Contacts of the helix formed by residues 74 - 84 (chain G) 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 74 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45G ALA* 3.5 26.5 - - + +
46G LYS* 4.1 18.8 - - - +
47G GLY* 4.4 4.4 - - - +
50G TYR* 3.8 9.0 - - + +
73G SER* 1.3 79.2 - - - +
75G GLY* 1.3 57.8 + - - +
76G ALA 3.1 5.9 + - - -
77G MET* 3.7 11.1 + - + +
78G THR* 3.3 21.8 + - - -
269G GLY* 5.7 0.2 - - - -
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Residues in contact with GLY 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G LEU* 3.7 18.6 - - - +
50G TYR* 3.6 21.2 + - - -
71G GLY* 3.3 7.4 - - - -
72G ALA 2.8 16.6 + - - -
74G ALA* 1.3 78.6 - - - +
76G ALA* 1.3 57.6 + - - +
77G MET 3.5 0.2 - - - -
78G THR* 4.0 2.9 - - - -
79G ALA* 3.2 27.2 + - - +
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Residues in contact with ALA 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G GLY 4.1 2.5 - - - -
72G ALA* 3.4 4.1 + - - -
73G SER 3.2 14.8 + - - +
74G ALA 3.1 0.8 - - - -
75G GLY* 1.3 77.7 - - - +
77G MET* 1.3 62.6 + - - +
79G ALA* 4.2 0.3 - - - +
80G SER* 3.3 21.3 + - - -
238G VAL* 3.9 24.2 - - + +
265G VAL* 3.6 19.2 - - + +
268G SER* 3.6 29.2 - - - +
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Residues in contact with MET 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G GLY* 6.0 6.5 - - - -
73G SER 4.3 1.3 + - - +
74G ALA* 3.7 11.2 + - + +
75G GLY 3.5 0.2 - - - -
76G ALA* 1.3 78.2 - - - +
78G THR* 1.3 62.0 + - - +
80G SER* 2.4 33.3 + - - +
81G ILE* 3.0 16.1 + - + +
94G LEU* 5.1 5.2 - - - -
95G ILE* 4.8 17.5 - - - -
98G LEU* 4.2 23.1 - - + -
100G ILE* 4.9 12.8 - - + -
118G PHE* 3.5 33.9 - - + -
122G LEU* 3.8 19.7 - - + -
125G ILE* 5.9 0.9 - - + -
265G VAL* 3.6 14.5 - - + +
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Residues in contact with THR 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G LEU* 3.7 24.2 - - + -
47G GLY* 4.4 8.8 + - - -
50G TYR* 3.4 31.1 - - + +
53G MET* 5.0 0.9 - - + -
54G ILE* 4.0 21.5 - - + -
74G ALA 3.3 15.6 + - - -
75G GLY* 4.2 0.2 - - - -
76G ALA 3.5 0.4 - - - -
77G MET* 1.3 80.5 - - - +
79G ALA* 1.3 60.8 + - - +
81G ILE* 3.4 17.5 - - + +
82G LEU* 3.4 20.0 - - + +
95G ILE* 4.4 10.2 - - + +
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Residues in contact with ALA 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G LEU* 4.1 5.3 - - + +
69G VAL* 3.4 23.0 - - + +
70G SER 3.8 24.7 - - - +
71G GLY* 4.3 1.3 - - - +
75G GLY 3.2 19.4 + - - +
76G ALA* 4.2 2.2 - - - +
77G MET 3.2 0.4 - - - -
78G THR* 1.3 78.2 - - - +
80G SER* 1.3 58.7 + - - +
82G LEU* 3.4 2.0 + - - +
83G ALA* 2.9 28.4 + - - +
236G LEU* 3.9 12.6 - - + -
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Residues in contact with SER 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76G ALA 3.3 12.7 + - - -
77G MET* 2.4 28.9 + - - +
79G ALA* 1.3 77.5 - - - +
81G ILE* 1.3 61.1 + - - +
83G ALA* 3.1 3.3 + - - +
84G VAL* 2.9 30.2 + - - +
126G TYR* 2.9 39.6 + - - -
218G LEU* 5.8 0.3 - - - +
236G LEU* 4.0 19.6 - - - +
261G ILE* 4.7 0.2 - - - -
265G VAL* 4.1 4.7 - - - -
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Residues in contact with ILE 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G ILE* 5.1 2.7 - - + -
77G MET* 3.0 21.5 + - + +
78G THR* 3.4 16.4 - - - +
80G SER* 1.3 85.3 + - - +
82G LEU* 1.3 66.0 + - + +
84G VAL* 3.3 13.9 - - - +
86G MET* 3.3 41.5 + - + +
91G ILE* 3.8 33.8 - - + +
94G LEU* 4.7 11.9 - - + -
95G ILE* 4.2 21.8 - - + -
122G LEU* 6.1 0.7 - - + -
125G ILE* 4.5 22.0 - - + -
126G TYR* 5.0 3.1 - - + -
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Residues in contact with LEU 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G LEU* 3.8 28.5 - - + -
40G LEU* 5.4 1.6 - - + -
53G MET* 5.5 0.2 - - + -
54G ILE* 4.0 31.6 - - + -
57G LEU* 6.3 0.7 - - + -
63G ILE* 4.6 22.2 - - + +
66G LEU* 6.1 0.9 - - + -
69G VAL* 4.5 11.2 - - + -
78G THR* 3.4 23.3 + - + +
79G ALA* 3.6 6.7 - - - +
80G SER 3.1 0.4 - - - -
81G ILE* 1.3 83.0 - - + +
83G ALA* 1.3 60.3 + - - +
84G VAL 3.3 0.4 + - - -
85G GLY* 3.6 8.3 + - - -
86G MET 5.3 1.6 - - - +
91G ILE* 4.0 23.1 - - + -
232G LEU 4.0 2.6 - - - +
234G LYS* 3.4 19.8 - - + +
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Residues in contact with ALA 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G VAL* 3.7 14.6 - - + +
79G ALA 2.9 17.6 + - - +
80G SER* 3.1 6.5 + - - +
82G LEU* 1.3 77.4 - - - +
84G VAL* 1.3 59.2 + - - +
85G GLY 3.2 0.9 - - - -
218G LEU* 3.9 8.5 - - + +
233G ILE* 3.5 13.3 - - - +
234G LYS* 3.1 33.7 + - - +
236G LEU* 3.7 22.9 - - + -
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Residues in contact with VAL 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G SER 2.9 11.2 + - - +
81G ILE* 3.3 26.2 - - + +
83G ALA* 1.3 77.1 - - - +
85G GLY* 1.3 55.9 + - - +
86G MET* 3.6 17.9 - - + +
125G ILE* 5.6 1.1 - - + +
126G TYR* 4.4 20.4 - - + +
129G GLN* 3.9 17.9 - - + -
130G MET* 3.6 31.6 - - + +
133G HIS* 3.2 20.3 + - - -
218G LEU* 4.2 13.5 - - + -
233G ILE* 3.5 9.8 - - - +
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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