Contacts of the strand formed by residues 80 - 84 (chain B) in PDB entry 4DQ0
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 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B SER* 4.0 9.2 - - - +
46B LEU* 3.8 22.0 - - + +
49B ALA* 3.9 13.5 - - + -
55B VAL* 3.5 37.0 - - + +
57B ALA* 4.0 15.9 - - + -
68B VAL* 3.8 27.4 - - + -
72B LYS* 2.8 40.7 + - + +
77B LEU* 3.1 20.8 + - + +
78B ASP 3.2 0.8 - - - -
79B ASN* 1.3 79.1 - - - +
81B HIS* 1.3 66.1 + - - +
82B THR* 4.8 3.6 - - + -
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Residues in contact with HIS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASP* 3.6 26.9 + - - -
55B VAL 2.9 12.1 + - - -
56B ASP* 3.4 20.5 + - - +
57B ALA* 2.7 28.2 + - - +
58B TRP* 4.7 1.4 - - - -
72B LYS* 4.5 10.5 + - - +
78B ASP 3.6 23.8 + - - -
79B ASN 3.8 4.1 + - - -
80B LEU* 1.3 77.8 + - - +
82B THR* 1.3 64.6 + - - +
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Residues in contact with THR 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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57B ALA* 3.2 14.1 - - + +
58B TRP* 4.5 0.7 - - - -
65B ILE* 3.8 14.8 - - + -
68B VAL* 3.7 33.4 - - + -
69B GLU* 2.3 44.7 + - + +
72B LYS* 5.7 1.1 - - + -
80B LEU* 4.8 4.7 - - + -
81B HIS* 1.3 80.3 - - - +
83B ARG* 1.3 64.6 + - - +
111D LYS* 3.6 15.5 + - - -
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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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57B ALA 3.0 5.5 + - - +
58B TRP* 3.3 56.7 - - + +
59B ASP 3.0 24.6 + - - +
65B ILE* 3.9 4.5 - - - +
82B THR* 1.3 78.2 - - - +
84B VAL* 1.3 66.9 + - - +
85B VAL* 3.4 19.3 + - + +
90B LEU* 4.1 11.3 - - - +
91B THR 5.2 2.8 + - - -
92B PHE* 5.0 2.8 - - - +
88C ASN 4.1 6.3 + - - -
89C ASN* 3.7 28.9 + - - +
111D LYS* 5.1 3.8 - - - +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASP 3.0 3.6 - - - +
60B LYS* 3.7 21.5 - - - +
62B ALA* 3.8 26.2 - - + +
65B ILE* 3.7 30.1 - - + -
83B ARG* 1.3 74.9 + - - +
85B VAL* 1.3 66.6 + - - +
86C ASP* 6.0 1.1 - - - +
89C ASN* 3.3 14.1 - - - +
110D ALA* 6.4 0.2 - - + -
111D LYS* 4.1 18.8 - - + +
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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