Contacts of the helix formed by residues 106 - 111 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303E TYR* 3.1 13.5 + - - -
101G ASN 4.1 2.4 - - - +
102G SER 2.9 24.6 - - - +
103G MET 2.8 8.7 + - - -
105G HIS* 1.3 96.8 + - - +
107G LYS* 1.3 65.3 + - - +
108G HIS* 3.0 20.7 - - + -
109G VAL* 2.9 26.5 + - + +
110G PHE* 3.5 7.4 - - + -
215G PHE* 5.5 1.3 - - + -
317G LYS 5.5 0.2 - - - -
318G CYS* 3.3 22.7 - - - +
319G HIS* 3.3 26.3 - - - +
322G MET* 5.0 0.7 - - - +
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Residues in contact with LYS 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345E TYR* 3.8 19.5 + - + +
103G MET 3.2 2.8 + - - -
104G TYR* 3.2 37.6 + - - +
105G HIS 3.8 1.4 - - - -
106G ASN* 1.3 76.8 - - - +
108G HIS* 1.3 52.8 + - - +
110G PHE* 2.9 3.6 + - - +
111G LYS* 2.7 38.6 + - + +
131G LYS 4.1 17.0 - - - -
132G ALA* 3.4 28.6 - - + +
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Residues in contact with HIS 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347E THR* 4.1 27.3 + - + +
382E LEU* 3.1 52.7 + - + +
383E CYS* 5.4 2.0 - - + -
105G HIS 4.6 0.6 + - - -
106G ASN* 3.0 38.0 - - + -
107G LYS* 1.3 78.4 - - - +
109G VAL* 1.3 75.0 + - + +
111G LYS* 4.3 10.0 + - - +
113G LYS* 5.5 1.2 - - - +
317G LYS 5.5 3.2 + - - -
319G HIS* 4.6 5.9 - - + +
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Residues in contact with VAL 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G ASN* 2.9 20.3 + - + +
108G HIS* 1.3 105.1 - - + +
110G PHE* 1.3 61.7 + - + +
113G LYS* 3.0 26.4 - - - +
181G ILE* 3.4 13.7 - - + +
213G LEU* 3.3 35.0 - - + -
215G PHE* 4.3 15.3 - - + -
317G LYS* 5.2 10.3 - - + +
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Residues in contact with PHE 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G SER 4.3 0.4 - - - -
103G MET* 3.6 44.0 - - + -
106G ASN 3.5 14.6 - - - -
107G LYS 2.9 2.3 + - - +
109G VAL* 1.3 81.4 - - + +
111G LYS* 1.3 68.1 + - - +
112G ASP 3.1 1.0 + - - -
113G LYS* 2.9 17.9 + - - +
115G VAL* 3.8 19.3 - - + -
129G ALA* 4.5 10.1 - - + -
132G ALA* 3.6 33.2 - - + +
133G GLY 3.5 5.2 - - - +
134G ALA* 3.5 7.0 - - + +
181G ILE* 3.6 30.3 - - + -
183G ILE* 4.3 4.3 - - + -
215G PHE* 3.8 36.8 - + - -
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Residues in contact with LYS 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G LYS* 2.7 21.4 + - + +
108G HIS* 4.3 8.9 - - - +
109G VAL 3.6 1.6 - - - -
110G PHE* 1.3 71.3 - - - +
112G ASP* 1.3 95.9 + - - +
113G LYS* 3.2 11.3 + - - +
132G ALA 4.1 1.1 + - - +
133G GLY* 3.3 16.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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