Contacts of the helix formed by residues 201 - 205 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ARG* 3.2 9.2 + - - -
197A SER 3.5 12.2 + - - -
198A PHE 2.7 21.3 + - - -
200A PHE* 1.3 82.4 - - - +
202A ASP* 1.3 65.6 + - - +
203A ARG 3.3 4.3 + - - -
204A GLY 2.9 12.1 + - - -
446A PHE* 4.4 7.4 - - - -
451A LEU* 5.1 6.7 - - - -
455A GLN* 5.7 1.3 - - - -
459A LEU* 4.2 12.1 - - - +
462A ASN* 4.3 3.7 + - - +
3000A NDP 2.9 29.4 + - - -
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Residues in contact with ASP 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A SER* 1.3 75.3 - - - +
203A ARG* 1.3 58.4 + - + +
204A GLY 3.1 3.7 + - - -
205A ILE* 3.7 7.1 + - - +
244A ASN* 3.2 37.3 - - + +
245A LEU 4.8 3.3 - - - +
455A GLN* 3.7 21.9 + - - +
458A ARG* 2.6 54.3 + - - +
462A ASN* 5.1 3.4 + - - +
3000A NDP 4.7 2.9 + - - +
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Residues in contact with ARG 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ASN* 4.0 10.0 - - - +
198A PHE 4.5 4.3 - - - +
201A SER* 3.0 4.1 + - - +
202A ASP* 1.3 74.2 - - + +
204A GLY* 1.3 62.5 + - - +
205A ILE 3.1 3.0 + - - -
206A PRO* 3.9 14.3 - - + +
213A ASN* 3.7 12.9 - - - +
215A TYR* 4.6 3.0 + - - -
242A ILE* 3.6 33.1 - - - +
244A ASN* 3.6 23.1 - - - +
3000A NDP 3.0 105.3 + - + +
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Residues in contact with GLY 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A VAL 3.9 1.0 - - - +
127A ARG* 3.7 5.3 - - - -
128A ASP 3.2 33.9 + - - +
198A PHE 4.2 1.5 + - - -
199A LEU* 3.1 30.9 + - - -
201A SER 2.9 11.2 + - - -
202A ASP 3.1 0.2 - - - -
203A ARG* 1.3 78.5 - - - +
205A ILE* 1.3 64.2 + - - +
206A PRO* 3.7 3.4 - - - +
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Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A THR* 4.1 19.1 - - - -
126A VAL* 4.5 0.9 - - - -
127A ARG* 3.8 44.4 - - + +
130A ARG* 4.1 6.5 - - - +
202A ASP 3.7 7.4 + - - +
203A ARG 3.1 0.2 - - - -
204A GLY* 1.3 85.7 - - - +
206A PRO* 1.3 62.4 - - - +
244A ASN* 3.5 4.2 - - - +
245A LEU* 2.8 41.5 + - + +
247A VAL* 4.6 11.4 - - + -
250A ALA* 3.8 34.5 - - + -
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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