Contacts of the helix formed by residues 205 - 208 (chain B) in PDB entry 1SID
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 ASP 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B GLY 4.8 0.9 - - - +
177B LEU* 2.5 40.0 - - - +
178B VAL* 4.1 10.5 - - + -
193B ILE* 3.4 23.2 - - + +
197B THR* 5.4 3.1 - - - +
200B ASP 4.8 1.0 - - - +
201B MET* 3.8 13.4 - - + -
202B VAL* 3.1 34.4 + - - +
204B LYS* 1.3 70.6 - - - +
206B GLN* 1.3 54.1 + - - +
207B VAL 2.5 5.4 + - - -
209B ASN* 2.8 32.2 + - - +
212B SER* 3.0 14.9 + - - +
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Residues in contact with GLN 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLN* 3.4 27.8 + - - +
73A TYR* 2.6 30.2 + - - +
75A TRP* 3.6 10.8 - - + -
300A ARG* 2.7 33.2 + - - +
177B LEU* 4.6 0.3 - - - +
178B VAL* 2.8 25.8 + - + +
179B THR 2.7 26.1 + - - +
180B ASP* 3.6 10.5 + - - +
181B ALA* 3.3 20.3 - - + +
202B VAL 3.5 3.3 + - - +
203B ASN* 2.8 18.1 + - - +
205B ASP* 1.3 78.1 - - - +
207B VAL* 1.3 51.2 + - - +
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Residues in contact with VAL 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASN* 3.0 22.0 - - - +
55A PRO* 4.6 10.1 - - + -
73A TYR* 3.5 52.7 - - + +
74A GLY* 3.9 14.8 - - - -
300A ARG* 4.1 7.6 - - - +
302A LEU* 5.5 0.4 - - - +
303A PRO* 3.4 9.8 - - + +
177B LEU* 2.6 28.3 - - - +
204B LYS* 2.7 16.4 + - + +
205B ASP 2.5 5.3 + - - -
206B GLN* 1.3 82.0 - - + +
208B LEU* 1.3 71.8 + - - +
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Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A PHE* 3.2 53.1 - - + -
54A ASN* 3.2 24.0 - - - +
130A VAL* 4.7 11.0 - - + -
303A PRO* 4.0 18.8 - - + -
175B GLN* 3.4 21.8 - - - +
177B LEU* 3.0 5.4 - - + -
204B LYS* 2.9 10.7 + - - +
207B VAL* 1.3 82.0 - - - +
209B ASN* 1.3 58.7 + - - +
210B PRO* 2.8 26.7 - - + +
213B LYS* 5.4 2.5 - - - +
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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