Contacts of the helix formed by residues 79 - 84 (chain A) in PDB entry 4KYI
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 ALA 79 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.2 5.6 - - + +
69A VAL* 3.3 24.3 - - + +
70A SER 3.3 29.8 - - - +
71A GLY* 4.2 1.3 - - - +
75A GLY 2.7 22.1 + - - +
76A ALA 4.3 1.3 - - - +
78A THR* 1.3 72.7 - - - +
80A SER* 1.3 57.9 + - - +
81A ILE 3.5 0.2 - - - -
82A LEU* 3.9 5.8 - - - +
83A ALA 3.3 15.9 + - - -
236A LEU* 3.3 19.3 - - + +
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ALA 3.3 14.1 + - - -
77A MET* 2.4 28.9 + - - +
79A ALA* 1.3 76.9 - - - +
81A ILE* 1.3 59.4 + - - +
82A LEU 3.1 4.9 - - - -
83A ALA* 3.5 2.8 + - - +
84A VAL* 3.3 25.3 + - - +
126A TYR* 2.7 37.9 + - - -
218A LEU* 5.8 0.5 - - - +
236A LEU* 3.8 23.2 - - - +
261A ILE* 4.6 0.7 - - - +
265A VAL* 3.9 2.9 - - - -
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A MET* 3.2 16.4 + - + +
78A THR* 3.4 20.0 - - + +
80A SER* 1.3 82.2 + - - +
82A LEU* 1.3 58.4 + - + +
84A VAL* 3.8 9.6 - - - -
86A MET* 3.4 37.3 + - + +
91A ILE* 3.8 25.4 - - + +
94A LEU* 4.4 14.8 - - + -
95A ILE* 3.6 35.7 - - + -
122A LEU* 6.1 0.7 - - + -
125A ILE* 4.1 26.5 - - + -
126A TYR* 4.4 3.8 - - + -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.1 26.5 - - + -
40A LEU* 5.5 2.5 - - + -
53A MET* 5.7 0.2 - - + -
54A ILE* 3.9 34.3 - - + -
63A ILE* 4.3 18.4 - - + -
66A LEU* 5.9 2.0 - - + -
69A VAL* 4.5 13.0 - - + -
78A THR* 3.5 18.1 + - + +
79A ALA* 3.9 7.2 - - - +
80A SER 3.1 0.2 - - - -
81A ILE* 1.3 79.9 - - - +
83A ALA* 1.3 59.7 + - - +
84A VAL 3.1 2.0 - - - -
85A GLY* 3.1 18.9 + - - +
86A MET 5.1 1.1 - - - +
91A ILE* 3.8 23.8 - - + -
232A LEU 3.9 0.9 - - - +
234A LYS* 3.6 17.8 - - + +
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A VAL* 3.7 12.3 - - + -
79A ALA 3.3 16.3 + - - +
80A SER 3.5 5.4 + - - +
82A LEU* 1.3 78.7 - - - +
84A VAL* 1.3 59.6 + - - +
85A GLY 3.2 0.2 - - - -
218A LEU* 3.7 17.8 - - + +
233A ILE* 3.4 15.1 - - - +
234A LYS* 3.2 42.9 + - - +
236A LEU* 3.8 8.3 - - + -
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A SER 3.3 11.2 + - - +
81A ILE* 3.6 20.6 - - + +
82A LEU 3.1 1.2 - - - -
83A ALA* 1.3 77.3 - - - +
85A GLY* 1.3 59.6 + - - +
86A MET* 3.6 19.1 - - + +
125A ILE* 5.6 0.4 - - + +
126A TYR* 4.2 19.1 - - + +
129A GLN* 3.8 24.0 - - + +
130A MET* 3.6 32.8 - - + -
133A HIS* 3.0 23.0 + - - -
218A LEU* 4.8 8.3 - - + -
233A ILE* 3.6 7.0 - - + +
261A ILE* 6.4 0.4 - - + -
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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