Contacts of the strand formed by residues 198 - 204 (chain A) in PDB entry 5ODS
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 ALA 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ILE* 5.7 0.7 - - - -
168A THR* 5.4 0.9 - - - -
181A MET* 4.9 1.6 - - - -
196A GLY 3.8 0.2 - - - -
197A HIS* 1.3 79.8 - - - +
199A ALA* 1.3 59.9 + - - +
218A PHE* 3.2 2.9 - - - +
219A ALA 2.7 35.6 + - - +
261A PRO* 4.0 16.2 - - + -
262A VAL 4.1 2.7 - - - +
263A ALA* 3.9 37.0 - - - +
264A MET* 3.5 7.8 - - + +
275A LEU* 4.4 2.2 - - + -
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Residues in contact with ALA 199 (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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157A ARG* 3.1 25.3 + - - -
166A LEU* 3.5 29.2 - - + -
168A THR* 5.2 2.3 + - - +
181A MET* 3.9 6.7 - - - -
198A ALA* 1.3 77.5 - - - +
200A SER* 1.3 64.1 + - - +
216A PHE* 3.8 4.0 - - + -
217A CYS 3.2 12.1 - - - +
218A PHE* 3.5 13.2 - - + -
264A MET* 3.8 10.0 + - - +
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Residues in contact with SER 200 (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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157A ARG* 2.9 30.6 + - - +
166A LEU* 5.2 0.2 - - - +
199A ALA* 1.3 78.4 - - - +
201A PHE* 1.3 73.5 + - - +
216A PHE* 3.8 3.0 - - - -
217A CYS* 2.8 35.0 + - - +
264A MET* 3.8 15.3 - - - -
266A ILE* 3.5 27.9 + - - +
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Residues in contact with PHE 201 (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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157A ARG* 3.9 13.8 + - + +
158A THR* 3.5 33.7 - - - +
159A ASP* 3.8 27.1 - - + -
164A TRP* 3.9 25.6 - + + -
166A LEU* 3.9 22.2 - - + -
183A LEU* 3.7 24.9 - - + -
200A SER* 1.3 86.3 + - - +
202A ALA* 1.3 62.9 + - - +
203A GLN* 6.0 0.4 - - - +
214A THR* 4.8 5.8 - - + -
215A LEU 3.3 14.4 - - - +
216A PHE* 3.6 28.9 - + + -
233A VAL* 4.9 2.2 - - + -
266A ILE* 4.0 2.6 - - - +
268A GLU* 4.8 1.4 - - - +
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Residues in contact with ALA 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 PHE* 1.3 76.6 - - - +
203A GLN* 1.3 63.5 - - - +
213A SER 3.5 1.4 - - - +
214A THR* 3.6 2.3 - - - +
215A LEU* 2.6 48.5 + - + +
266A ILE* 3.8 28.9 - - + -
268A GLU* 3.4 15.0 - - - +
287A LEU* 3.9 17.9 - - + -
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Residues in contact with GLN 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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159A ASP* 4.1 7.7 + - - +
160A ALA* 3.8 31.5 - - + +
161A LYS* 4.3 14.8 - - - +
201A PHE* 6.0 0.2 - - - +
202A ALA* 1.3 72.1 - - - +
204A PHE* 1.3 61.9 + - - +
212A GLU* 4.0 36.6 - - - +
213A SER 3.5 7.6 - - - +
214A THR* 3.0 41.3 + - - +
268A GLU* 3.0 32.7 + - - +
271A ASP* 4.7 5.9 - - - +
287A LEU* 5.1 0.5 - - - +
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Residues in contact with PHE 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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203A GLN* 1.3 74.6 - - - +
205A LYS* 1.3 68.6 + - - +
206A MET* 3.7 20.9 + - + -
212A GLU* 4.3 1.9 - - - +
213A SER* 2.9 40.2 + - - +
215A LEU* 3.6 32.5 - - + -
243A PHE* 3.9 23.6 - + - -
271A ASP* 3.7 33.0 - - + -
287A LEU* 4.1 12.8 - - + -
288A GLU* 3.6 41.5 - - + -
350A ARG* 5.1 0.7 - - - -
354A ARG* 4.1 14.6 - - - -
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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