Contacts of the strand formed by residues 201 - 206 (chain A) in PDB entry 5KJH
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 TYR 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A PHE* 3.5 5.5 - - - -
196A HIS* 2.9 38.9 + + + -
198A ASN* 3.5 32.7 + - - -
200A ARG* 1.3 81.1 + - - +
202A VAL* 1.3 64.1 + - - +
213A LEU* 3.6 26.0 - - + -
214A TRP 3.2 7.6 - - - +
215A ALA* 3.9 20.0 - - + -
250A PHE* 3.9 13.5 - - + -
273A PHE* 3.6 30.5 - + - -
274A SER 4.8 5.2 + - - -
275A SER* 4.6 7.0 - - - -
277A ASP* 4.9 0.7 + - - +
278A PRO 4.2 2.6 + - - -
279A ILE* 3.7 19.3 - - + +
280A PRO* 3.2 24.7 - - + +
299A PHE* 4.2 9.2 - + - -
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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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163A ILE* 4.7 1.8 - - + -
165A ILE* 4.4 3.6 - - + -
181A LEU* 3.8 25.1 - - + -
193A VAL* 3.7 28.3 - - + -
194A ALA 3.3 5.4 - - - +
195A PHE* 3.7 21.1 - - + -
201A TYR* 1.3 78.9 - - - +
203A LEU* 1.3 65.4 + - - +
204A SER* 5.1 1.3 - - - -
213A LEU* 3.4 3.6 - - - -
214A TRP* 2.8 40.5 + - + +
216A LEU* 3.7 32.8 - - + -
250A PHE* 4.5 1.3 - - - -
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Residues in contact with LEU 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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193A VAL* 3.2 6.9 - - - +
194A ALA* 2.8 35.7 + - + +
202A VAL* 1.3 73.1 - - - +
204A SER* 1.3 59.6 + - - +
211A ILE* 4.4 13.7 - - + -
212A ASN 3.3 10.5 - - - +
213A LEU* 4.0 16.6 - - + -
235A PHE* 6.4 0.2 - - + -
248A VAL* 3.7 24.6 - - + +
249A ALA* 3.6 34.5 - - - +
250A PHE* 3.4 37.9 - - + -
255A ILE* 3.9 17.5 - - + -
270A ILE* 5.3 0.9 - - + -
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Residues in contact with SER 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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163A ILE* 3.8 29.2 - - - -
186A HIS* 2.7 29.4 + - - -
190A LEU* 4.6 1.3 - - - -
192A SER 3.3 6.7 - - - -
193A VAL* 4.9 0.4 - - - -
202A VAL* 5.1 0.2 - - - -
203A LEU* 1.3 75.1 - - - +
205A ALA* 1.3 63.9 + - - +
211A ILE* 3.5 2.8 - - - +
212A ASN* 3.0 30.2 + - - +
214A TRP* 2.9 25.8 + - - -
248A VAL* 4.5 2.0 - - - -
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Residues in contact with ALA 205 (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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186A HIS* 4.1 2.8 + - - -
190A LEU* 3.7 8.8 - - - +
191A LEU 2.9 18.7 + - - -
192A SER* 3.0 18.1 + - - +
204A SER* 1.3 76.2 - - - +
206A GLY* 1.3 59.0 + - - +
210A VAL 3.4 15.0 - - - +
211A ILE* 4.0 7.4 - - + -
245A VAL* 3.6 32.5 - - + +
248A VAL* 4.3 12.8 - - + -
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Residues in contact with GLY 206 (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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189A ASP 3.5 12.3 - - - -
190A LEU* 4.1 4.4 - - - +
191A LEU* 3.6 10.1 - - - -
205A ALA* 1.3 76.9 - - - +
207A HIS* 1.3 63.5 + - - -
208A ASP* 3.2 4.3 + - - -
209A GLN* 3.2 9.0 + - - -
210A VAL 4.0 4.6 + - - -
245A VAL* 3.0 33.3 + - - -
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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