Contacts of the strand formed by residues 77 - 82 (chain D) in PDB entry 1YY9
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 GLN 77 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D THR* 4.3 11.3 - - + +
22D CYS 3.5 3.1 - - - -
23D THR* 3.5 28.0 + - - +
29D LEU* 3.5 1.6 - - - +
71D LYS* 3.3 4.5 - - - +
72D ASP* 2.9 33.9 + - + +
75D LYS* 3.4 41.1 + - + +
76D SER* 1.3 75.1 - - - +
78D VAL* 1.3 63.0 + - - +
79D PHE* 3.6 29.0 - - + -
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Residues in contact with VAL 78 (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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20D ILE 3.8 0.3 - - - +
21D THR* 3.3 5.4 - - - +
22D CYS* 2.8 49.1 + - + +
24D VAL* 5.3 1.6 - - + -
29D LEU* 3.7 30.5 - - + -
34D VAL* 3.9 17.3 - - + -
36D TRP* 3.6 28.3 - - + +
51D ILE* 3.9 8.5 - - + -
69D ILE* 3.8 9.9 - - + -
70D ASN 3.4 11.9 - - - +
71D LYS* 4.2 6.7 - - + -
77D GLN* 1.3 77.1 - - - +
79D PHE* 1.3 66.9 + - - +
80D PHE 4.1 0.4 - - - -
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Residues in contact with PHE 79 (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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20D ILE 3.6 3.4 - - - -
21D THR* 3.3 36.1 - - + -
68D SER 3.5 1.7 - - - +
69D ILE* 3.4 4.8 - - - -
70D ASN* 2.8 56.5 + - + +
71D LYS* 4.3 3.1 - - - -
72D ASP* 4.3 17.7 - - + -
75D LYS* 5.6 3.1 - - - -
77D GLN* 3.6 34.3 - - + -
78D VAL* 1.3 74.5 - - - +
80D PHE* 1.3 63.0 + - - +
81D LYS* 5.1 1.3 - - - +
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Residues in contact with PHE 80 (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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18D LEU* 4.1 20.6 - - + -
19D SER* 3.3 6.6 - - - -
20D ILE* 3.0 40.6 + - + +
36D TRP* 3.4 56.0 - + + -
48D LEU* 3.8 29.6 - - + -
67D LEU* 3.7 29.8 - - + -
68D SER 3.7 2.9 - - - -
69D ILE* 4.3 12.3 - - + -
79D PHE* 1.3 71.1 - - - +
81D LYS* 1.3 62.6 + - - +
82D MET* 3.9 22.9 - - + -
93D TYR* 4.0 9.2 - + - -
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Residues in contact with LYS 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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17D SER* 3.6 21.5 - - - +
18D LEU 3.4 4.0 - - - +
19D SER* 3.7 17.9 - - - +
66D ARG 4.4 0.2 - - - -
67D LEU* 3.6 6.6 - - - +
68D SER* 2.6 54.3 + - - +
70D ASN* 6.2 0.9 - - - +
79D PHE 5.1 0.9 - - - +
80D PHE* 1.3 76.7 - - - +
82D MET* 1.3 60.8 + - - +
83D ASN* 3.8 19.7 + - - +
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Residues in contact with MET 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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17D SER* 3.3 4.7 - - - -
18D LEU* 3.0 31.7 + - + +
38D ARG* 3.8 4.3 - - - +
48D LEU* 5.1 2.0 - - - -
63D PHE* 4.3 15.3 - - - -
66D ARG* 3.2 21.3 - - + +
67D LEU* 3.6 20.9 - - + -
80D PHE* 3.9 18.6 - - + -
81D LYS* 1.3 74.7 - - - +
83D ASN* 1.3 68.9 + - - +
85D LEU* 3.3 22.9 - - + +
89D ASP* 3.6 27.4 - - - +
93D TYR* 3.5 27.6 - - + +
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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