Contacts of the strand formed by residues 120 - 127 (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 LYS 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ALA 4.9 0.7 - - - +
20A GLY* 2.9 34.7 + - - +
21A VAL* 5.7 0.2 - - - -
22A PHE* 2.5 52.6 + - + +
23A ASP* 4.5 0.4 - - - +
24A ASP* 2.8 32.6 + - - +
112A ILE* 4.3 5.8 - - - -
113A LEU 3.1 7.6 - - - +
114A THR* 3.7 26.5 - - + +
115A TYR* 3.8 9.8 - - - -
118A GLY 4.3 4.5 - - - +
119A LYS* 1.3 78.6 - - - +
121A GLY* 1.3 59.4 + - - +
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Residues in contact with GLY 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 PHE* 3.9 7.2 - - - -
111A LYS 3.8 0.2 - - - +
112A ILE* 3.5 5.0 - - - +
113A LEU* 2.8 33.2 + - - +
115A TYR* 3.7 19.3 - - - -
120A LYS* 1.3 76.9 - - - +
122A VAL* 1.3 65.9 + - - +
142A SER* 5.7 0.7 - - - -
144A HIS* 6.5 0.4 - - - -
146A ILE* 5.8 0.2 - - - -
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Residues in contact with VAL 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 PHE* 3.7 20.2 - - + -
27A VAL* 3.8 25.8 - - + -
110A TYR* 3.8 17.7 - - + -
111A LYS 3.3 9.4 - - - +
112A ILE* 4.1 4.9 - - + -
115A TYR* 4.8 0.4 + - - -
121A GLY* 1.3 78.5 - - - +
123A ARG* 1.3 63.8 + - - +
124A TYR* 3.5 38.1 - - + +
141A PHE 3.8 4.5 - - - +
142A SER* 3.7 17.1 + - - -
143A ASP 4.7 1.7 + - - -
144A HIS 5.6 0.7 + - - -
145A ILE 4.4 7.6 + - - +
146A ILE* 3.8 12.8 - - + +
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Residues in contact with ARG 123 (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 TYR* 3.1 6.6 - - - +
111A LYS 2.8 40.1 + - - +
113A LEU* 3.4 31.2 - - + +
115A TYR* 5.1 2.8 + - - +
121A GLY 5.7 0.2 - - - +
122A VAL* 1.3 76.2 - - - +
124A TYR* 1.3 63.3 + - - +
125A LEU* 3.4 14.7 - - + +
140A GLN* 2.9 29.4 + - + -
141A PHE 3.2 6.1 - - - +
142A SER* 4.5 7.9 + - - +
157A PHE* 3.4 38.2 - - - -
166A LEU 3.0 19.6 + - - -
167A LEU* 3.6 12.9 + - + +
169A GLU 2.8 24.4 + - - -
170A MET* 3.4 20.2 - - - +
1196A SO4 3.7 3.0 + - - -
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Residues in contact with TYR 124 (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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27A VAL* 4.0 0.5 - - - +
28A ARG 2.9 28.2 + - - -
30A ARG* 3.4 49.5 - - + -
35A TRP* 3.7 20.6 - + + -
107A TYR* 3.6 18.6 - + + -
109A GLY 3.8 0.4 - - - -
110A TYR* 3.6 15.0 - - + -
122A VAL* 3.5 25.5 - - + +
123A ARG* 1.3 72.0 - - - +
125A LEU* 1.3 63.2 + - - +
126A PHE* 3.6 16.0 - - + -
140A GLN* 3.2 3.1 - - - -
141A PHE* 2.8 41.6 + - + +
142A SER* 5.7 0.2 - - - -
143A ASP* 5.3 0.2 - - - -
145A ILE 3.7 8.3 - - - -
146A ILE* 3.0 24.8 + - - -
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Residues in contact with LEU 125 (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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107A TYR* 3.6 6.3 - - - -
108A ALA* 2.7 43.8 + - + +
109A GLY 2.8 17.2 + - - +
111A LYS* 4.1 34.8 - - + +
123A ARG* 3.4 32.1 - - + +
124A TYR* 1.3 74.0 - - - +
126A PHE* 1.3 62.1 + - - +
139A VAL 3.5 4.5 - - - -
140A GLN* 3.9 13.7 - - + +
163A GLN* 3.7 40.2 - - + +
167A LEU* 4.5 4.7 - - + -
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Residues in contact with PHE 126 (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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31A ALA 4.3 0.7 - - - -
32A LEU* 3.7 44.0 - - + -
35A TRP* 3.9 12.3 - + - -
92A ILE* 5.2 0.2 - - + -
105A TYR* 4.0 28.0 - - + -
106A ASN 3.3 9.0 - - - +
107A TYR* 3.6 46.7 - + + -
108A ALA* 4.3 0.9 - - - +
124A TYR* 3.6 15.5 - - + -
125A LEU* 1.3 73.6 - - - +
127A GLU* 1.3 59.2 + - - +
138A TYR* 3.6 0.7 - - - -
139A VAL* 2.7 34.5 + - + +
141A PHE* 3.7 31.4 - + - -
163A GLN* 2.8 18.6 + - - -
1198A SO4 5.2 1.3 - - - -
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Residues in contact with GLU 127 (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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105A TYR* 3.5 5.6 - - - -
106A ASN* 2.8 41.6 + - + +
108A ALA* 4.9 9.3 - - + +
126A PHE* 1.3 76.0 - - - +
128A CYS* 1.3 73.4 + - - +
129A LYS* 3.8 33.2 + - + +
137A LYS* 3.3 8.9 - - - +
138A TYR* 3.9 23.9 + - + -
163A GLN* 4.5 6.8 - - - +
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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