Contacts of the helix formed by residues 99 - 104 (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 ASP 99 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48G ILE* 5.0 6.9 - - - +
96G GLU 3.8 11.3 - - - +
97G GLY 3.0 18.6 + - - +
98G LEU* 1.3 79.3 - - - +
100G ILE* 1.3 64.1 + - - +
101G THR* 3.0 11.8 + - - +
102G LYS* 3.1 48.3 + - - +
103G LEU* 3.6 13.3 + - - +
180G THR* 5.3 3.6 + - - -
181G LYS* 5.1 0.9 + - - -
391G ARG* 5.1 14.2 + - - -
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Residues in contact with ILE 100 (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* 4.7 17.5 - - + -
47G GLY* 4.7 18.4 - - - +
48G ILE* 5.8 5.6 - - + -
77G MET* 4.9 17.0 - - + -
98G LEU* 4.1 7.8 - - + +
99G ASP* 1.3 73.9 - - - +
101G THR* 1.3 63.1 + - - +
102G LYS 3.4 0.2 - - - -
103G LEU* 3.3 23.5 + - + +
104G LEU* 3.7 13.6 + - + +
118G PHE* 4.7 20.4 - - + -
275G PHE* 4.6 21.8 - - + -
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Residues in contact with THR 101 (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* 5.9 0.9 + - - -
99G ASP* 3.0 7.1 + - - +
100G ILE* 1.3 78.3 - - - +
102G LYS* 1.3 68.7 + - + +
103G LEU 3.2 3.5 + - - -
104G LEU* 3.3 30.9 + - + +
384G THR* 4.0 21.7 + - - +
385G SER* 4.1 23.0 + - - -
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Residues in contact with LYS 102 (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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99G ASP* 3.1 46.1 + - - +
101G THR* 1.3 85.8 - - + +
103G LEU* 1.3 60.9 + - - +
104G LEU 3.4 3.4 - - - +
180G THR* 3.7 23.9 - - - +
181G LYS* 4.2 24.1 - - + +
186G LEU* 3.7 19.2 - - - +
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Residues in contact with LEU 103 (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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98G LEU* 3.6 29.2 - - + -
99G ASP 3.7 9.0 - - - +
100G ILE* 3.5 22.7 - - + +
101G THR 3.1 1.2 - - - -
102G LYS* 1.3 79.6 - - - +
104G LEU* 1.3 65.5 + - - +
105G ASP* 3.5 5.5 + - - +
117G ARG* 3.5 19.6 - - - +
118G PHE* 3.9 35.5 + - + +
121G ILE* 3.6 27.1 - - + -
180G THR* 3.6 34.1 - - + -
186G LEU* 4.8 4.7 - - + -
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Residues in contact with LEU 104 (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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100G ILE* 3.7 11.7 - - + +
101G THR* 3.3 25.4 - - + +
102G LYS 3.4 3.7 - - - +
103G LEU* 1.3 79.4 - - - +
105G ASP* 1.3 58.5 + - - +
106G ASN* 3.5 31.2 + - - +
113G ALA* 3.9 19.1 - - + -
117G ARG* 4.2 10.6 + - - -
274G LEU* 5.6 3.1 - - + +
275G PHE* 4.6 17.3 - - + -
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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