Contacts of the strand formed by residues 77 - 82 (chain I) in PDB entry 4DKE
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 77 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I SER* 4.4 3.8 - - - -
22I CYS 3.2 22.9 - - - +
23I ALA* 4.1 12.1 - - + +
29I PHE* 4.1 4.3 - - - -
71I ALA* 3.3 5.7 - - - +
72I ASP 2.9 29.4 + - - -
75I LYS* 2.9 26.2 + - - +
76I ASN* 1.3 75.0 + - - +
78I ALA* 1.3 68.2 - - - +
79I TYR* 3.6 34.3 - - + +
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Residues in contact with ALA 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I SER* 3.3 4.3 - - - -
22I CYS* 2.7 53.1 + - + +
29I PHE* 4.3 8.3 - - + -
34I ILE* 4.1 24.7 - - + -
36I TRP* 4.4 7.6 - - - +
51I ILE* 5.7 1.8 - - + -
69I ILE* 5.8 0.7 - - + -
70I SER 3.4 9.6 - - - +
71I ALA* 4.2 6.1 - - + +
77I THR* 1.3 73.4 - - - +
79I TYR* 1.3 67.0 + - - +
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Residues in contact with TYR 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I ARG* 3.4 43.7 - - - +
20I LEU 3.3 7.2 - - - +
21I SER* 3.4 26.5 - - - -
36I TRP* 3.3 13.8 + - - -
68I THR 4.5 0.2 - - - -
69I ILE* 3.4 3.1 - - - +
70I SER* 2.8 54.9 + - - +
71I ALA* 4.5 1.6 - - - -
72I ASP* 4.0 16.4 - - + +
75I LYS* 4.0 21.5 + - - +
77I THR* 3.6 38.1 - - + +
78I ALA* 1.3 77.4 - - - +
80I LEU* 1.3 60.2 + - - +
81I GLN 4.1 1.3 - - - +
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Residues in contact with LEU 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I ARG* 3.5 2.3 - - - -
20I LEU* 3.0 39.4 + - + +
36I TRP* 3.5 40.9 - - + +
48I VAL* 5.0 1.6 - - + -
49I ALA* 4.4 14.1 - - + -
67I PHE* 4.0 27.8 - - + -
68I THR 3.6 14.4 - - - +
69I ILE* 4.5 0.9 - - + -
79I TYR* 1.3 74.2 - - - +
81I GLN* 1.3 60.4 + - - +
82I MET* 3.7 36.2 + - + +
90I TYR* 4.1 17.7 - - + -
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Residues in contact with GLN 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I SER* 4.0 11.1 + - - -
18I LEU 3.9 4.0 - - - -
19I ARG* 3.5 36.2 + - - +
66I ARG 3.8 0.2 - - - +
67I PHE* 3.1 6.9 - - - +
68I THR* 2.8 49.4 + - - +
70I SER* 6.0 0.9 - - - +
79I TYR* 4.1 2.0 - - + +
80I LEU* 1.3 73.5 - - - +
82I MET* 1.3 95.2 + - + +
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Residues in contact with MET 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I GLY 4.2 0.5 - - - +
17I SER* 3.1 7.6 + - - -
18I LEU* 2.8 52.8 + - + +
20I LEU* 3.7 28.7 - - + -
66I ARG 3.8 1.8 - - - -
67I PHE* 3.6 36.6 - - + -
80I LEU* 3.7 25.1 - - + +
81I GLN* 1.3 80.7 - - - +
82I ASN* 1.3 76.4 + - - +
90I TYR* 3.8 11.9 - - - -
109I VAL* 3.9 26.0 - - + -
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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