Contacts of the strand formed by residues 76 - 80 (chain B) in PDB entry 6DBT
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 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B PRO* 1.3 72.5 - - - +
77B ILE* 1.3 62.8 + - - +
91B LEU 3.5 5.5 - - - +
92B ILE* 3.7 1.6 - - - -
93B HIS 3.0 42.1 + - - +
94B GLY 4.0 0.4 - - - +
140B HIS* 3.3 38.5 - - + +
141B THR* 4.2 0.9 - - + -
142B LEU* 4.0 21.3 - - + +
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Residues in contact with ILE 77 (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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20B SER* 3.3 31.4 - - - +
21B LEU 5.4 2.9 - - - +
22B LEU* 3.6 22.2 - - + -
75B PRO* 3.6 22.7 - - + +
76B ALA* 1.3 76.2 - - - +
78B ALA* 1.3 65.9 + - - +
79B HIS* 4.6 0.9 - - + +
90B TYR* 3.5 31.0 - - + -
91B LEU 3.6 3.6 - - - -
92B ILE* 4.3 15.7 - - + -
142B LEU* 4.2 9.4 + - - +
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Residues in contact with ALA 78 (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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77B ILE* 1.3 78.4 - - - +
79B HIS* 1.3 59.8 + - - +
80B PHE 3.0 5.4 + - - -
90B TYR* 3.5 1.5 - - - -
91B LEU* 2.8 40.0 + - + +
142B LEU* 3.6 45.8 - - + +
143B SER* 4.3 1.3 - - - +
144B VAL* 4.2 14.1 - - + -
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Residues in contact with HIS 79 (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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23B ASP 4.5 3.5 + - - -
77B ILE* 4.3 2.0 - - - +
78B ALA* 1.3 67.6 - - - +
80B PHE* 1.3 65.9 + - - +
81B GLU* 3.0 40.8 + - + +
82B ALA 4.3 4.0 - - - -
88B GLU* 4.6 18.6 + - - -
89B CYS 4.0 4.5 - - - -
90B TYR* 3.0 44.8 + + + -
144B VAL* 3.6 13.5 - - - +
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Residues in contact with PHE 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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78B ALA 3.0 5.9 + - - -
79B HIS* 1.3 70.2 + - - +
81B GLU* 1.3 72.6 + - - +
82B ALA 3.7 0.3 + - - -
83B GLN* 3.3 42.8 - - + -
84B ASP 5.0 4.5 - - - -
85B GLY 5.6 1.3 - - - -
86B LYS 4.6 9.9 - - - -
87B PRO* 6.0 0.7 - - + -
88B GLU* 6.0 0.4 - - - -
89B CYS* 2.9 66.5 + - + +
90B TYR 4.4 0.4 - - - +
91B LEU* 4.4 19.3 - - + -
108B MET* 5.2 6.1 - - - -
144B VAL* 4.1 18.6 - - + -
151B THR* 4.7 3.8 - - + -
187B LEU* 3.5 34.8 - - + -
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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