Contacts of the strand formed by residues 79 - 84 (chain B) in PDB entry 2YD7
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 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B CYS 3.4 7.9 - - - -
46B GLN* 4.0 3.6 - - - -
55B ILE* 4.4 0.7 - - - -
73B GLU* 3.4 7.8 - - - +
74B PHE* 2.9 55.2 + - - +
75B ASP* 3.9 1.6 - - - +
77B GLY 4.0 3.1 - - - -
78B SER* 1.3 80.5 - - - +
80B SER* 1.3 61.9 + - - -
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Residues in contact with SER 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B CYS 2.8 31.9 + - - -
55B ILE* 3.5 33.8 + - - +
57B TRP* 2.8 24.4 + - - -
71B VAL* 3.1 23.0 - - - +
72B ILE 3.5 5.3 - - - -
73B GLU* 4.4 4.7 - - - +
74B PHE* 3.3 3.2 - - - -
79B GLY* 1.3 76.1 - - - -
81B VAL* 1.3 64.0 + - - +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B SER* 4.0 16.6 - - - +
43B PHE 3.3 8.1 - - - +
44B ILE* 4.0 13.0 - - + -
57B TRP* 4.2 3.1 - - - -
70B GLU 3.5 1.4 - - - +
71B VAL* 3.2 5.9 - - - +
72B ILE* 2.7 45.3 + - + +
74B PHE* 3.9 9.6 - - + -
80B SER* 1.3 77.5 + - - +
82B LEU* 1.3 71.2 + - - +
83B ARG* 4.4 1.1 - - + +
160B PHE* 4.8 1.6 - - + -
163B PHE 3.7 19.3 - - - +
164B LEU* 3.8 21.5 - - + -
165B PRO* 3.9 15.5 - - + -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ALA 3.8 1.2 - - - +
42B SER* 3.1 4.2 - - - -
43B PHE* 2.8 51.3 + - + +
57B TRP* 3.6 45.3 - - + +
64B VAL* 4.2 17.9 - - + -
69B PHE* 4.3 15.3 - - + -
70B GLU 3.5 12.8 - - - +
71B VAL* 4.0 15.3 - - + -
81B VAL* 1.3 71.8 - - - +
83B ARG* 1.3 58.8 + - - +
84B ILE* 4.2 12.9 + - + +
96B TYR* 4.2 25.1 - - + -
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Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL* 3.8 20.0 - - + +
41B ALA 3.4 2.7 - - - -
42B SER* 4.0 15.7 + - - +
68B ARG 3.6 1.7 - - - +
69B PHE* 3.4 2.3 - - - +
70B GLU* 2.7 49.9 + - + +
72B ILE* 3.9 11.7 - - + -
81B VAL* 3.8 2.2 + - + -
82B LEU* 1.3 74.4 - - - +
84B ILE* 1.3 64.9 + - - +
85B GLN* 2.8 36.4 + - + +
160B PHE* 5.4 1.0 - - - +
163B PHE* 3.3 54.9 - - + +
200B GLU* 2.8 42.2 + - - -
211B TYR* 4.1 4.4 - - - -
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Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL* 3.4 2.9 - - - +
41B ALA* 2.8 35.4 + - + +
43B PHE* 4.3 17.3 - - + -
68B ARG* 3.4 8.5 - - - +
69B PHE* 3.6 47.6 - - + -
82B LEU* 4.4 13.9 - - + +
83B ARG* 1.3 76.1 - - - +
85B GLN* 1.3 64.8 + - - +
87B LEU* 3.8 15.6 - - + +
92B ASP* 3.6 24.2 - - - +
96B TYR* 4.5 2.7 - - + -
113B LEU* 3.7 26.7 - - + -
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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