Contacts of the strand formed by residues 197 - 202 (chain A) in PDB entry 1N99
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 ARG 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A GLU* 1.3 78.2 + - - +
198A THR* 1.3 72.2 + - - +
199A ILE* 4.1 19.2 + - + -
233A LEU* 6.3 1.3 - - + -
267A ILE 3.8 0.9 - - - +
268A THR* 3.4 0.5 - - - -
269A ILE* 2.8 42.3 + - + +
110B MSE 2.4 55.6 + - - +
191B ARG* 3.7 36.2 - - - +
192B ASP 4.5 3.2 + - - -
194B PRO* 3.7 34.0 + - + +
195B PHE* 3.7 22.4 - - + -
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Residues in contact with THR 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLU* 4.2 8.1 + - - +
197A ARG* 1.3 84.7 + - - +
199A ILE* 1.3 65.5 - - - +
200A THR* 5.3 1.3 - - - +
266A THR* 3.7 26.7 - - + -
267A ILE 3.3 3.4 - - - +
268A THR* 2.6 29.3 + - - +
110B MSE 4.3 30.8 - - + +
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Residues in contact with ILE 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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197A ARG* 4.2 10.3 - - + +
198A THR* 1.3 79.3 - - - +
200A THR* 1.3 65.3 + - - +
201A MSE 3.6 22.0 - - + +
230A ASN* 3.8 31.4 - - + +
231A GLY 4.1 9.4 - - - +
232A LEU* 3.9 23.6 - - + +
233A LEU* 5.9 0.7 - - + -
266A THR* 3.4 1.4 - - - -
267A ILE 2.7 36.7 + - - +
269A ILE* 4.0 18.4 - - + -
191B ARG* 3.9 31.9 - - - +
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Residues in contact with THR 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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198A THR* 5.3 1.4 - - - +
199A ILE* 1.3 72.4 - - - +
201A MSE 1.3 66.5 + - - +
230A ASN* 3.5 21.8 + - - +
264A VAL* 3.7 21.1 - - + -
265A VAL 3.5 3.8 - - - -
266A THR* 2.9 28.1 + - - +
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Residues in contact with MSE 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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199A ILE* 3.6 33.0 - - + +
200A THR* 1.3 83.9 - - - +
202A HIS* 1.3 65.7 + - - +
209A VAL* 4.1 21.8 - - + -
211A PHE* 4.7 0.2 - - - -
226A SER* 3.2 31.9 - - - +
227A ALA* 3.8 25.6 - - - -
230A ASN* 3.9 8.3 - - + +
232A LEU* 4.3 16.4 - - + -
264A VAL* 3.5 3.8 - - - -
265A VAL 2.6 36.8 + - - +
267A ILE* 3.6 33.9 - - + -
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Residues in contact with HIS 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 MSE 1.3 77.1 - - - +
203A LYS* 1.3 79.6 + - - +
204A ASP* 3.5 5.9 + - + -
208A HIS 4.4 0.3 - - - +
209A VAL* 3.9 5.2 - - - +
226A SER* 2.8 33.4 + - - -
229A ARG* 4.2 20.4 + - - -
230A ASN* 6.1 1.3 - - - -
263A THR* 3.2 21.0 - - + +
264A VAL* 4.6 5.6 - - + -
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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