Contacts of the strand formed by residues 205 - 210 (chain A) in PDB entry 5H15
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 LEU 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A PHE* 3.5 5.9 - - - -
199A HIS* 2.9 58.8 + - + +
202A ASP* 3.2 34.7 + - + +
204A ASN* 1.3 77.5 - - - +
206A LEU* 1.3 59.3 + - - +
217A LEU* 4.0 14.4 - - + -
218A TRP 3.3 10.8 - - - +
219A ASN* 4.3 18.2 - - + +
226A VAL* 4.6 9.2 - - + -
244A TYR* 3.4 2.9 + - - -
274A ILE* 4.0 39.3 - - + -
277A SER* 5.1 0.2 - - - +
278A TYR* 4.9 0.4 - - - +
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Residues in contact with LEU 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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164A ALA* 4.1 5.6 - - + -
172A ILE* 3.8 33.9 - - + -
174A ILE* 4.1 6.7 - - + -
186A TYR* 5.4 0.4 - - + -
196A LEU* 3.8 27.8 - - + -
197A LYS 3.5 20.4 - - - +
198A PHE* 3.5 41.3 - - + -
204A ASN 3.3 1.2 + - - -
205A LEU* 1.3 72.1 - - - +
207A LEU* 1.3 62.3 + - - +
217A LEU* 3.5 2.0 - - - -
218A TRP* 2.8 45.2 + - + +
220A ILE* 4.0 17.3 - - + -
244A TYR* 4.1 1.6 - - - -
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Residues in contact with LEU 207 (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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195A GLU 3.9 0.5 - - - +
196A LEU* 3.2 5.7 - - - -
197A LYS* 2.8 45.9 + - + +
206A LEU* 1.3 75.4 - - - +
208A SER* 1.4 60.2 + - - +
209A VAL* 4.6 3.0 - - + +
215A LEU* 4.1 19.1 - - + -
216A ARG 3.3 20.0 - - - +
217A LEU* 4.4 6.7 - - + +
229A PHE* 4.5 5.2 - - + -
242A ALA* 3.8 19.3 - - + -
243A ASP 5.0 0.2 - - - +
244A TYR* 3.5 21.0 + - + +
251A ILE* 3.7 49.1 - - + -
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Residues in contact with SER 208 (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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172A ILE* 3.8 21.1 - - - -
189A HIS* 3.0 29.1 + - - -
193A ILE* 4.0 6.3 - - - -
195A GLU 3.4 5.2 - - - -
196A LEU* 3.8 8.3 - - - -
206A LEU 4.1 0.8 + - - -
207A LEU* 1.4 72.1 - - - +
209A VAL* 1.3 61.9 + - - +
215A LEU* 3.3 4.9 - - - +
216A ARG* 2.9 29.8 + - - +
218A TRP* 2.9 21.5 + - - -
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Residues in contact with VAL 209 (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 HIS* 4.4 0.2 - - - -
193A ILE* 3.4 4.5 - - - -
194A ASN 2.8 26.3 + - - -
195A GLU* 2.9 39.4 + - + +
207A LEU* 4.6 5.4 - - + -
208A SER* 1.3 76.6 - - - +
210A SER* 1.3 61.6 + - - +
214A ALA 3.9 2.9 - - - -
215A LEU* 3.8 15.5 - - + -
239A VAL* 3.6 27.4 - - + +
240A LEU 3.9 11.4 - - - -
241A SER* 4.0 1.8 - - - +
242A ALA* 3.5 31.0 - - + +
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Residues in contact with SER 210 (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 HIS* 3.2 34.5 - - - -
190A GLY 2.7 27.0 + - - -
191A ASN 3.7 0.9 + - - -
192A ALA 3.0 13.0 + - - -
193A ILE* 4.4 0.2 - - - -
194A ASN* 4.0 3.8 - - - +
209A VAL* 1.3 76.1 - - - +
211A LYS* 1.4 62.9 + - - +
212A ASP* 3.1 8.6 + - - -
213A HIS* 3.2 13.4 + - - -
214A ALA 3.0 6.9 + - - +
239A VAL* 2.9 27.5 + - - +
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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