Contacts of the strand formed by residues 197 - 204 (chain A) in PDB entry 3C7N
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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182A TYR* 2.9 31.0 + - - -
186A LYS* 4.1 17.4 - - - +
188A ASP* 3.3 34.4 + - - +
189A LEU* 3.7 19.8 - - - +
190A PRO* 3.5 17.6 - - + +
195A LYS* 4.4 7.4 - - - +
196A PRO* 1.3 71.0 - - - +
198A ILE* 1.3 61.9 + - - +
199A VAL* 3.5 16.3 + - + -
214A MET 3.4 3.5 - - - +
215A ALA* 3.4 0.3 - - - -
216A PHE* 2.9 36.5 + - + +
336A ASP* 4.1 18.2 - - + +
337A PHE* 3.7 22.4 - - + -
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Residues in contact with ILE 198 (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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196A PRO* 3.8 15.7 + - + +
197A ARG* 1.3 73.6 - - - +
199A VAL* 1.3 59.4 + - - +
213A ILE* 3.2 32.3 - - + -
214A MET 3.3 2.5 - - - +
215A ALA* 3.5 28.7 - - + -
224A LEU* 3.9 8.1 - - + -
330A LEU* 3.8 22.2 - - + -
334A GLU* 3.5 23.3 - - + +
335A VAL* 3.5 12.4 - - + -
336A ASP* 2.7 35.2 + - - +
337A PHE 3.5 4.7 + - - +
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Residues in contact with VAL 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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182A TYR* 3.6 21.3 - - + +
197A ARG* 3.7 19.5 - - + -
198A ILE* 1.3 75.5 - - - +
200A ALA* 1.3 64.4 + - - +
201A PHE* 3.4 30.0 - - + -
213A ILE* 4.3 1.8 - - - -
214A MET 2.8 34.6 + - - -
216A PHE* 3.6 22.9 - - + -
337A PHE* 3.4 16.2 - - + +
339A GLU* 3.8 20.2 - - + -
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Residues in contact with ALA 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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199A VAL* 1.3 75.4 - - - +
201A PHE* 1.3 60.1 + - - +
202A VAL 4.2 0.2 - - - -
211A CYS* 5.2 0.4 - - - -
212A SER 3.7 4.9 - - - +
213A ILE* 3.8 16.8 - - + -
335A VAL* 4.1 11.2 - - + +
337A PHE 2.9 7.5 + - - -
338A VAL* 3.3 9.2 - - + +
339A GLU 2.8 26.0 + - - +
358A PHE* 3.4 37.7 - - + -
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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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175A VAL* 3.5 25.2 - - + +
178A ALA* 4.4 10.8 - - + -
179A GLY* 4.3 2.0 - - - -
182A TYR* 3.5 34.3 - + + -
199A VAL* 3.4 29.4 - - + -
200A ALA* 1.3 74.2 - - - +
202A VAL* 1.3 62.6 + - - +
203A ASP 4.2 0.2 - - - -
210A THR 3.9 0.9 - - - +
211A CYS* 3.4 4.5 - - - -
212A SER 2.9 32.5 + - - +
214A MET* 4.1 18.4 - - + -
216A PHE* 3.5 22.0 - + - -
339A GLU* 3.4 19.1 - - + +
341A ILE* 5.2 4.5 - - + -
366A LEU* 3.4 33.4 - - + -
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Residues in contact with VAL 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 78.4 - - - +
203A ASP* 1.3 60.7 + - - +
204A ILE* 3.3 29.1 + - + -
209A TYR* 3.7 15.5 - - + +
210A THR 3.6 2.2 - - - -
211A CYS* 4.2 9.9 - - + -
338A VAL* 4.4 5.4 - - + -
339A GLU 3.0 9.0 + - - +
340A ILE* 3.5 8.2 - - + +
341A ILE* 2.9 25.3 + - - +
345A THR* 4.1 0.5 - - - +
354A ILE* 3.3 33.4 - - + -
358A PHE* 3.9 26.2 - - + -
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Residues in contact with ASP 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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174A ASP* 4.2 6.1 - - - +
175A VAL* 4.0 17.7 - - + +
201A PHE 4.2 0.8 + - - -
202A VAL* 1.3 72.1 - - - +
204A ILE* 1.3 61.6 + - - +
205A GLY 3.3 13.0 + - - -
208A SER 3.2 11.6 - - - +
210A THR* 2.9 25.1 + - - +
341A ILE* 3.0 37.3 - - + +
342A GLY* 3.5 5.0 - - - -
372A ILE* 3.7 3.6 - - - +
671A BEF 2.6 34.8 - - - -
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Residues in contact with ILE 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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202A VAL* 3.3 23.6 - - + -
203A ASP* 1.3 72.6 - - - +
205A GLY* 1.3 59.9 + - - +
208A SER 3.6 2.0 - - - -
209A TYR* 3.4 24.7 - - + -
232A PHE* 3.7 43.7 - - + +
233A GLY* 4.0 4.3 - - - -
317A VAL* 6.5 0.4 - - + -
341A ILE 3.5 3.6 + - - -
342A GLY 3.2 9.5 - - - +
344A THR* 3.1 38.6 + - - +
345A THR* 3.1 27.3 - - + +
350A LEU* 4.7 15.3 - - + -
354A ILE* 5.0 3.8 - - + -
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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