Contacts of the strand formed by residues 121 - 127 (chain A) in PDB entry 4O65
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 TRP 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.7 24.7 - - + -
90A LEU* 3.9 27.8 - - + -
110A LEU* 4.3 13.0 - - + -
112A THR* 3.9 17.8 + - - -
119A ASN 3.4 17.8 + - - -
120A ARG* 1.3 88.7 + - + +
122A GLU* 1.3 60.0 + - - +
147A LEU* 4.0 24.9 - - + -
148A SER 3.3 12.1 - - - -
149A ALA* 3.6 30.3 - - + -
150A LEU* 4.0 4.1 - - - +
155A TYR* 3.6 48.8 - + + -
157A ALA* 5.7 0.4 - - + -
176A ILE* 4.1 12.6 - - + -
178A VAL* 3.8 8.7 - - + -
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Residues in contact with GLU 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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57A LYS* 2.6 37.0 + - - -
77A ASP* 4.0 4.5 - - - +
121A TRP* 1.3 75.8 - - - +
123A PHE* 1.3 73.4 + - - +
124A ILE* 5.7 1.8 - - + +
147A LEU* 3.1 7.4 - - - -
148A SER* 2.8 39.9 + - - +
150A LEU* 4.0 21.3 - - + +
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Residues in contact with PHE 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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108A ILE 4.3 0.2 - - - -
109A SER* 3.8 25.6 - - - -
110A LEU* 3.9 7.2 - - + -
122A GLU* 1.3 85.8 - - - +
124A ILE* 1.3 61.3 + - - +
125A SER 3.6 19.5 - - - +
126A ARG* 3.2 60.1 - - + +
145A LEU* 3.7 26.9 - - + -
146A CYS 3.7 5.8 - - - -
147A LEU* 3.8 22.9 - - + +
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Residues in contact with ILE 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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77A ASP 5.9 0.4 - - - +
80A GLY* 4.0 8.7 - - - +
81A CYS* 3.8 29.6 - - + +
86A ARG* 3.8 18.6 - - - +
89A VAL* 3.6 30.1 - - + -
122A GLU* 5.7 1.8 - - - +
123A PHE* 1.3 78.9 - - - +
125A SER* 1.3 63.6 + - - +
146A CYS* 2.8 22.0 + - - +
147A LEU 3.7 16.8 - - - +
148A SER* 3.8 13.7 - - - +
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Residues in contact with SER 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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81A CYS* 4.2 9.3 - - - +
123A PHE* 3.6 9.2 - - - +
124A ILE* 1.3 85.7 - - - +
126A ARG* 1.3 66.3 + - - +
144A LYS* 4.5 4.4 - - - +
146A CYS* 2.9 43.8 + - - +
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Residues in contact with ARG 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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107A TRP* 6.2 1.4 - - - +
108A ILE* 3.0 36.6 + - + +
109A SER* 4.1 5.9 - - - -
123A PHE* 3.2 57.4 - - + +
125A SER* 1.3 82.2 - - - +
127A ASP* 1.3 61.8 + - - +
128A PRO 3.4 15.7 - - - +
129A PRO* 3.4 20.6 - - + +
130A GLY 5.1 8.3 - - - -
131A ASN* 6.3 0.9 - - - +
144A LYS 3.3 6.7 - - - +
145A LEU* 4.3 8.1 - - + -
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Residues in contact with ASP 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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108A ILE* 5.3 0.6 - - - +
126A ARG* 1.3 74.6 - - - +
128A PRO* 1.3 74.2 - - - +
129A PRO* 3.6 9.4 - - - +
142A PRO* 4.7 8.6 - - - +
143A TYR* 3.1 7.4 - - - +
144A LYS* 2.8 47.6 + - + +
145A LEU* 5.0 1.9 - - - +
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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