Contacts of the strand formed by residues 57 - 64 (chain B) in PDB entry 2YYU
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 ALA 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU 2.8 9.9 + - - +
32B PHE* 3.6 27.4 - - + -
33B VAL* 2.9 28.9 + - - +
55B GLY 4.2 0.4 + - - -
56B HIS* 1.3 73.8 - - - +
58B VAL* 1.3 61.1 + - - +
84B ASP* 3.3 16.8 - - + +
116B ARG* 5.7 2.0 - - - +
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 3.9 4.0 - - - -
33B VAL* 3.4 7.9 - - + +
35B VAL* 3.8 25.6 - - + -
48B VAL* 4.5 14.6 - - + +
51B LEU* 3.8 29.2 - - + -
52B LYS* 4.2 18.2 - - + -
56B HIS 4.3 2.0 - - - +
57B ALA* 1.3 78.6 - - - +
59B PHE* 1.3 62.1 + - - +
60B LEU* 3.9 20.1 + - + +
83B ALA* 3.9 2.3 - - - -
84B ASP* 2.7 43.2 + - - +
85B LEU 3.2 6.1 + - - +
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Residues in contact with PHE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.1 12.6 - - + -
32B PHE* 3.8 15.9 - - + -
33B VAL 2.7 15.3 + - - +
34B LYS* 3.2 33.6 - - + -
35B VAL 2.8 32.4 + - - -
58B VAL* 1.3 73.1 - - - +
60B LEU* 1.3 73.2 + - - +
61B ASP* 3.3 7.0 + - + -
85B LEU* 3.3 40.8 - - + -
86B VAL* 4.1 4.5 - - - -
87B ASN* 3.6 30.3 - - - -
118B ILE* 4.2 9.4 - - + -
161B VAL* 5.1 2.9 - - + -
181B VAL* 4.6 14.1 - - + -
213B VAL* 5.1 2.2 - - + -
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Residues in contact with LEU 60 (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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35B VAL* 3.7 22.9 - - + +
40B TYR* 4.0 19.1 - - + -
48B VAL* 3.6 28.5 - - + -
58B VAL* 3.9 7.1 + - + -
59B PHE* 1.3 72.5 - - - +
61B ASP* 1.3 60.3 + - - +
62B LEU* 3.3 19.1 + - + +
64B LEU* 6.1 0.5 - - - +
78B LEU* 3.8 28.2 - - + +
81B VAL* 4.2 13.5 - - + -
83B ALA* 4.0 19.7 - - + -
85B LEU 2.8 11.9 + - - +
86B VAL* 3.4 26.4 - - + +
87B ASN* 3.8 2.3 + - - +
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Residues in contact with ASP 61 (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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66A ASP* 4.7 2.4 - - - +
34B LYS* 3.0 49.4 + - + +
35B VAL 2.9 11.3 + - - +
36B GLY* 3.6 15.7 - - - -
37B MET* 3.8 7.1 + - - +
59B PHE* 3.3 7.0 + - + -
60B LEU* 1.3 68.4 - - - +
62B LEU* 1.3 60.6 + - - +
63B LYS* 2.7 34.0 + - - +
87B ASN* 2.8 22.5 + - - -
2301B C5P 3.8 5.2 + - - -
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Residues in contact with LEU 62 (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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37A MET* 6.0 0.2 - - - +
41A TYR* 3.9 31.2 + - + +
35B VAL 4.3 2.9 - - - +
36B GLY 4.0 11.0 - - - +
37B MET* 3.6 24.4 - - - +
40B TYR* 3.8 47.1 - - + -
41B TYR* 4.1 12.6 + - + +
60B LEU* 3.3 20.9 + - + +
61B ASP* 1.3 82.2 - - - +
63B LYS* 1.3 73.1 + - - +
64B LEU* 3.2 15.6 + - + +
78B LEU* 4.4 14.6 - - + -
87B ASN* 3.4 0.4 + - - -
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Residues in contact with LYS 63 (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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37A MET* 5.5 0.3 - - - +
63A LYS 5.4 1.7 - - - +
65A HIS* 3.5 19.0 + - - +
66A ASP* 2.7 38.1 + - - +
37B MET* 4.4 1.6 - - + +
61B ASP* 2.7 40.4 + - - +
62B LEU* 1.3 80.3 - - - +
64B LEU* 1.3 67.1 + - - +
65B HIS* 3.2 4.7 + - - +
87B ASN* 2.9 27.2 + - - +
88B VAL* 4.1 2.9 - - - +
89B HIS* 3.5 29.6 + - + +
120B VAL* 3.8 22.2 - - + -
123B LEU* 3.8 13.9 - - + -
161B VAL* 6.0 3.1 - - - -
2301B C5P 4.6 5.7 + - - -
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A MET* 3.9 22.2 - - + -
41A TYR* 4.2 8.5 - - + +
60B LEU 6.1 0.4 - - - +
62B LEU* 3.8 25.6 - - + -
63B LYS* 1.3 71.3 - - - +
65B HIS* 1.3 58.4 + - - +
66B ASP 4.1 0.9 - - - -
71B VAL* 4.1 17.3 - - + -
74B ALA* 3.7 30.3 - - + -
75B MET* 4.0 21.8 - - + -
78B LEU* 4.1 17.0 - - + -
86B VAL* 6.0 0.2 - - + -
87B ASN 3.2 13.8 + - - +
88B VAL* 3.3 18.8 - - + +
89B HIS 3.1 20.4 + - - -
96B MET* 3.7 4.5 - - - +
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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