Contacts of the strand formed by residues 78 - 83 (chain D) in PDB entry 3EYF
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D SER* 5.2 6.5 + - - -
22D CYS 3.4 8.3 - - - -
23D GLU* 4.6 11.9 - - + +
29D PHE* 3.5 8.2 - - - -
72D ARG* 3.6 0.3 - - - -
73D ASP* 2.8 39.1 + - - +
76D LYS* 3.0 30.7 - - + +
77D ASN* 1.3 78.9 - - - +
79D MET* 1.3 68.5 + - - +
80D SER* 4.6 5.0 + - - -
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Residues in contact with MET 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D SER* 3.3 6.6 + - - -
22D CYS* 3.0 43.0 + - + +
29D PHE* 3.9 15.7 - - + -
34D ILE* 4.3 18.6 - - + -
36D TRP* 2.9 46.7 - - + +
51D ILE* 3.9 20.0 - - + -
70D ILE* 3.7 10.5 - - + -
71D SER 3.1 14.8 - - - +
72D ARG* 4.1 4.0 - - + +
78D THR* 1.3 78.8 - - - +
80D SER* 1.3 92.3 + - - +
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Residues in contact with SER 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ARG* 3.4 38.5 + - - -
20D LEU 3.3 6.0 + - - -
21D SER* 3.5 13.9 + - - -
69D THR 3.7 1.4 - - - +
70D ILE* 3.4 5.2 - - - -
71D SER* 2.9 38.3 + - - +
72D ARG* 4.7 0.4 - - - +
78D THR* 4.6 5.2 + - - -
79D MET* 1.3 83.2 + - - +
81D LEU* 1.3 61.1 + - - +
82D GLN 4.2 0.2 - - - -
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU 3.8 0.3 - - - +
19D ARG* 3.2 7.2 - - - -
20D LEU* 2.8 45.5 + - + +
36D TRP* 3.6 45.5 - - + +
48D LEU* 5.6 0.7 - - + -
49D THR* 4.3 9.2 - - + -
60D TYR* 5.3 0.2 - - + -
68D PHE* 4.3 23.8 - - + -
69D THR 3.7 16.8 - - - +
70D ILE* 4.1 12.8 - - + -
80D SER* 1.3 73.8 - - - +
82D GLN* 1.3 63.0 + - - +
83D MET* 3.6 28.8 + - + +
94D TYR* 4.7 3.8 - - + -
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Residues in contact with GLN 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D SER* 4.2 6.1 + - - -
18D LEU 3.3 21.0 + - - -
19D ARG* 3.3 44.3 + - - +
67D ARG 3.2 3.5 - - - +
68D PHE* 3.1 6.2 - - - -
69D THR* 2.9 55.2 + - + +
80D SER 4.2 0.4 - - - -
81D LEU* 1.3 70.8 - - - +
83D MET* 1.3 62.4 + - - +
84D ASN* 3.2 32.1 + - - +
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Residues in contact with MET 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D GLY 4.0 0.5 - - - +
17D SER* 3.2 5.0 + - - -
18D LEU* 2.8 47.9 + - + +
20D LEU* 3.5 37.9 - - + -
68D PHE* 3.4 45.5 - - + -
81D LEU* 3.9 17.3 - - + +
82D GLN* 1.3 75.1 - - - +
84D ASN* 1.3 63.8 + - - +
86D LEU* 4.0 14.1 - - + +
94D TYR* 3.7 17.3 - - + -
121D VAL* 4.2 15.0 - - + -
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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