Contacts of the helix formed by residues 106 - 111 (chain C) in PDB entry 5DST
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 ASN 106 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A TYR* 3.1 13.7 + - - -
102C SER* 2.8 26.6 - - - +
103C MET 2.9 9.8 + - - +
105C HIS* 1.3 96.4 + - - +
107C LYS* 1.3 64.3 + - - +
108C HIS* 3.1 21.5 - - + -
109C VAL* 3.0 25.8 + - + +
110C PHE* 3.6 6.0 - - + -
215C PHE* 5.4 1.8 - - + -
318C CYS* 3.2 24.0 - - - +
319C HIS* 3.2 27.0 - - - +
322C MET* 5.0 0.7 - - - +
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Residues in contact with LYS 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A TYR* 4.0 16.2 + - + +
103C MET 3.9 2.2 - - - -
104C TYR* 3.1 39.8 + - - +
105C HIS 3.8 1.4 - - - -
106C ASN* 1.3 75.6 - - - +
108C HIS* 1.3 57.3 + - - +
110C PHE 3.1 2.3 + - - +
111C LYS* 2.9 33.6 + - + +
131C LYS 4.1 15.7 - - - -
132C ALA* 3.4 30.4 - - + +
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Residues in contact with HIS 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A THR* 4.2 25.6 + - + +
382A LEU* 3.1 52.2 + - + +
383A CYS* 5.3 2.2 - - + -
105C HIS 4.9 0.2 + - - -
106C ASN* 3.1 38.3 - - + -
107C LYS* 1.3 79.1 + - - +
109C VAL* 1.3 74.0 + - + +
111C LYS* 4.2 10.6 + - - +
113C LYS* 5.4 1.6 - - - +
317C LYS 5.2 3.6 + - - -
319C HIS* 4.5 5.3 - - + +
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Residues in contact with VAL 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C ASN* 3.0 20.8 + - + +
108C HIS* 1.3 102.0 - - + +
110C PHE* 1.3 63.3 - - + +
113C LYS* 2.9 26.6 - - - +
181C ILE* 3.4 13.4 - - + +
213C LEU* 3.3 35.2 - - + -
215C PHE* 4.2 15.3 - - + -
317C LYS 4.7 11.4 - - - +
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Residues in contact with PHE 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C SER 4.4 0.2 - - - -
103C MET* 3.7 50.3 - - + -
106C ASN 3.6 14.8 - - - -
107C LYS 3.1 2.7 + - - +
109C VAL* 1.3 82.1 - - + +
111C LYS* 1.3 67.0 + - - +
112C ASP 3.1 0.9 + - - -
113C LYS* 2.8 18.7 + - - +
115C VAL* 3.9 18.8 - - + -
129C ALA* 4.5 9.4 - - + -
132C ALA* 3.7 25.1 - - + +
133C GLY 4.2 0.9 - - - -
134C ALA* 3.5 11.4 - - - +
181C ILE* 3.6 28.7 - - + -
183C ILE* 4.4 5.6 - - + -
215C PHE* 3.8 39.3 - + - -
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Residues in contact with LYS 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C LYS* 2.9 17.3 + - + +
108C HIS* 4.2 8.7 + - - +
109C VAL 3.6 1.6 - - - -
110C PHE* 1.3 75.2 - - - +
112C ASP* 1.3 93.6 + - - +
113C LYS* 3.2 10.4 + - - +
132C ALA 4.5 1.3 - - - +
133C GLY* 3.4 15.3 - - - +
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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