Contacts of the strand formed by residues 106 - 114 (chain A) in PDB entry 4ARH
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 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A LYS* 4.2 19.0 + - - +
105A TYR* 1.3 77.1 - - - +
107A TYR* 1.3 66.8 + - - +
108A ALA* 4.6 0.2 - - - +
126A PHE* 3.3 3.4 - - - -
127A GLU* 2.8 40.7 + - + +
129A LYS* 3.4 49.4 - - - +
1198A SO4 3.2 21.0 + - - +
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Residues in contact with TYR 107 (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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29A ASP* 2.5 48.2 + - + -
30A ARG 3.3 23.4 + - - -
31A ALA* 5.8 1.1 - - - -
106A ASN* 1.3 75.0 - - - +
108A ALA* 1.3 58.3 + - - +
109A GLY* 3.4 39.1 - - - -
110A TYR* 3.7 1.0 + - - -
124A TYR* 3.6 15.8 - + + -
125A LEU 3.6 10.8 - - - -
126A PHE* 3.6 30.6 - + + -
1198A SO4 2.7 31.3 + - - +
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Residues in contact with ALA 108 (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 ASN 3.6 3.8 + - - +
107A TYR* 1.3 73.9 - - - +
109A GLY* 1.3 61.5 + - - +
111A LYS* 5.6 2.6 + - - -
125A LEU* 2.7 36.6 + - + +
126A PHE* 4.6 1.6 - - - +
127A GLU* 4.9 8.5 - - + +
163A GLN* 4.4 12.1 - - + +
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Residues in contact with GLY 109 (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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29A ASP* 4.2 2.9 - - - -
107A TYR* 3.4 35.8 - - - -
108A ALA* 1.3 81.6 - - - +
110A TYR* 1.3 59.9 + - - -
124A TYR 3.7 0.3 - - - -
125A LEU* 2.8 28.2 + - - +
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Residues in contact with TYR 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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24A ASP 5.3 1.6 + - - -
27A VAL* 3.5 36.1 + - + +
28A ARG* 4.1 6.5 - - - -
29A ASP* 3.3 46.9 - - - -
107A TYR* 3.9 1.3 - - - -
109A GLY* 1.3 73.9 - - - -
111A LYS* 1.3 76.9 + - - +
112A ILE* 4.0 19.3 - - + +
122A VAL* 3.8 8.1 - - + -
123A ARG 3.1 11.9 - - - +
124A TYR* 3.6 18.4 - - + -
125A LEU* 4.4 1.1 - - - -
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Residues in contact with LYS 111 (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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108A ALA 5.6 2.2 + - - -
110A TYR* 1.3 83.0 + - - +
112A ILE* 1.3 64.2 + - - +
113A LEU* 3.8 10.5 + - + +
122A VAL* 3.3 4.3 - - - -
123A ARG* 2.8 38.4 + - + +
125A LEU* 4.1 25.7 - - + +
164A GLN* 4.7 10.9 - - - +
167A LEU* 3.9 38.1 - - + +
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Residues in contact with ILE 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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22A PHE* 4.2 10.8 - - + -
24A ASP* 3.6 45.1 - - + +
27A VAL* 3.9 21.5 - - + -
110A TYR* 4.0 21.0 - - + +
111A LYS* 1.3 75.5 - - - +
113A LEU* 1.3 69.8 + - - +
114A THR* 4.3 2.4 + - - +
120A LYS* 4.3 7.9 - - - -
121A GLY 3.5 8.1 - - - +
122A VAL* 4.1 13.7 - - + -
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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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111A LYS* 4.4 13.7 - - + +
112A ILE* 1.3 81.5 - - - +
114A THR* 1.3 62.6 + - - +
115A TYR* 3.9 25.6 - - + +
120A LYS* 3.1 8.1 - - - +
121A GLY 2.8 37.2 + - - +
123A ARG* 3.4 46.9 - - + +
167A LEU* 4.2 28.5 - - + +
170A MET* 5.1 3.4 - - - -
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Residues in contact with THR 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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112A ILE* 4.3 2.3 + - - +
113A LEU* 1.3 75.6 - - - +
115A TYR* 1.3 76.2 + - - +
118A GLY* 4.2 12.3 - - - +
119A LYS 3.5 10.8 - - - +
120A LYS* 3.7 20.7 - - + +
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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