Contacts of the strand formed by residues 78 - 83 (chain D) in PDB entry 3KC3
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 VAL 78 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D VAL* 3.7 1.7 - - - -
70D LEU* 2.9 37.7 + - + +
71D GLY 4.6 8.0 + - - +
77D LYS* 1.3 81.6 - - - +
79D LEU* 1.3 62.1 + - - +
91D ALA* 3.6 26.9 - - + -
92D LEU 3.1 12.3 - - - +
93D LYS* 3.7 20.2 - - + -
138D MET* 3.8 7.4 - - + -
500D MK2 3.5 48.0 - - + +
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Residues in contact with LEU 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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65D VAL* 5.1 13.2 - - + -
66D THR 4.8 4.9 - - - +
67D SER* 3.3 31.4 - - - +
68D GLN 3.5 3.6 - - - +
69D VAL* 3.8 22.9 - - + -
70D LEU* 4.4 1.9 - - - +
77D LYS* 4.2 31.0 - - + +
78D VAL* 1.3 78.2 - - - +
80D GLN* 1.3 62.4 + - - +
81D ILE* 4.6 3.6 - - + -
91D ALA* 3.4 6.6 - - - +
92D LEU* 2.9 41.8 + - + +
94D MET* 5.2 10.3 - - + -
45E GLN* 5.3 6.5 - - - +
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Residues in contact with GLN 80 (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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66D THR* 2.6 35.9 + - - +
68D GLN* 2.7 59.5 + - + +
70D LEU* 3.3 29.9 - - + +
79D LEU* 1.3 74.8 - - - +
81D ILE* 1.3 62.6 + - - +
82D PHE* 3.2 17.8 - - + -
89D LYS* 3.3 25.0 - - + +
90D PHE 3.7 8.7 - - - +
140D CYS* 5.1 1.8 - - - -
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Residues in contact with ILE 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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59D ILE* 4.9 3.6 - - + -
63D TYR* 3.2 40.6 - - + -
64D LYS 3.4 10.1 - - - +
65D VAL* 3.7 28.7 - - + -
79D LEU* 4.6 1.6 - - + -
80D GLN* 1.3 80.8 - - - +
82D PHE* 1.3 63.5 + - - +
89D LYS* 3.4 5.4 - - - +
90D PHE* 2.7 54.0 + - + +
91D ALA 4.1 1.1 - - - +
92D LEU* 3.7 27.1 - - + +
137D VAL* 4.0 20.0 - - + -
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Residues in contact with PHE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D TYR* 3.3 4.5 - - - -
64D LYS* 2.7 51.7 + - + +
66D THR* 3.2 42.6 - - + -
68D GLN* 3.9 8.7 - - - -
80D GLN* 3.2 31.2 - - + -
81D ILE* 1.3 76.0 - - - +
83D ASN* 1.3 65.4 + - - +
87D GLN* 4.5 16.2 - - + +
88D GLU 3.2 17.7 - - - +
89D LYS* 3.8 19.3 - - + -
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Residues in contact with ASN 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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62D ASP* 4.3 5.4 + - - +
63D TYR* 3.7 28.3 + - + -
82D PHE* 1.3 74.6 - - - +
84D LYS* 1.3 59.6 + - - +
85D ARG* 2.8 33.7 + - - +
86D THR* 2.8 42.7 + - - +
87D GLN* 3.2 27.7 + - - +
88D GLU 3.2 11.0 + - - +
90D PHE* 3.7 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