Contacts of the strand formed by residues 78 - 83 (chain O) in PDB entry 3HAE
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 THR 78 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O SER* 4.6 9.2 - - - -
22O CYS 3.0 31.2 - - - +
23O ALA* 3.8 10.5 - - + +
29O PHE* 4.0 5.7 - - - -
72O ARG* 3.3 3.5 - - - +
73O ASP 2.9 34.3 + - - +
76O LYS* 3.0 27.8 + - - +
77O ASN* 1.3 76.4 - - - +
79O LEU* 1.3 59.8 + - - +
80O TYR* 3.9 22.4 + - + +
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Residues in contact with LEU 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O SER* 3.6 3.3 - - - -
22O CYS* 3.0 37.2 + - + +
29O PHE* 4.2 10.1 - - + -
34O MET* 3.7 26.0 - - + -
35O GLY 3.9 18.4 - - - +
36O TRP* 3.3 35.5 - - + +
51O ILE* 3.7 17.9 - - + -
70O ILE* 3.8 9.6 - - + -
71O SER 3.4 20.9 - - - +
72O ARG* 4.1 5.2 - - + -
78O THR* 1.3 72.3 - - - +
80O TYR* 1.3 61.7 + - - +
96O CYS* 3.9 17.5 - - - -
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Residues in contact with TYR 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19O ARG* 3.5 41.5 - - + +
20O LEU 3.3 7.4 - - - +
21O SER* 3.5 27.1 - - - -
36O TRP* 3.4 10.1 + - - -
70O ILE* 3.7 2.9 - - - +
71O SER* 2.9 47.7 + - - +
72O ARG* 4.2 6.7 - - - -
73O ASP* 4.2 16.4 - - + -
76O LYS* 3.9 23.4 - - - +
78O THR* 3.9 26.4 + - + +
79O LEU* 1.3 75.4 - - - +
81O LEU* 1.3 64.3 + - - +
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Residues in contact with LEU 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18O LEU 3.6 0.2 - - - +
19O ARG* 4.5 1.6 - - - -
20O LEU* 2.8 39.4 + - + +
36O TRP* 3.1 51.1 - - + +
48O VAL* 4.5 11.9 - - + -
49O SER* 4.4 9.9 - - - +
68O PHE* 4.5 10.8 - - + -
69O THR 3.7 5.2 - - - +
70O ILE* 3.9 26.7 - - + +
80O TYR* 1.3 70.8 - - - +
82O GLN* 1.3 62.5 + - - +
83O MET* 3.5 32.0 + - + +
94O TYR* 4.6 4.5 - - + -
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Residues in contact with GLN 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O SER* 4.1 12.1 - - - -
18O LEU 3.7 14.6 + - - -
19O ARG* 3.2 44.8 + - - +
67O ARG 3.8 0.7 - - - +
68O PHE* 3.1 7.6 - - - +
69O THR* 2.8 53.1 + - - +
80O TYR 4.3 0.2 - - - -
81O LEU* 1.3 71.4 - - - +
83O MET* 1.3 61.6 + - - +
84O ASN* 3.5 31.3 + - - +
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Residues in contact with MET 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O SER* 3.2 22.2 - - - -
18O LEU* 2.8 26.1 + - + +
20O LEU* 3.5 38.1 - - + -
67O ARG 3.9 2.2 - - - -
68O PHE* 3.4 42.0 - - + -
81O LEU* 3.6 17.0 - - + +
82O GLN* 1.3 78.2 - - - +
84O ASN* 1.3 69.9 + - - +
86O LEU* 4.0 15.7 - - + +
94O TYR* 4.1 16.8 - - - -
115O VAL* 3.8 19.7 - - + -
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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