Contacts of the strand formed by residues 72 - 77 (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 GLY 72 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D PRO* 3.9 4.3 - - - -
71D PRO* 1.3 75.8 - - - +
73D ALA* 1.3 61.8 + - - -
74D TYR* 3.5 8.2 - - - -
92D VAL* 2.9 37.1 + - - +
96D PRO* 3.7 18.5 - - - +
97D ALA* 4.7 3.1 - - - -
98D ASN* 3.6 9.4 - - - -
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Residues in contact with ALA 73 (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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49D ILE* 3.7 1.0 - - - -
50D PRO* 3.3 5.0 - - - +
72D GLY* 1.3 72.0 - - - -
74D TYR* 1.3 69.2 + - - +
89D LEU* 4.1 13.0 - - + -
90D ILE 3.3 8.3 - - - +
91D ALA* 4.5 1.3 - - - +
96D PRO* 3.6 14.7 - - + +
98D ASN* 2.7 39.9 + - - +
99D LEU* 4.3 14.1 - - + -
102D ILE* 3.7 19.2 - - + +
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Residues in contact with TYR 74 (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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48D MET 3.4 4.9 - - - -
49D ILE* 3.5 17.7 - - + -
50D PRO* 2.4 45.3 - - + +
53D ALA* 3.2 19.3 - - + +
56D PHE* 4.4 13.9 - + - -
66D LEU* 6.0 1.8 - - + -
68D VAL* 5.9 8.3 - - + -
69D THR 5.5 1.3 + - - -
70D GLN* 2.9 39.3 + - - +
72D GLY 3.5 11.4 - - - -
73D ALA* 1.3 79.2 - - - +
75D LEU* 1.3 61.6 + - - +
76D VAL* 3.9 5.7 + - + -
88D ALA 3.7 0.7 - - - +
89D LEU* 3.4 8.5 - - - +
90D ILE* 2.8 55.5 + - + +
92D VAL* 4.3 9.4 - - + -
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Residues in contact with LEU 75 (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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44D SER* 4.2 0.5 - - - -
45D ILE* 3.3 43.9 + - + +
48D MET* 2.9 39.5 + - + +
49D ILE* 4.6 1.2 - - - +
74D TYR* 1.3 74.9 - - - +
76D VAL* 1.3 64.9 + - - +
82D TYR* 5.2 0.7 - - - +
87D ILE* 4.1 10.3 - - + -
88D ALA 3.5 17.5 - - - +
89D LEU* 3.9 17.0 - - + +
102D ILE* 4.3 14.5 - - + +
107D LYS* 4.5 12.3 - - + -
111D VAL* 4.7 14.4 - - + -
115D LEU* 4.1 20.4 - - + -
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Residues in contact with VAL 76 (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* 5.4 5.2 - - + -
33D PHE* 4.9 13.0 - - + -
42D VAL* 5.4 4.3 - - + -
43D GLU 3.5 11.2 - - - +
45D ILE* 4.2 1.3 - - - -
56D PHE* 3.7 33.9 - - + -
66D LEU* 5.8 0.2 - - + -
74D TYR* 4.7 4.5 - - + +
75D LEU* 1.3 79.9 - - - +
77D LYS* 1.3 63.7 + - - +
87D ILE* 3.2 9.2 - - - +
88D ALA* 2.9 57.3 + - + +
90D ILE* 4.2 24.2 - - + -
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Residues in contact with LYS 77 (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* 4.1 6.5 - - - -
42D VAL* 3.3 4.7 - - - +
43D GLU* 2.9 67.2 + - + +
44D SER 4.7 3.4 - - - -
45D ILE* 3.7 21.3 - - + +
46D LYS* 5.3 10.8 - - - +
76D VAL* 1.3 77.2 - - - +
78D CYS* 1.3 65.3 + - - +
79D THR* 4.7 9.6 + - - +
82D TYR* 3.4 53.3 - - + +
86D MET 3.5 5.8 - - - +
87D ILE* 4.3 0.2 - - - +
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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