Contacts of the strand formed by residues 56 - 68 (chain O) in PDB entry 5IYB
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 VAL 56 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358N MET* 4.1 20.9 - - + -
366N ILE 5.8 0.4 - - - +
367N PHE* 3.8 33.0 - - + -
369N LYS 3.7 2.5 + - - +
370N ALA* 3.7 24.8 - - + +
371N ILE 4.0 1.9 + - - +
55O ARG* 1.3 79.7 - - - +
57O ASN* 1.3 74.6 + - - +
58O PHE* 4.3 4.6 - - + -
81O PHE* 4.4 17.5 - - + -
82O ARG 3.7 10.1 - - - +
83O GLU* 4.2 19.7 - - + +
88O ILE* 6.3 1.1 - - + -
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Residues in contact with ASN 57 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371N ILE 3.1 18.0 - - - +
372N GLY* 4.5 0.5 + - - -
56O VAL* 1.3 74.9 - - - +
58O PHE* 1.3 82.7 + - - +
59O ARG* 4.5 12.6 - - - +
81O PHE* 3.6 1.7 - - - -
82O ARG* 2.7 61.8 + - + +
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Residues in contact with PHE 58 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351N PHE* 3.4 35.0 - + + -
353N LEU* 3.7 20.6 - - + -
370N ALA* 3.8 26.2 - - + -
371N ILE 3.5 18.8 - - - -
372N GLY* 3.5 16.8 - - - -
373N ASP 3.6 15.0 + - - -
56O VAL* 4.3 4.7 - - + -
57O ASN* 1.3 87.1 + - - +
59O ARG* 1.3 74.8 + - - +
76O LEU* 5.1 9.2 - - + -
79O VAL* 5.2 0.7 - - + -
80O GLU 3.6 5.6 - - - -
81O PHE* 3.3 35.7 - + + -
95O ILE* 5.5 9.2 - - + -
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Residues in contact with ARG 59 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373N ASP* 3.4 22.7 - - + +
374N ALA* 5.4 0.7 - - - -
57O ASN* 4.5 13.7 - - - +
58O PHE* 1.3 82.9 - - - +
60O GLY* 1.3 57.8 + - - +
76O LEU* 5.2 1.9 - - - +
79O VAL* 3.2 24.6 - - - +
80O GLU* 2.8 57.4 + - + +
82O ARG* 3.7 23.3 - - + +
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Residues in contact with GLY 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373N ASP 3.6 4.0 + - - -
374N ALA* 3.2 24.9 - - - -
375N GLU* 3.4 4.0 + - - +
59O ARG* 1.3 79.3 - - - +
61O SER* 1.3 64.4 + - - -
76O LEU* 5.0 1.8 - - - -
78O ASP 3.6 15.9 - - - -
79O VAL* 4.3 3.8 - - - -
80O GLU 4.9 0.2 - - - -
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Residues in contact with SER 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375N GLU* 3.4 11.9 + - - +
60O GLY* 1.3 74.3 + - - -
62O LEU* 1.3 60.3 + - - +
76O LEU* 3.3 9.0 - - - +
77O ASN* 2.9 56.3 + - - -
78O ASP* 4.0 4.7 + - - +
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Residues in contact with LEU 62 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349N TRP* 3.5 42.4 - - + +
351N PHE* 5.0 5.6 - - + -
374N ALA* 4.4 10.0 - - + +
375N GLU 2.6 18.9 + - - +
376N TRP* 3.3 37.6 - - + -
60O GLY 4.2 0.6 + - - -
61O SER* 1.3 73.0 - - - +
63O ASN* 1.3 59.4 + - - +
64O THR 3.3 23.6 - - - +
65O TYR* 4.2 14.6 - - + -
74O PHE* 4.1 10.3 - - + -
75O VAL 4.0 0.2 - - - +
76O LEU* 3.8 28.0 - - + -
77O ASN* 4.3 2.2 - - - +
205P ARG* 5.1 2.9 + - - -
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Residues in contact with ASN 63 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322N ASP* 5.0 4.3 - - - +
326N GLN* 3.7 32.8 + - - +
376N TRP* 3.4 16.7 + - - -
61O SER 3.7 2.0 + - - -
62O LEU* 1.3 73.0 - - - +
64O THR* 1.3 74.3 + - - +
75O VAL* 3.1 19.0 + - + +
77O ASN* 3.1 29.6 + - + +
92O LYS* 4.6 9.7 - - - +
189P ASN* 3.4 2.9 + - - +
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Residues in contact with THR 64 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322N ASP* 5.7 1.8 - - - +
326N GLN* 4.5 3.1 + - - +
62O LEU* 3.3 12.1 - - - +
63O ASN* 1.3 97.4 - - - +
65O TYR* 1.3 63.7 + - - +
74O PHE* 3.5 0.2 - - - -
75O VAL* 3.0 55.4 + - - +
188P ARG* 3.2 51.6 - - + +
189P ASN* 4.0 10.5 - - - +
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Residues in contact with TYR 65 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349N TRP* 4.3 18.8 - + + -
376N TRP* 4.2 11.9 - + - -
62O LEU* 4.2 20.4 - - + -
64O THR* 1.3 77.3 - - - +
66O ARG* 1.3 63.2 + - - +
72O TRP* 5.3 0.7 - + - -
73O THR 3.2 7.0 - - - -
74O PHE* 3.5 20.4 - + + -
187P ALA 4.5 0.3 - - - +
188P ARG* 2.5 32.2 + - - +
189P ASN* 2.9 41.4 + - + -
190P ALA* 2.9 42.7 - - - +
191P GLU* 4.2 10.8 - - + -
203P ARG* 2.6 51.1 + - + +
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Residues in contact with ARG 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327N GLU* 3.3 30.1 + - - -
65O TYR* 1.3 78.2 - - - +
67O PHE* 1.3 64.5 + - - +
68O CYS* 4.5 13.7 - - - -
72O TRP* 3.4 9.3 - - - -
73O THR* 2.5 74.2 + - - +
74O PHE* 4.1 0.6 - - - -
94O LYS* 6.1 1.0 - - - +
184P ALA* 3.0 25.4 + - - +
185P LEU* 3.0 27.9 + - - +
186P ARG 3.4 8.1 + - - -
187P ALA 2.8 21.1 + - - +
188P ARG* 4.3 3.9 - - - +
190P ALA 3.2 9.4 + - - +
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Residues in contact with PHE 67 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339N TYR* 4.2 2.5 - + - -
66O ARG* 1.3 78.2 - - - +
68O CYS* 1.3 59.5 + - - +
70O ASN* 3.6 43.3 - - - -
71O VAL 3.2 12.3 - - - -
72O TRP* 3.3 61.9 - + + -
184P ALA* 4.5 1.4 - - - +
190P ALA 3.8 5.5 + - - -
191P GLU* 3.7 11.3 - - + +
192P TYR* 2.6 53.7 + - - +
193P ASN* 3.3 39.9 - - + -
196P ARG* 6.2 0.2 - - - -
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Residues in contact with CYS 68 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66O ARG* 4.5 21.1 - - - -
67O PHE* 1.3 77.4 - - - +
69O ASP* 1.3 70.0 + - + +
70O ASN 3.2 3.4 - - - +
71O VAL* 2.9 33.1 + - - +
73O THR* 5.9 1.3 - - - -
181P LYS* 5.5 3.4 - - + +
184P ALA* 4.3 16.6 - - + -
185P LEU* 5.1 8.5 - - - -
192P TYR* 3.5 14.4 - - + +
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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