Contacts of the strand formed by residues 87 - 92 (chain D) in PDB entry 2P80
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 ILE 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D PHE* 3.6 14.2 + - - +
21D ALA* 3.9 13.5 - - - +
45D ILE* 4.7 3.6 - - + -
75D LEU* 4.1 20.2 - - + -
76D VAL 3.2 15.3 - - - +
77D LYS* 4.1 0.4 - - + -
82D TYR* 3.4 34.5 - - + -
85D GLY 3.0 14.1 + - - +
86D MET* 1.3 79.0 - - - +
88D ALA* 1.3 66.2 + - - +
89D LEU 5.4 0.2 - - - +
111D VAL* 4.0 20.9 - - + +
114D ARG* 4.5 6.2 - - + -
115D LEU* 4.1 31.6 - - + +
118D VAL* 5.3 5.6 - - + -
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Residues in contact with ALA 88 (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 PHE* 4.0 20.9 - - + -
21D ALA* 3.3 12.8 - - - +
23D ILE* 4.0 19.3 - - + -
33D PHE* 5.2 2.0 - - + -
74D TYR 3.7 0.3 - - - +
75D LEU* 3.5 8.1 - - - +
76D VAL* 2.9 49.1 + - + +
87D ILE* 1.3 78.3 - - - +
89D LEU* 1.3 60.4 + - - +
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Residues in contact with LEU 89 (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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21D ALA 2.8 12.5 + - - +
22D TYR* 3.5 30.3 - - + -
23D ILE* 2.8 26.9 + - - +
73D ALA* 4.1 18.4 - - + -
74D TYR 3.4 20.4 - - - +
75D LEU* 3.9 17.9 - - + +
87D ILE* 5.4 0.6 - - + +
88D ALA* 1.3 73.1 - - - +
90D ILE* 1.3 66.5 + - - +
91D ALA* 5.2 2.9 - - + -
99D LEU* 4.2 24.2 - - + -
102D ILE* 4.8 5.6 - - + -
115D LEU* 4.5 10.1 - - + -
118D VAL* 5.0 4.0 - - + +
119D ILE* 4.2 17.7 - - + -
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Residues in contact with ILE 90 (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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23D ILE* 3.3 35.0 - - + +
25D ALA* 4.7 5.8 - - + -
31D VAL* 4.7 6.1 - - + -
33D PHE* 4.3 14.6 - - + -
66D LEU* 4.0 26.0 - - + -
68D VAL* 4.5 9.9 - - + -
72D GLY 3.7 1.2 - - - +
73D ALA* 3.3 4.7 - - - +
74D TYR* 2.8 46.7 + - + +
76D VAL* 4.2 24.2 - - + -
89D LEU* 1.3 77.5 - - - +
91D ALA* 1.3 61.0 + - - +
92D VAL* 4.0 19.3 - - + -
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Residues in contact with ALA 91 (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 TYR* 3.9 28.0 - - + +
23D ILE 2.7 12.1 + - - +
24D LYS* 3.0 14.4 - - + +
25D ALA 2.9 29.9 + - - -
72D GLY 3.8 4.0 - - - -
73D ALA* 4.5 2.5 - - + +
89D LEU* 4.0 4.9 + - + -
90D ILE* 1.3 73.4 - - - +
92D VAL* 1.3 57.9 + - - +
93D GLY 4.9 1.3 - - - +
96D PRO* 4.6 17.7 - - + -
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Residues in contact with VAL 92 (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 ALA* 3.3 5.6 - - + +
26D ASN 4.1 4.0 - - - +
27D PRO* 3.9 30.1 - - + -
68D VAL* 4.2 20.2 - - + -
69D THR 4.4 1.6 - - - +
70D GLN 3.5 24.9 - - - +
71D PRO* 3.4 12.5 - - + +
72D GLY* 2.9 41.6 + - - +
74D TYR* 4.3 8.3 - - + -
90D ILE* 4.1 18.6 - - + -
91D ALA* 1.3 71.9 - - - +
93D GLY* 1.3 65.8 + - - +
94D ASP 4.9 0.9 - - - +
96D PRO* 5.0 2.5 - - - +
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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