Contacts of the strand formed by residues 92 - 97 (chain B) in PDB entry 4YO0
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 SER 92 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B SER* 4.6 8.4 - - - -
41B CYS 3.2 13.0 - - - -
42B LYS* 3.3 18.5 - - - +
48B ILE* 3.8 6.0 - - - +
86B ILE* 3.7 2.4 - - - +
87B ASP* 2.8 37.4 + - - +
90B SER* 2.9 31.9 + - - -
91B ASN* 1.3 74.6 - - - +
93B ALA* 1.3 64.5 + - - +
94B LEU* 4.9 5.2 - - - -
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Residues in contact with ALA 93 (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 SER* 3.4 4.0 - - - -
41B CYS* 2.8 37.5 + - + +
48B ILE* 3.8 4.0 - - + +
53B VAL* 3.6 33.9 - - + -
55B TRP* 3.8 12.1 - - + +
85B SER 3.5 6.1 - - - +
86B ILE* 3.7 17.3 - - + -
92B SER* 1.3 75.5 - - - +
94B LEU* 1.3 63.6 + - - +
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LYS* 4.8 26.7 - - + +
39B LEU 3.3 5.2 - - - +
40B SER* 3.8 24.5 - - - -
55B TRP* 3.7 5.8 + - - -
83B SER 3.8 0.3 - - - +
84B GLY* 3.4 4.9 - - - -
85B SER* 2.9 50.7 + - - +
87B ASP* 4.0 28.9 - - + +
92B SER* 4.7 5.2 - - - +
93B ALA* 1.3 83.6 - - - +
95B LEU* 1.3 59.6 + - - +
96B THR* 3.9 6.9 + - - +
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Residues in contact with LEU 95 (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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37B VAL 3.8 0.7 - - - +
38B LYS* 3.5 1.8 - - - -
39B LEU* 2.8 47.3 + - + +
55B TRP* 3.4 42.6 - - + -
67B MET* 4.8 3.1 - - + -
68B ILE* 3.6 26.7 - - + -
82B PHE* 4.3 22.2 - - + -
83B SER 3.5 16.4 - - - +
94B LEU* 1.3 71.7 - - - +
96B THR* 1.3 59.9 + - - +
97B ILE* 4.0 4.3 + - + +
108B TYR* 3.6 35.9 - - + -
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Residues in contact with THR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B THR* 3.7 27.4 - - + -
37B VAL 3.4 5.6 - - - +
38B LYS* 2.7 37.4 + - + +
81B ARG 3.4 2.3 - - - +
82B PHE* 3.5 2.1 - - - -
83B SER* 2.9 46.2 + - - +
84B GLY 6.1 0.2 - - - -
85B SER* 4.9 3.5 + - - -
94B LEU* 3.9 7.0 + - - +
95B LEU* 1.3 73.9 - - - +
97B ILE* 1.4 63.9 + - - +
98B ASN* 4.1 15.9 - - - +
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER 3.7 1.9 - - - +
36B THR* 3.3 2.6 - - - -
37B VAL* 2.8 45.5 + - + +
39B LEU* 4.6 7.6 - - + -
81B ARG* 3.4 10.8 - - + +
82B PHE* 3.4 39.7 - - + -
95B LEU* 4.6 7.9 - - + +
96B THR* 1.4 77.3 - - - +
98B ASN* 1.3 70.8 + - - +
100B VAL* 4.0 7.6 - - + -
104B ASP* 3.8 20.0 - - + +
108B TYR* 4.1 11.4 - - + +
125B LEU* 3.8 29.2 - - + -
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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
------------------------------------------------------------
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