Contacts of the strand formed by residues 200 - 205 (chain C) in PDB entry 1SA0
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 CYS 200 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C LYS 3.7 1.3 + - - +
167C LEU* 3.4 16.0 - - - +
168C GLU 3.3 18.7 + - - +
198C SER* 3.6 0.8 + - - -
199C ASP* 1.3 82.5 - - - +
201C ALA* 1.3 63.8 + - - +
202C PHE* 4.0 31.4 - - - -
255C PHE* 5.3 3.4 - - - -
256C GLN* 3.9 21.3 - - + +
259C LEU* 5.1 4.9 - - - -
260C VAL* 4.0 14.4 - - + -
265C ILE* 3.3 11.4 + - - +
266C HIS 4.0 0.2 - - - -
268C PRO* 4.3 13.0 - - - -
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Residues in contact with ALA 201 (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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168C GLU* 3.1 39.7 - - + +
170C SER* 4.8 3.1 - - - +
200C CYS* 1.3 74.6 - - - +
202C PHE* 1.3 63.8 + - - +
203C MET* 3.9 0.7 - - + -
265C ILE* 3.5 10.8 + - + -
266C HIS 3.6 0.8 + - - -
267C PHE* 3.2 33.3 - - + +
268C PRO* 2.8 25.6 - - - +
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Residues in contact with PHE 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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167C LEU* 4.3 9.0 - - + -
168C GLU 2.8 15.9 + - - +
169C PHE* 3.6 32.9 - + + -
170C SER* 3.1 22.9 + - - +
200C CYS* 4.0 18.2 - - - -
201C ALA* 1.3 72.6 - - - +
203C MET* 1.3 64.5 + - - +
204C VAL* 4.2 5.9 - - + +
238C ILE* 4.0 21.1 - - + -
255C PHE* 3.9 25.1 - + - -
259C LEU* 4.3 3.6 - - + -
268C PRO* 3.8 34.1 - - + -
270C ALA* 5.1 8.1 - - + -
378C LEU* 3.8 33.7 - - + -
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Residues in contact with MET 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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141C PHE* 3.8 21.5 - - + -
170C SER* 3.6 7.4 - - - +
172C TYR* 3.4 33.4 - - + -
201C ALA* 3.8 3.8 + - + -
202C PHE* 1.3 74.7 - - - +
204C VAL* 1.3 65.1 + - - +
267C PHE* 4.7 10.7 - - + +
268C PRO 4.4 8.6 + - - +
270C ALA* 5.6 3.5 + - - +
302C MET* 4.1 5.9 - - - +
303C VAL* 3.5 45.8 - - + +
384C ILE* 4.0 15.5 - - + -
387C ALA* 3.9 11.7 - - + -
388C TRP* 3.6 35.9 - - + -
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Residues in contact with VAL 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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169C PHE* 5.5 8.7 - - + -
170C SER 2.8 17.4 + - - +
171C ILE* 3.4 15.5 - - + +
172C TYR* 2.9 25.3 + - - +
202C PHE* 4.2 7.9 - - + +
203C MET* 1.3 79.8 - - - +
205C ASP* 1.3 64.6 + - - +
206C ASN* 3.4 2.2 + - - +
209C ILE* 3.8 18.6 - - + -
231C ILE* 4.3 24.5 - - + -
234C ILE* 5.6 2.2 - - + -
235C VAL* 6.5 0.2 - - + -
270C ALA* 6.4 0.2 - - + -
302C MET* 3.4 34.5 - - + -
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Residues in contact with ASP 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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172C TYR* 3.6 21.0 - - + +
174C ALA* 3.8 6.8 - - - +
203C MET 4.1 0.8 - - - -
204C VAL* 1.3 69.6 - - - +
206C ASN* 1.3 60.2 + - - +
207C GLU* 2.6 33.9 + - - +
208C ALA* 3.0 22.9 + - + +
209C ILE* 3.2 15.2 + - - +
302C MET 2.7 17.2 + - - +
303C VAL* 3.5 18.8 - - + +
304C LYS* 3.2 25.9 + - - +
390C ARG* 3.4 16.5 + - - -
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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