Contacts of the strand formed by residues 108 - 120 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B LYS* 1.3 81.2 + - + +
109B SER* 1.3 77.3 + - - +
110B PHE* 4.8 7.4 - + + -
156B GLY* 4.7 8.1 - - - -
157B ARG 3.3 22.4 - - - -
158B TYR* 4.0 20.2 - + + -
405B TYR* 4.4 2.0 - - - +
406B PHE* 3.2 64.5 + + + +
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ALA* 5.2 0.5 - - - +
107B LYS 4.1 1.2 + - - -
108B PHE* 1.3 86.0 - - - +
110B PHE* 1.3 63.6 + - - +
111B GLU* 4.4 0.9 + - - +
156B GLY* 3.7 2.1 - - - -
157B ARG* 2.9 56.4 + - - +
403B PRO* 5.8 2.0 - - - +
404B TYR 3.4 15.0 - - - -
405B TYR* 3.7 31.2 - - - -
406B PHE* 4.4 1.8 - - - +
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Residues in contact with PHE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PHE* 4.8 8.1 - + + -
109B SER* 1.3 75.7 - - - +
111B GLU* 1.3 58.5 + - - +
112B THR* 3.6 23.3 + - - -
154B LEU* 4.3 24.2 - - + -
155B THR 3.0 33.9 - - - -
156B GLY* 4.2 5.4 - - - -
402B PHE 3.6 3.3 - - - +
403B PRO* 4.6 0.2 - - - -
404B TYR* 3.0 37.0 + - + +
406B PHE* 4.1 20.1 - + + -
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU* 5.7 0.2 - - - +
109B SER* 4.4 0.9 - - - +
110B PHE* 1.3 71.6 - - - +
112B THR* 1.3 63.4 + - - +
113B GLY* 5.3 0.7 - - - +
153B ASP 3.7 1.0 - - - +
154B LEU* 3.9 0.9 - - - -
155B THR* 3.0 53.6 + - - +
157B ARG* 2.8 34.6 + - + +
401B LYS* 3.8 41.3 + - + +
402B PHE 3.7 4.7 - - - -
403B PRO* 4.0 31.1 - - + +
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B PHE* 3.6 24.4 + - - -
111B GLU* 1.3 72.4 - - - +
113B GLY* 1.3 62.0 + - - +
114B ILE* 5.1 1.1 - - + +
152B LEU* 4.2 20.4 - - + -
153B ASP 3.5 4.7 - - - +
154B LEU* 4.3 7.2 - - + +
401B LYS* 3.4 1.7 - - - -
402B PHE* 2.8 54.3 + - + -
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Residues in contact with GLY 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLU* 4.2 1.3 - - - +
112B THR* 1.3 76.2 - - - +
114B ILE* 1.3 60.5 + - - -
115B THR* 4.9 2.0 - - - -
151B THR 3.5 1.0 - - - +
152B LEU* 3.2 12.2 - - - +
153B ASP* 2.7 46.2 + - - +
155B THR* 5.6 0.2 + - - -
400B LEU 3.4 8.1 - - - -
401B LYS* 4.2 10.8 - - - -
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Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B THR* 5.1 1.5 - - + +
113B GLY* 1.3 71.3 - - - -
115B THR* 1.3 62.1 + - - +
150B TRP* 4.1 32.1 - - + -
151B THR 3.1 30.5 - - - +
152B LEU* 4.0 18.2 - - + +
399B SER* 3.4 1.6 - - - -
400B LEU* 2.8 60.3 + - + +
401B LYS* 5.6 0.2 - - - +
402B PHE* 5.1 6.8 - - + -
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLY 4.9 1.4 - - - -
114B ILE* 1.3 79.3 + - - +
116B TYR* 1.3 63.5 + - - +
117B ALA* 5.2 2.9 - - + -
149B ASN 3.5 1.2 - - - +
150B TRP* 3.3 9.8 - - - -
151B THR* 2.9 44.7 + - - -
153B ASP* 4.7 8.3 + - - -
397B THR* 3.7 22.2 - - + -
398B PHE 3.4 13.0 - - - +
399B SER* 3.5 12.6 - - - -
401B LYS* 6.0 1.0 - - - +
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Residues in contact with TYR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A ASP* 4.5 2.5 - - - -
363A ASN* 3.5 18.0 + - - -
115B THR* 1.3 75.0 - - - +
117B ALA* 1.3 71.1 + - - +
118B ARG* 3.7 9.7 - - + -
148B ASP* 3.0 41.2 + - + -
149B ASN 3.4 4.9 - - - -
150B TRP* 3.5 43.2 - + + -
396B PHE* 3.7 24.5 - + - -
397B THR* 3.3 5.9 - - - +
398B PHE* 2.8 58.2 + + + +
502B LDA 3.6 30.6 - - + +
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B THR* 5.2 2.9 - - + -
116B TYR* 1.3 82.2 - - - +
118B ARG* 1.3 60.0 + - - +
119B TYR* 4.1 14.1 + - + +
147B ALA 3.7 2.9 - - - +
148B ASP* 3.9 1.0 - - - -
149B ASN* 2.9 44.4 + - + +
394B PRO* 4.6 4.3 - - + -
396B PHE 3.4 5.4 - - - +
397B THR* 3.6 22.0 - - + +
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A ASP* 5.8 0.8 + - - -
362A ALA* 5.2 2.0 - - - +
363A ASN* 3.8 34.2 + - - +
390A THR* 4.6 10.7 - - + +
392A ASP* 5.0 4.0 + - - -
116B TYR* 3.7 13.4 + - - +
117B ALA* 1.3 71.9 - - - +
119B TYR* 1.3 72.9 + - - +
120B ASP* 4.6 7.5 + - + +
146B LYS* 3.8 41.0 - - - +
147B ALA 3.7 4.6 + - - +
148B ASP* 2.7 42.4 + - - -
394B PRO* 3.3 6.8 - - - +
395B ASP* 2.9 27.9 + - + +
396B PHE* 3.2 39.1 + - + +
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Residues in contact with TYR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ALA* 4.1 13.9 - - + +
118B ARG* 1.3 84.7 + - - +
120B ASP* 1.3 63.4 + - - +
121B ALA* 6.4 0.2 - - + -
145B ILE 4.4 3.4 - - - +
146B LYS* 3.5 3.5 - - - -
147B ALA* 3.1 50.1 + - + +
149B ASN* 4.1 22.4 + - + -
391B ASP 6.0 0.7 - - - -
392B ASP 5.5 3.4 - - - -
393B ALA 4.7 3.1 - - - -
394B PRO* 3.6 43.6 - - + +
395B ASP* 4.6 4.0 - - - +
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Residues in contact with ASP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A THR* 6.1 1.1 - - - -
391A ASP* 3.5 31.2 + - - +
392A ASP* 5.2 7.3 - - - +
118B ARG* 4.6 8.1 + - - +
119B TYR* 1.3 76.3 - - - +
121B ALA* 1.3 70.8 + - - +
122B ARG* 5.4 0.7 - - - +
144B ARG* 5.1 3.8 - - - +
145B ILE 3.8 4.7 - - - -
146B LYS* 3.8 25.1 - - - +
391B ASP* 5.7 3.5 - - - +
395B ASP* 3.6 25.8 + - - +
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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