Contacts of the helix formed by residues 104 - 109 (chain A) in PDB entry 4HKC
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 PHE 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A THR* 3.8 28.3 - - + +
31A GLU* 3.8 45.1 - - + -
33A GLY* 4.0 15.7 - - - +
100A LEU* 2.9 32.2 + - + +
102A GLU 3.6 0.4 - - - -
103A LYS* 1.4 128.4 - - + +
105A LEU* 1.3 64.1 - - + +
106A ILE 3.7 1.3 - - - -
107A PRO* 3.7 1.8 - - - -
108A ASN* 2.8 37.1 + - - +
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Residues in contact with LEU 105 (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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30A THR* 3.5 23.6 - - + -
36A LEU* 3.9 18.4 - - + -
44A LEU* 3.7 21.3 - - + -
97A VAL* 5.2 0.9 - - + +
100A LEU* 3.1 16.6 + - + +
101A LEU* 3.7 33.7 - - + +
104A PHE* 1.3 80.5 - - + +
106A ILE* 1.3 63.1 + - - +
108A ASN* 3.9 1.3 - - - +
109A ALA* 3.1 25.1 + - - +
118A TYR* 3.7 43.9 - - + +
121A MET* 5.1 3.1 - - + -
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Residues in contact with ILE 106 (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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101A LEU* 2.9 31.7 + - + +
102A GLU* 3.7 23.6 - - - +
105A LEU* 1.3 70.9 - - - +
107A PRO* 1.4 65.5 - - + +
109A ALA* 3.3 20.3 + - - +
115A LYS* 5.2 5.8 - - + +
118A TYR* 3.8 27.4 - - + +
119A LEU* 4.1 23.6 - - + +
122A LYS* 3.8 21.3 - - + +
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Residues in contact with PRO 107 (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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101A LEU 3.5 4.3 - - - +
102A GLU* 3.2 26.7 - - - +
103A LYS 3.9 12.6 - - - +
104A PHE 3.6 9.4 - - - +
106A ILE* 1.4 93.8 - - + +
108A ASN* 1.3 62.2 + - - +
109A ALA 3.6 2.6 + - - +
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Residues in contact with ASN 108 (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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33A GLY 2.8 27.8 + - - +
34A ALA* 4.7 0.4 - - - -
35A GLU* 3.2 33.6 + - + +
103A LYS 4.6 2.6 + - - -
104A PHE* 2.8 35.6 + - - +
105A LEU* 3.9 2.7 - - - +
107A PRO* 1.3 81.1 - - - +
109A ALA* 1.4 60.3 + - - +
110A SER* 3.0 12.4 + - - -
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Residues in contact with ALA 109 (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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35A GLU* 3.7 7.4 - - - -
105A LEU 3.1 18.0 + - - +
106A ILE* 3.3 13.4 + - - +
107A PRO 3.3 3.0 - - - +
108A ASN* 1.4 72.5 - - - +
110A SER* 1.3 61.6 + - - +
111A GLN 3.4 1.7 + - - -
114A SER* 3.4 17.3 - - - +
115A LYS* 3.8 34.2 - - + +
118A TYR* 4.0 11.0 - - + -
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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