Contacts of the helix formed by residues 46 - 49 (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 LYS 46 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44G GLY 4.9 2.2 - - - -
45G ALA* 1.3 83.4 - - - +
47G GLY* 1.3 64.1 + - - +
48G ILE* 3.2 18.7 + - + +
49G SER* 3.6 19.9 + - - +
50G TYR* 4.3 5.0 - - - -
74G ALA* 4.1 8.3 - - - +
100G ILE* 4.7 16.2 - - + -
101G THR* 5.9 0.6 + - - -
274G LEU* 6.5 0.9 - - - -
376G THR* 4.7 1.8 - - - +
379G VAL* 3.7 29.3 - - + +
380G THR 3.7 18.4 + - - +
381G THR* 5.1 2.9 - - - +
383G ASN 3.4 21.6 + - - -
384G THR* 4.5 7.5 - - - +
385G SER 4.8 1.2 - - - +
386G PRO* 4.7 9.1 - - - +
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Residues in contact with GLY 47 (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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46G LYS* 1.3 73.1 - - - +
48G ILE* 1.3 65.4 + - - +
49G SER 3.2 1.7 + - - -
50G TYR* 3.6 13.9 + - - +
51G LEU 3.9 2.4 + - - -
74G ALA* 4.4 10.3 - - - +
77G MET* 6.0 7.0 - - - -
78G THR* 4.4 10.9 + - - -
95G ILE* 3.4 27.8 - - - +
100G ILE* 4.7 12.0 - - - +
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Residues in contact with ILE 48 (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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46G LYS* 3.2 15.4 - - + -
47G GLY* 1.3 80.0 - - - +
49G SER* 1.3 63.8 + - - +
50G TYR 3.2 0.9 - - - -
51G LEU* 3.3 16.7 + - + +
52G GLY 4.4 0.3 + - - -
95G ILE* 3.3 35.7 - - + +
96G GLU* 4.8 9.9 - - + +
98G LEU 4.5 7.9 - - - +
99G ASP* 5.0 6.5 - - - +
100G ILE* 5.8 5.6 - - + -
379G VAL* 5.7 5.4 - - + -
391G ARG* 4.3 36.1 - - + +
394G ALA* 4.2 7.7 - - + +
395G VAL* 4.0 26.3 - - + +
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Residues in contact with SER 49 (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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45G ALA* 4.6 4.9 - - - -
46G LYS* 3.7 19.1 + - - +
47G GLY 3.2 0.4 - - - -
48G ILE* 1.3 79.4 - - - +
50G TYR* 1.3 65.8 + - - +
52G GLY 4.3 0.7 + - - -
311G ALA* 5.2 1.1 - - - -
374G ILE* 3.4 37.2 - - - +
375G ASN 5.7 0.2 - - - -
376G THR* 3.5 27.1 - - - +
379G VAL* 4.9 2.3 + - - +
394G ALA* 4.0 25.2 - - - +
398G GLY* 4.0 5.0 - - - -
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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