Contacts of the strand formed by residues 78 - 83 (chain B) in PDB entry 3DGG
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B SER* 4.0 4.5 - - - -
22B CYS 3.4 8.1 - - - +
23B LYS* 3.4 35.1 - - + +
29B PHE* 3.5 5.3 - - - -
72B SER* 3.4 3.1 - - - -
73B ASP 3.0 30.4 + - - -
76B SER* 2.8 36.5 + - - -
77B SER* 1.3 74.3 + - - +
79B ALA* 1.3 67.8 + - - +
80B TYR* 3.6 31.0 + - + +
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Residues in contact with ALA 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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21B SER* 3.5 2.3 - - - -
22B CYS* 2.7 45.5 + - + +
29B PHE* 3.8 9.9 - - + -
34B MET* 4.0 29.4 - - + -
36B TRP* 3.8 12.0 - - - +
51B ILE* 4.4 9.6 - - + -
71B THR 3.5 8.1 - - - +
72B SER* 4.3 2.0 - - - +
78B THR* 1.3 75.1 - - - +
80B TYR* 1.3 60.6 + - - +
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Residues in contact with TYR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LYS* 3.5 32.5 - - + -
20B MET 3.3 14.4 - - - +
21B SER* 3.9 14.4 - - - -
36B TRP* 3.9 5.7 + - - -
69B THR 4.4 0.2 - - - -
70B LEU* 3.4 8.5 - - - +
71B THR* 2.8 56.7 + - - +
72B SER* 4.5 1.1 - - - -
73B ASP* 4.0 17.8 + - + +
76B SER* 3.9 11.8 + - - -
78B THR* 3.6 36.8 - - + +
79B ALA* 1.3 74.5 - - - +
81B MET* 1.3 60.3 + - - +
82B GLU 4.3 0.2 - - - -
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Residues in contact with MET 81 (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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18B VAL 3.5 1.9 - - - +
19B LYS* 3.4 3.5 - - - -
20B MET* 2.9 70.5 + - + +
36B TRP* 3.7 34.7 - - + -
48B ILE* 3.7 27.6 - - + -
68B ALA* 4.5 2.7 - - + -
69B THR 3.5 2.7 - - - +
70B LEU* 3.4 24.5 - - + -
80B TYR* 1.3 73.2 - - - +
82B GLU* 1.3 71.2 + - - +
83B LEU* 4.0 10.9 + - + -
94B TYR* 3.5 24.0 - - + -
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Residues in contact with GLU 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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17B SER* 2.5 34.1 + - - -
18B VAL* 3.3 17.2 + - - -
19B LYS* 3.8 32.1 + - + +
67B LYS 3.6 1.4 - - - +
68B ALA* 3.3 5.2 - - - +
69B THR* 2.8 54.8 + - + +
80B TYR* 5.4 0.4 - - - +
81B MET* 1.3 71.2 - - - +
83B LEU* 1.3 63.0 + - - +
84B SER* 4.9 2.8 - - - -
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Residues in contact with LEU 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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17B SER* 3.2 6.5 + - - -
18B VAL* 2.9 35.4 + - + -
20B MET* 3.3 30.5 - - + -
48B ILE* 5.5 0.7 - - + -
64B PHE* 5.3 4.3 - - + -
67B LYS* 3.4 24.9 - - + -
68B ALA* 3.9 21.8 - - + -
81B MET* 4.0 9.6 - - + -
82B GLU* 1.3 73.2 - - - +
84B SER* 1.3 60.2 + - - +
86B LEU* 3.7 18.0 - - + +
90B ASP* 5.4 0.7 - - + -
94B TYR* 3.6 33.0 - - + +
115B LEU* 4.1 12.3 - - + -
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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