Contacts of the strand formed by residues 80 - 87 (chain D) in PDB entry 5CYP
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 ARG 80 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D LYS* 4.8 4.5 - - + +
20D GLN 2.9 18.9 + - - +
21D GLY* 3.3 28.9 + - - +
22D PHE* 2.8 25.8 + - - +
23D GLU* 6.3 1.0 - - - +
73D ASP* 3.4 41.3 + - + -
74D ILE 3.7 7.4 - - - +
75D GLU* 4.7 5.2 - - + +
79D VAL* 1.3 74.4 - - - +
81D MET* 1.3 66.0 + - - +
82D LYS* 4.1 14.9 - - - +
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Residues in contact with MET 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D PHE* 3.2 11.0 - - + +
24D PHE* 5.8 5.2 - - + -
73D ASP* 3.5 3.6 - - - -
74D ILE* 2.8 42.3 + - + +
79D VAL 3.7 2.4 + - - +
80D ARG* 1.3 80.2 - - - +
82D LYS* 1.3 60.9 + - - +
83D LEU* 3.4 8.8 + - + +
266D ILE* 5.7 10.1 - - + -
270D MET* 6.4 2.2 - - + -
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Residues in contact with LYS 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D PHE 2.9 14.4 + - - +
23D GLU* 4.0 19.4 - - + +
24D PHE* 3.4 16.9 + - - +
25D ASN* 4.8 0.5 - - - +
71D THR* 4.9 7.6 - - + -
72D HIS 3.9 0.4 - - - -
73D ASP* 3.9 18.2 - - - +
80D ARG* 4.1 13.2 - - - +
81D MET* 1.3 70.0 - - - +
83D LEU* 1.3 63.9 + - - +
84D THR* 3.3 8.9 + - - -
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Residues in contact with LEU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D PHE* 3.6 24.2 - - + +
26D ILE* 3.9 26.9 - - + -
43D LEU* 4.5 18.6 - - + -
44D PHE* 3.7 28.4 - - + -
70D ILE 3.7 1.0 - - - +
71D THR* 3.4 1.7 - - - -
72D HIS 2.9 41.9 + - - +
74D ILE* 4.7 13.5 - - + -
81D MET* 3.4 7.1 + - + +
82D LYS* 1.3 73.2 - - - +
84D THR* 1.3 64.5 + - - +
85D VAL* 4.4 2.9 - - + -
262D ARG* 4.8 8.7 - - - +
266D ILE* 4.0 17.9 - - + -
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Residues in contact with THR 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D PHE 2.9 7.5 + - - +
25D ASN* 3.3 23.1 + - - +
26D ILE* 2.8 27.5 + - - +
69D SER* 4.2 18.8 - - - +
70D ILE 3.2 7.6 - - - +
71D THR* 3.0 30.0 + - - +
82D LYS* 3.3 4.9 + - - +
83D LEU* 1.3 74.1 - - - +
85D VAL* 1.3 64.8 + - - +
86D ILE* 4.1 12.0 + - + +
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ILE* 3.2 13.7 - - + +
28D VAL* 4.6 10.1 - - + -
40D ILE* 3.6 43.5 - - + -
43D LEU* 4.1 25.4 - - + -
44D PHE* 3.6 26.0 - - + -
68D LYS 3.7 2.1 - - - +
70D ILE* 2.8 39.3 + - - +
83D LEU* 4.4 7.6 - - + -
84D THR* 1.3 76.9 - - - +
86D ILE* 1.3 65.3 + - - +
87D ASP 3.7 0.9 + - - -
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Residues in contact with ILE 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ASN* 4.4 18.8 - - + -
26D ILE 2.9 18.1 + - - +
27D MET* 3.6 23.2 - - + +
28D VAL* 3.2 25.2 + - - +
67D ILE* 3.6 30.3 - - + -
68D LYS 3.5 6.1 - - - +
69D SER* 3.7 16.8 - - - +
84D THR* 4.3 9.6 - - + -
85D VAL* 1.3 72.9 - - - +
87D ASP* 1.3 62.0 + - - +
88D THR 3.8 0.5 + - - -
107D PHE* 3.8 15.0 - - + -
131D THR 5.2 2.5 - - - +
133D VAL* 3.7 29.8 - - + -
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Residues in contact with ASP 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D VAL* 3.3 17.1 - - - +
36D LYS* 4.3 1.7 - - - +
37D SER* 2.9 25.2 + - - -
40D ILE* 3.5 20.9 - - + +
64D THR* 3.3 14.6 + - + +
66D GLU 4.1 0.3 - - - +
67D ILE* 3.3 7.3 - - - +
68D LYS* 2.8 42.7 + - + +
70D ILE* 5.2 6.2 - - + +
85D VAL 3.7 2.2 + - - -
86D ILE* 1.3 73.4 - - - +
88D THR* 1.3 70.6 + - - +
302D MG 3.1 14.9 - - - -
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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