Contacts of the helix formed by residues 201 - 205 (chain C) in PDB entry 1DGH
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 SER 201 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127C ARG* 3.3 9.9 + - - -
197C SER 3.4 11.7 + - - -
198C PHE 2.5 22.5 + - - -
200C PHE* 1.3 82.8 - - - +
202C ASP* 1.3 66.6 + - - +
203C ARG 3.4 4.3 + - - -
204C GLY 3.1 9.9 + - - -
446C PHE* 4.4 7.9 - - - -
451C LEU* 5.1 7.9 - - - -
455C GLN* 5.6 2.5 - - - -
459C LEU* 4.4 10.3 - - - +
462C ASN* 4.2 3.4 + - - +
3001C NDP 3.0 28.9 + - - -
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Residues in contact with ASP 202 (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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127C ARG* 5.5 0.2 + - - -
201C SER* 1.3 78.7 - - - +
203C ARG* 1.3 61.0 + - + +
204C GLY 3.1 4.2 + - - -
205C ILE* 3.6 6.4 + - - +
244C ASN* 3.2 34.5 - - + +
245C LEU 4.7 3.3 - - - +
455C GLN* 3.9 18.8 + - - +
458C ARG* 2.6 51.9 + - - +
462C ASN* 5.2 1.8 + - - +
3001C NDP 5.1 2.9 - - - +
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Residues in contact with ARG 203 (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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149C ASN* 4.1 9.5 - - - +
198C PHE 4.6 2.7 - - - +
201C SER* 3.2 3.7 + - - +
202C ASP* 1.3 74.6 - - + +
204C GLY* 1.3 63.0 + - - +
205C ILE* 3.1 3.0 + - - -
206C PRO* 3.7 15.9 - - + +
213C ASN* 4.1 6.1 - - - +
215C TYR* 4.8 2.6 + - - -
242C ILE* 3.3 42.1 - - + +
244C ASN* 3.3 22.6 - - - +
3001C NDP 3.1 99.9 + - + +
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Residues in contact with GLY 204 (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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126C VAL 4.0 0.7 - - - +
127C ARG* 3.5 4.6 - - - -
128C ASP 3.3 32.6 + - - +
198C PHE 4.2 1.7 + - - -
199C LEU* 3.0 33.4 + - - -
201C SER 3.1 6.2 + - - -
202C ASP 3.0 4.2 - - - -
203C ARG* 1.3 78.1 - - - +
205C ILE* 1.3 64.1 + - - +
206C PRO* 3.8 2.7 - - - +
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Residues in contact with ILE 205 (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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125C THR 4.0 17.3 - - - -
126C VAL* 4.9 0.4 - - - -
127C ARG* 3.7 45.1 - - + +
130C ARG* 4.0 8.5 - - - +
202C ASP 3.6 5.7 + - - +
203C ARG 3.1 0.6 - - - -
204C GLY* 1.3 85.3 - - - +
206C PRO* 1.3 63.9 - - - +
244C ASN* 3.6 4.0 - - - +
245C LEU* 2.9 44.5 + - + +
247C VAL* 4.6 10.8 - - + -
250C ALA* 3.7 34.8 - - + -
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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