Contacts of the helix formed by residues 125 - 130 (chain C) in PDB entry 3DVA
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300B PHE* 3.9 9.0 - - - +
302B GLN* 5.3 7.6 - - + -
120C LEU* 3.0 34.8 + - + +
121C PHE* 4.7 2.3 + - - +
123C ARG* 5.5 0.9 - - + -
124C GLY* 1.3 75.7 - - - +
126C PHE* 1.3 78.5 + + - +
127C HIS* 3.1 39.8 + - + +
128C GLY* 3.0 15.1 + - - -
129C ASN* 4.1 2.1 + - - +
335C THR* 3.7 15.1 - - + +
336C PRO 2.8 27.5 + - - -
337C LYS* 4.7 2.5 - - - -
338C GLN* 3.4 32.9 + - + +
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Residues in contact with PHE 126 (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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300B PHE* 3.3 35.7 - - + -
125C HIS* 1.3 81.7 + + - +
127C HIS* 1.3 69.5 + - + +
129C ASN* 3.0 17.5 + - - +
130C GLN* 3.5 36.4 + - + +
338C GLN* 3.1 44.5 + - + -
342C ASP* 3.8 34.5 - - + -
343C LEU* 4.3 7.9 - - + -
346C ILE* 4.2 24.0 - - + -
102D TYR 4.6 1.3 - - - +
103D ARG 4.7 0.5 - - - +
105D GLY* 4.6 3.5 + - - -
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Residues in contact with HIS 127 (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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116C TYR* 2.9 30.9 + + - -
117C GLN* 2.9 43.5 + - - -
120C LEU* 3.6 22.9 - - + -
125C HIS* 3.1 25.4 + - + +
126C PHE* 1.3 82.9 - - + +
128C GLY* 1.3 58.9 + - - +
130C GLN* 2.7 38.4 + - + +
335C THR* 4.2 10.1 - - + -
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Residues in contact with GLY 128 (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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113C LEU* 4.0 13.7 - - - +
117C GLN* 3.2 40.9 - - - +
120C LEU* 3.7 15.0 - - - +
121C PHE* 4.1 4.6 - - - +
125C HIS 3.0 10.3 + - - -
127C HIS* 1.3 79.2 - - - +
129C ASN* 1.3 63.8 + - - +
130C GLN 3.7 0.3 + - - -
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Residues in contact with ASN 129 (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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126B GLU* 5.9 0.4 + - - -
300B PHE* 3.6 20.4 - - - -
121C PHE* 3.5 25.4 - - - +
125C HIS 4.1 1.0 + - - +
126C PHE 3.0 8.6 + - - +
128C GLY* 1.3 80.6 - - - +
130C GLN* 1.3 55.0 + - - +
131C ILE* 2.8 26.5 + - - +
139C PRO* 3.5 34.2 - - + +
140C PRO* 5.1 0.2 - - - +
103D ARG* 2.7 36.5 + - - +
104D THR* 3.8 14.7 - - - +
107D ARG* 4.5 0.3 - - - +
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Residues in contact with GLN 130 (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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117C GLN* 2.9 19.5 + - - -
126C PHE* 3.8 30.8 - - - +
127C HIS* 2.7 44.4 + - + +
128C GLY 3.4 0.2 - - - -
129C ASN* 1.3 72.7 - - - +
131C ILE* 1.3 66.9 + - - +
132C PRO* 3.5 1.7 - - - +
346C ILE* 5.4 1.6 - - - +
104D THR 3.6 18.2 - - - +
105D GLY* 2.9 27.1 + - - +
107D ARG* 4.4 3.6 - - + -
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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