 1.1 - - - +
115A LEU* 2.7 32.0 + - + +
116A ASP* 3.8 13.2 - - - +
118A ALA* 1.3 73.4 - - - +
120A ALA* 1.3 60.2 + - - +
122A LEU* 3.3 11.4 + - + +
124A ASN* 2.9 34.7 + - - +
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Residues in contact with ALA 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 ASP 3.0 17.4 + - - +
117A ALA* 3.3 7.4 + - - +
119A LEU* 1.3 75.4 - - - +
121A ALA* 1.3 60.0 + - - +
123A GLY* 3.2 13.0 + - - -
124A ASN* 3.6 19.8 + - - +
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Residues in contact with ALA 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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22A SER* 3.8 17.7 - - - +
117A ALA 3.0 13.4 + - - +
118A ALA* 3.2 11.8 + - - +
120A ALA* 1.3 75.6 - - - +
122A LEU* 1.3 57.9 + - - +
123A GLY 3.3 1.3 + - - -
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Residues in contact with LEU 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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22A SER* 4.3 7.0 - - - -
23A LEU 4.0 32.8 - - - +
24A LYS* 4.2 9.6 - - + +
73A VAL* 5.5 1.8 - - + -
89A VAL* 3.5 32.5 - - + +
91A GLN* 3.7 36.3 + - + +
99A LEU* 6.2 0.2 - - + -
118A ALA 3.6 14.6 - - - +
119A LEU* 3.3 13.9 + - + +
120A ALA 3.2 1.2 - - - -
121A ALA* 1.3 76.8 - - - +
123A GLY* 1.3 59.5 + - - +
124A ASN* 4.2 4.0 - - - +
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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
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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