Contacts of the helix formed by residues 125 - 130 (chain G) in PDB entry 3DUF
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 HIS 125 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300F PHE* 3.9 6.5 - - - +
302F GLN* 4.9 7.6 - - + -
120G LEU* 3.2 32.7 + - + +
121G PHE* 5.0 2.2 - - - +
123G ARG* 5.5 0.9 - - + -
124G GLY* 1.3 76.6 - - - +
126G PHE* 1.3 87.4 + + - +
127G HIS* 3.1 41.1 + - + +
128G GLY* 2.9 17.2 + - - -
129G ASN* 4.1 2.4 + - - +
335G THR* 3.6 19.4 - - + +
336G PRO 3.1 24.6 + - - -
337G LYS* 4.9 2.9 - - - -
338G GLN* 3.1 23.6 + - + +
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Residues in contact with PHE 126 (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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300F PHE* 3.2 37.4 - - + -
125G HIS* 1.3 83.0 + + - +
127G HIS* 1.3 68.3 + - + +
129G ASN* 3.0 17.0 + - - +
130G GLN* 3.2 39.3 + - - -
337G LYS 6.0 0.2 - - - -
338G GLN* 2.7 44.3 + - + -
342G ASP* 3.9 29.6 - - + -
343G LEU* 4.2 9.0 - - + -
346G ILE* 4.4 17.3 - - + -
102H TYR 5.0 0.7 - - - +
105H GLY* 4.8 6.3 - - - -
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Residues in contact with HIS 127 (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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116G TYR* 3.1 31.1 + + - -
117G GLN* 3.0 33.1 + - + +
120G LEU* 3.6 22.2 - - + -
125G HIS* 3.0 26.1 + - + +
126G PHE* 1.3 87.3 - - + +
128G GLY* 1.3 58.1 + - - +
130G GLN* 3.1 28.0 + - + +
335G THR* 4.2 10.8 - - + -
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Residues in contact with GLY 128 (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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113G LEU* 4.2 12.1 - - - +
117G GLN* 3.3 39.5 - - - +
120G LEU* 3.6 16.7 - - - +
121G PHE* 4.2 4.5 - - - +
125G HIS 2.9 10.5 + - - -
127G HIS* 1.3 78.3 - - - +
129G ASN* 1.3 63.2 + - - +
130G GLN 3.2 1.6 + - - -
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Residues in contact with ASN 129 (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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300F PHE* 4.3 15.1 - - + -
121G PHE* 3.4 31.7 - - - +
125G HIS 4.1 1.1 + - - +
126G PHE 3.0 11.3 + - - +
128G GLY* 1.3 79.5 - - - +
130G GLN* 1.3 57.0 + - - +
131G ILE* 2.8 27.4 + - - +
139G PRO* 3.5 27.0 - - + +
140G PRO* 5.0 0.8 + - - +
103H ARG* 3.0 36.3 + - - +
104H THR* 3.5 14.3 - - - +
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Residues in contact with GLN 130 (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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113G LEU* 5.4 0.2 - - - -
117G GLN* 3.0 18.8 + - - +
126G PHE* 3.2 37.5 + - - -
127G HIS* 3.1 37.4 + - + +
128G GLY 3.2 3.6 - - - -
129G ASN* 1.3 74.8 - - - +
131G ILE* 1.3 67.0 + - - +
132G PRO* 3.2 4.2 - - - +
346G ILE* 5.3 1.0 - - - +
104H THR 3.9 7.0 - - - +
105H GLY* 2.9 33.5 + - - +
107H ARG* 4.9 4.5 - - + +
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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