Contacts of the strand formed by residues 66 - 71 (chain B) in PDB entry 5E0T
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 LEU 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B PHE* 3.6 36.1 - - + +
28B TRP 3.5 0.7 - - - +
29B ASP* 3.6 3.5 - - - +
30B ILE* 2.9 41.6 + - + +
64B ARG 3.4 11.6 + - - +
65B ASN* 1.3 76.3 - - - +
67B ALA* 1.3 60.5 + - - +
68B MET* 4.0 17.5 - - + -
92B ALA* 4.2 16.4 - - + -
93B GLU 3.9 10.8 - - - +
94B ASP* 3.1 31.2 - - - +
95B ASN* 4.9 0.9 - - - +
96B ALA* 4.5 10.8 - - + +
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Residues in contact with ALA 67 (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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27B CYS* 3.5 21.8 - - - -
28B TRP 3.5 4.7 - - - -
29B ASP* 3.9 7.4 - - - +
66B LEU* 1.3 75.6 - - - +
68B MET* 1.3 61.9 + - - +
69B GLY 3.7 1.9 + - - -
123B VAL* 5.9 1.8 - - + -
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Residues in contact with MET 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PHE* 4.7 0.7 - - + -
27B CYS* 3.2 3.0 - - - -
28B TRP* 2.7 51.1 + - + +
30B ILE* 3.4 31.0 - - + -
66B LEU* 4.4 15.7 - - + -
67B ALA* 1.3 71.6 - - - +
69B GLY* 1.3 63.0 + - - +
70B VAL* 3.6 6.8 + - + +
90B LEU* 6.2 1.1 - - + -
92B ALA* 4.2 14.8 - - - -
96B ALA* 4.7 4.3 - - + -
99B LEU* 3.8 42.0 - - + -
118B LEU* 4.0 34.1 - - + -
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Residues in contact with GLY 69 (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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26B ALA 3.8 0.4 - - - -
27B CYS* 4.4 4.2 - - - -
67B ALA 3.7 4.6 + - - -
68B MET* 1.3 70.8 - - - +
70B VAL* 1.3 57.6 + - - -
118B LEU* 3.2 17.8 - - - +
119B MET* 3.1 39.8 + - - -
121B LEU* 3.7 23.6 - - - -
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLU* 3.2 6.9 - - - +
26B ALA 2.9 28.6 + - - +
28B TRP* 3.5 38.1 - - + +
68B MET* 3.7 10.5 - - + +
69B GLY* 1.3 81.9 - - - +
71B ASN* 1.3 77.7 + - - +
72B LEU* 3.4 5.7 + - + +
75B MET* 3.9 22.7 - - + -
99B LEU* 5.3 0.4 - - + -
116B MET* 4.1 12.8 - - + -
117B LYS 5.7 0.4 - - - -
118B LEU* 3.7 18.4 - - + +
119B MET* 4.2 4.9 - - - +
121B LEU* 3.8 2.6 - - - +
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Residues in contact with ASN 71 (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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24B ASN* 3.8 7.0 - - - +
25B GLU* 4.8 2.0 - - - +
70B VAL* 1.3 77.5 - - - +
72B LEU* 1.3 57.3 + - - +
73B THR* 2.9 25.0 + - - -
74B SER* 2.9 29.2 + - - +
75B MET 3.0 22.2 + - - -
116B MET* 4.4 1.7 - - - +
117B LYS 5.3 7.2 + - - +
119B MET* 3.8 31.9 - - + +
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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