Contacts of the strand formed by residues 396 - 405 (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 396 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A ASP* 3.5 33.0 - - + -
363A ASN* 4.0 3.8 - - - -
365A GLY* 4.5 0.4 - - - -
389A MET* 3.8 31.9 - - + -
390A THR* 4.0 23.1 - - + -
116B TYR* 3.7 20.9 - + - -
117B ALA* 3.4 1.2 - - - +
118B ARG* 3.2 40.7 + - + +
385B LEU* 4.3 3.6 - - + -
386B ALA 3.4 13.0 - - - +
387B ILE* 4.9 0.4 - - - -
394B PRO* 3.4 3.2 - - - +
395B ASP* 1.3 81.7 - - - +
397B THR* 1.3 72.7 + - - +
398B PHE* 3.3 43.5 - + - -
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Residues in contact with THR 397 (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* 3.7 21.3 - - + -
116B TYR 3.3 15.7 - - - +
117B ALA* 3.6 7.7 - - + +
366B TYR* 5.1 3.0 - - - -
384B ASN* 3.4 5.0 - - - +
385B LEU* 4.7 0.2 - - - -
386B ALA* 3.1 41.8 + - + +
394B PRO* 3.6 19.8 - - - +
396B PHE* 1.3 86.3 + - - +
398B PHE* 1.3 61.4 + - - +
399B SER* 4.7 4.5 + - - +
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Residues in contact with PHE 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A PHE* 3.9 30.5 - + - -
337A VAL* 3.7 33.2 - - + -
338A SER 5.2 0.2 - - - -
339A ASP* 4.1 16.4 - - + -
389A MET* 5.1 1.3 - - + -
115B THR* 3.4 1.2 - - - +
116B TYR* 2.8 52.8 + + + +
384B ASN 3.6 4.9 - - - +
385B LEU* 4.0 16.2 - - + -
396B PHE* 3.3 38.1 - + - -
397B THR* 1.3 72.6 - - - +
399B SER* 1.3 64.2 + - - +
502B LDA 5.1 1.6 - - + -
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Residues in contact with SER 399 (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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114B ILE 3.4 4.9 - - - -
115B THR* 3.5 24.5 - - - +
382B VAL 3.7 1.5 + - - +
383B PRO* 3.4 4.9 - - - +
384B ASN* 3.1 49.9 + - - +
397B THR* 4.7 3.9 + - - +
398B PHE* 1.3 79.6 - - - +
400B LEU* 1.3 66.8 + - - +
401B LYS* 5.2 8.6 - - - +
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Residues in contact with LEU 400 (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 4.1 0.5 - - - +
113B GLY* 3.4 1.9 - - - -
114B ILE* 2.8 47.9 + - + +
381B ILE* 4.0 22.7 - - + -
382B VAL 3.5 1.8 - - - -
383B PRO* 4.0 27.4 - - + -
399B SER* 1.3 74.2 - - - +
401B LYS* 1.3 63.1 + - - +
402B PHE* 3.8 24.0 - - + -
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Residues in contact with LYS 401 (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* 3.2 37.6 + - - -
111B GLU* 3.8 33.3 + - + +
112B THR 3.4 5.8 - - - +
113B GLY* 4.5 8.3 - - - -
380B THR 3.6 1.4 - - - +
381B ILE* 3.6 2.3 - - - +
382B VAL* 3.0 48.1 + - + +
399B SER* 5.2 8.7 - - - +
400B LEU* 1.3 82.1 - - - +
402B PHE* 1.3 64.8 + - - +
403B PRO* 3.4 6.8 - - + +
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Residues in contact with PHE 402 (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 2.4 - - - +
111B GLU* 4.2 0.8 - - - +
112B THR* 2.8 49.2 + - + +
113B GLY* 5.4 0.2 - - - -
114B ILE* 5.1 6.5 - - + -
379B LEU* 3.9 18.5 - - + +
380B THR 3.5 4.5 - - - -
381B ILE* 4.0 39.7 - - + -
400B LEU* 3.8 39.7 - - + -
401B LYS* 1.3 75.6 - - - +
403B PRO* 1.3 65.5 - - - +
404B TYR* 3.1 5.2 + - - +
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Residues in contact with PRO 403 (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* 6.1 0.4 - - - +
109B SER* 5.8 2.7 - - - +
110B PHE 4.6 0.9 - - - +
111B GLU* 4.0 33.8 - - + +
378B ASN 3.4 2.4 - - - +
379B LEU* 3.4 5.4 - - - +
380B THR* 3.1 52.6 + - - +
382B VAL* 4.2 10.5 - - + -
401B LYS* 3.4 9.0 - - + +
402B PHE* 1.3 84.0 - - - +
404B TYR* 1.3 59.5 + - - +
405B TYR* 3.7 26.8 - - + +
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Residues in contact with TYR 404 (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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109B SER* 3.4 3.4 - - - -
110B PHE* 3.0 38.0 + - + +
376B SER* 5.9 0.7 - - - -
378B ASN* 3.5 27.6 + - + +
379B LEU* 4.6 20.9 - - + -
402B PHE 3.1 6.2 + - - +
403B PRO* 1.3 72.5 - - - +
405B TYR* 1.3 78.3 + - - +
406B PHE* 3.7 38.0 + + + -
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Residues in contact with TYR 405 (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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94B ASN* 5.3 3.1 - - - -
97B ASN* 3.0 30.9 + - - +
103B ALA* 3.7 21.7 - - + +
105B ASN* 4.7 9.2 - - + -
106B GLY* 4.8 16.6 - - - -
107B LYS 5.8 0.2 - - - -
108B PHE 5.0 2.0 - - - +
109B SER* 3.7 23.1 - - - -
377B GLU 4.9 5.4 - - - +
378B ASN* 2.7 57.0 + - - +
380B THR* 4.0 13.2 - - - -
403B PRO* 3.7 29.7 - - + +
404B TYR* 1.3 80.6 - - - +
406B PHE* 1.3 60.4 + - - +
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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