Contacts of the helix formed by residues 102 - 106 (chain A) in PDB entry 1AST
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 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ALA 4.4 5.8 + - - -
92A HIS* 3.5 16.4 - + - -
96A HIS* 3.0 13.1 + + - -
101A TYR* 1.3 77.5 - - - +
103A GLU* 1.3 65.2 + - - +
104A HIS* 3.4 25.0 + + + +
105A THR* 3.1 27.0 + - - +
106A ARG 3.8 4.5 + - - -
127A ASN 4.9 7.9 + - - -
131A ASP* 3.9 2.6 - - - +
147A MET* 3.5 5.8 - - - -
149A TYR* 3.0 21.5 + + - -
999A ZN 2.0 36.7 - - - -
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Residues in contact with GLU 103 (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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1A ALA 4.3 8.4 + - - +
101A TYR 3.7 1.2 + - - -
102A HIS* 1.3 72.6 - - - +
104A HIS* 1.3 58.9 + - - +
105A THR 3.0 4.9 + - - -
106A ARG* 3.1 37.9 + - - +
140A ASP 3.9 4.0 - - - +
141A TYR* 3.3 27.0 - - + -
142A GLN* 2.8 46.8 + - - +
145A SER* 3.9 15.7 + - - +
147A MET* 3.0 13.1 + - + +
148A HIS* 3.7 29.6 - - + +
189A GLN* 4.7 11.7 + - - -
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Residues in contact with HIS 104 (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 HIS* 3.4 29.4 + + + +
103A GLU* 1.3 77.3 - - - +
105A THR* 1.3 67.7 + - + +
106A ARG 3.5 0.7 - - - -
109A ARG* 2.9 34.1 + - - -
113A VAL* 4.8 1.9 - - + +
115A ILE* 5.0 2.2 - - + +
127A ASN 4.7 3.8 + - - -
128A PHE* 4.2 24.5 - + - -
141A TYR* 3.3 18.2 - - - +
147A MET 3.8 2.2 - - - -
148A HIS* 3.7 16.5 - - + +
149A TYR* 3.2 56.7 + + + -
154A PHE* 5.6 1.0 - - - -
164A ILE* 4.4 14.6 - - + -
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Residues in contact with THR 105 (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 HIS* 3.1 20.4 + - + +
103A GLU 3.1 0.2 - - - -
104A HIS* 1.3 95.4 - - + +
106A ARG* 1.3 64.8 + - - +
109A ARG* 4.1 5.2 - - - +
127A ASN 3.7 21.5 - - - +
128A PHE* 3.9 9.6 - - - -
129A ASP 3.3 23.6 - - - +
130A ILE* 3.4 2.3 - - - +
131A ASP* 2.6 57.2 + - - +
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Residues in contact with ARG 106 (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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1A ALA* 3.9 25.2 - - + +
102A HIS 3.8 2.0 + - - -
103A GLU* 3.1 40.4 + - - +
104A HIS 3.5 0.8 - - - -
105A THR* 1.3 81.5 - - - +
107A MET* 1.3 66.0 + - - +
108A ASP* 2.8 42.6 + - - +
109A ARG* 2.9 20.5 + - - +
130A ILE* 3.9 2.6 - - - +
131A ASP* 4.8 2.0 - - - -
136A TYR* 3.3 34.2 - - + -
139A GLU 2.9 22.4 + - - -
140A ASP* 3.6 16.2 + - - +
141A TYR* 3.3 31.3 - - + +
189A GLN* 4.4 11.3 + - - -
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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