Contacts of the strand formed by residues 108 - 119 (chain A) in PDB entry 5O67
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 PHE 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A LYS* 1.3 107.0 + - + +
109A SER* 1.3 64.3 + - - +
157A ARG 3.6 11.4 - - - -
158A TYR* 4.1 31.2 - + + -
405A TYR* 3.7 7.2 - - - -
406A PHE* 3.4 47.7 + + + +
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Residues in contact with SER 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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103A ALA* 4.5 1.9 - - - +
107A LYS 5.0 1.4 + - - -
108A PHE* 1.3 79.1 - - - +
110A PHE* 1.3 63.0 + - - +
111A GLU* 4.2 0.9 - - - -
155A THR 3.9 0.3 - - - +
156A GLY* 3.4 2.8 - - - -
157A ARG* 2.9 64.3 + - - +
403A PRO* 5.7 1.8 - - - -
404A TYR 3.3 15.7 - - - -
405A TYR* 3.9 24.7 - - - -
406A PHE* 4.0 5.8 - - - -
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Residues in contact with PHE 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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109A SER* 1.3 77.0 - - - +
111A GLU* 1.3 60.5 + - - +
112A THR* 4.0 15.9 + - + -
154A LEU* 3.5 38.6 - - + -
155A THR 3.2 26.0 - - - -
156A GLY* 4.4 5.8 - - - -
402A PHE 3.8 2.4 - - - +
403A PRO* 4.7 0.2 - - - -
404A TYR* 3.1 33.4 + - + +
406A PHE* 3.9 20.9 - - + -
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Residues in contact with GLU 111 (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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109A SER* 4.2 1.5 - - - -
110A PHE* 1.3 77.5 - - - +
112A THR* 1.3 62.1 + - - +
113A GLY* 4.3 9.9 + - - -
153A ASP* 3.8 4.3 - - - +
154A LEU* 3.7 5.0 - - - -
155A THR* 2.8 50.7 + - - +
157A ARG* 3.2 31.5 + - - +
401A LYS* 3.8 39.1 + - - +
402A PHE 3.7 3.8 - - - +
403A PRO* 4.0 28.3 - - + +
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Residues in contact with THR 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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110A PHE* 4.0 13.5 + - + -
111A GLU* 1.3 76.8 - - - +
113A GLY* 1.3 60.6 + - - +
152A LEU* 4.1 16.4 - - + -
153A ASP 3.6 2.7 - - - +
154A LEU* 4.0 20.9 - - + -
402A PHE* 3.0 52.5 + - + +
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Residues in contact with GLY 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 GLU* 4.2 4.4 + - - -
112A THR* 1.3 74.3 - - - +
114A ILE* 1.3 60.3 + - - -
115A THR* 4.9 2.9 - - - -
151A THR 4.4 0.4 - - - -
152A LEU* 3.3 13.0 - - - +
153A ASP* 2.8 42.9 + - - -
400A LEU 3.4 7.4 - - - -
401A LYS* 4.3 11.2 - - - -
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Residues in contact with ILE 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 THR 4.3 0.2 + - - -
113A GLY* 1.3 73.5 - - - +
115A THR* 1.3 64.6 + - - +
150A TRP* 3.8 33.9 - - + -
151A THR 3.4 19.7 - - - +
152A LEU* 4.6 14.6 - - + -
399A SER* 3.5 1.0 - - - -
400A LEU* 2.8 59.5 + - + +
402A PHE* 4.6 11.0 - - + -
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Residues in contact with THR 115 (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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113A GLY 4.9 1.0 - - - -
114A ILE* 1.3 79.6 + - - +
116A TYR* 1.3 64.0 + - - +
117A ALA* 5.0 2.5 - - + +
149A ASN 3.4 2.0 - - - +
150A TRP* 3.4 11.3 - - - -
151A THR* 3.1 43.2 + - - -
153A ASP* 4.6 9.4 + - - -
397A THR* 3.5 29.6 - - + -
398A PHE 3.6 5.4 - - - +
399A SER* 3.9 11.4 - - - +
401A LYS* 6.1 1.0 - - - +
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Residues in contact with TYR 116 (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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115A THR* 1.3 74.0 - - - +
117A ALA* 1.3 78.5 + - - +
118A ARG* 3.3 19.2 + - + -
148A ASP* 2.7 39.1 + - + -
149A ASN 3.3 5.6 - - - -
150A TRP* 3.7 46.0 - + + -
396A PHE* 4.1 30.7 - + - -
397A THR* 3.4 3.1 - - - +
398A PHE* 2.9 38.2 + - + +
339C ASP* 4.9 5.8 - - - -
363C ASN* 4.2 6.1 + - - -
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Residues in contact with ALA 117 (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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115A THR* 5.3 2.7 - - + -
116A TYR* 1.3 82.7 - - - +
118A ARG* 1.3 62.2 + - - +
119A TYR* 4.7 9.7 - - + +
147A ALA 4.1 0.3 - - - +
148A ASP* 3.7 0.2 - - - -
149A ASN* 2.8 43.6 + - + +
394A PRO* 4.3 10.8 - - + -
396A PHE 3.5 6.7 - - - +
397A THR* 3.7 22.2 - - + +
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Residues in contact with ARG 118 (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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116A TYR* 3.3 22.4 + - + +
117A ALA* 1.3 78.4 - - - +
119A TYR* 1.3 69.9 + - - +
120A ASP* 4.0 16.6 + - - -
146A LYS* 3.5 30.2 - - - +
147A ALA 3.6 4.9 + - - -
148A ASP* 2.8 27.0 + - - -
394A PRO* 3.5 2.0 - - - +
395A ASP* 2.9 28.4 + - + +
396A PHE* 3.4 35.6 + - + +
362C ALA 5.7 0.4 - - - -
363C ASN* 3.9 36.1 - - - +
390C THR* 4.6 9.2 - - + +
392C ASP* 5.3 2.6 + - - -
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Residues in contact with TYR 119 (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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117A ALA* 4.7 4.9 - - + +
118A ARG* 1.3 90.0 + - - +
120A ASP* 1.3 66.8 + - - +
145A ILE 4.3 2.7 - - - +
146A LYS* 3.8 4.2 - - - -
147A ALA* 3.3 45.3 + - + -
149A ASN* 4.1 31.2 + - + +
175A ARG* 6.4 0.4 - - - -
391A ASP 5.9 1.6 - - - -
392A ASP 5.7 2.0 - - - -
393A ALA 4.7 2.2 - - - -
394A PRO* 3.6 43.2 - - + +
395A ASP* 4.2 6.5 - - - -
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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