Contacts of the helix formed by residues 109 - 117 (chain B) in PDB entry 1ZJA
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 HIS 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B ILE 3.8 8.1 - - - +
67B SER* 3.4 32.4 + - - +
68B ASP* 4.4 4.6 - - - -
69B TYR* 3.7 36.7 + + - -
105B SER* 3.8 11.7 - - - +
106B SER 3.2 17.1 + - - +
108B GLN* 1.3 79.9 - - - +
110B GLU* 1.3 74.0 + - + +
111B TRP* 2.9 63.1 + + - +
112B PHE* 2.9 13.3 + - - +
113B LYS* 3.1 10.4 + - - +
127B TYR* 4.3 2.7 - - - +
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B SER 4.3 3.8 + - - +
108B GLN 3.6 2.8 + - - +
109B HIS* 1.3 80.5 + - + +
111B TRP* 1.3 66.3 + - + +
113B LYS* 3.7 34.6 + - - +
114B SER* 2.9 32.1 + - - +
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Residues in contact with TRP 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B TYR* 4.1 20.6 - + - -
105B SER* 5.3 0.2 - - - -
109B HIS* 2.9 33.0 + + - +
110B GLU* 1.3 81.7 - - + +
112B PHE* 1.3 58.8 + - - +
114B SER* 3.6 2.0 - - - -
115B SER* 2.8 29.1 + - - -
123B TYR* 3.7 28.8 - + - +
126B TYR* 3.7 25.4 - + + -
127B TYR* 3.4 11.8 - - + +
171B LEU* 4.0 19.1 - - + -
178B LEU* 3.9 12.3 - - + -
181B GLU* 3.6 46.1 + - + -
182B LEU* 4.0 20.4 - - + -
185B MET* 5.9 2.5 - - + -
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Residues in contact with PHE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B SER 4.1 7.4 - - - +
107B ASP* 3.4 34.3 - - + +
109B HIS 2.9 8.4 + - - +
111B TRP* 1.3 77.1 - - - +
113B LYS* 1.3 66.8 + - - +
114B SER 3.1 0.9 - - - -
115B SER* 4.0 1.3 - - - -
116B ARG* 2.9 57.9 + - - +
127B TYR* 3.4 35.7 + + + +
129B TRP* 3.6 31.4 - + - -
160B TYR* 3.8 28.9 - + + -
169B PRO* 3.5 27.4 - - + -
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ASP 4.1 9.0 - - - +
108B GLN* 3.5 41.8 + - - +
109B HIS 3.1 9.7 + - - +
110B GLU* 3.4 37.5 + - - +
112B PHE* 1.3 76.6 - - - +
114B SER* 1.3 63.9 + - - +
116B ARG* 3.5 21.4 - - - +
117B ALA* 3.5 10.7 + - - +
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B GLU* 2.9 21.9 + - - +
111B TRP 3.6 3.4 - - - -
113B LYS* 1.3 77.2 - - - +
115B SER* 1.3 64.6 + - - +
117B ALA* 3.2 17.9 + - - +
121B ASN* 3.1 17.7 + - - +
123B TYR* 3.7 30.3 - - - -
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Residues in contact with SER 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B TRP 2.8 20.4 + - - -
112B PHE* 3.3 4.7 + - - -
114B SER* 1.3 72.5 - - - +
116B ARG* 1.3 60.4 + - - +
121B ASN* 3.2 19.5 + - - -
123B TYR* 2.8 28.4 + - - +
124B ARG* 3.0 26.4 + - - -
127B TYR* 3.5 16.0 - - - -
129B TRP* 3.0 22.2 + - - -
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Residues in contact with ARG 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ASP* 4.3 17.3 + - - +
108B GLN* 5.6 2.6 - - - +
112B PHE* 2.9 45.2 + - + +
113B LYS* 3.5 13.9 - - - +
115B SER* 1.3 76.1 - - - +
117B ALA* 1.3 65.8 + - - +
118B SER 3.4 1.2 + - - -
124B ARG* 3.8 7.0 + - - +
129B TRP* 3.6 20.4 - - + -
152B LYS 5.5 1.0 + - - -
153B ASP* 2.8 39.3 + - - +
155B VAL* 3.5 22.3 - - + +
156B THR* 4.1 1.4 - - - +
160B TYR* 4.0 21.0 + - - -
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ASP* 6.0 0.5 - - - +
113B LYS 3.7 9.6 - - - +
114B SER* 3.2 15.2 + - - +
116B ARG* 1.3 82.2 - - + +
118B SER* 1.3 63.8 + - - +
121B ASN* 5.7 0.2 - - - -
155B VAL* 3.3 20.1 - - - +
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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