Contacts of the strand formed by residues 208 - 213 (chain A) in PDB entry 5E8A
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 HIS 208 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLU* 2.5 61.1 + - + +
207A ASP* 1.3 92.2 + - + +
209A PHE* 1.3 67.5 + - - +
210A LYS* 4.3 1.8 - - + -
220A GLN* 3.5 43.4 + - + +
221A TYR 3.2 24.5 - - - +
222A ASN* 3.9 4.5 + - - +
223A HIS* 3.3 11.7 + - - -
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Residues in contact with PHE 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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126A VAL* 4.7 7.6 - - + -
149A PHE* 4.3 22.4 - + + -
156A ALA* 5.1 3.6 - - + -
157A PHE* 3.6 52.7 - + + -
202A VAL* 3.9 21.3 - - + -
203A LEU 3.7 3.1 - - - -
204A VAL* 4.1 23.1 - - + -
208A HIS* 1.3 73.5 - - - +
210A LYS* 1.3 59.8 + - - +
211A VAL* 4.2 1.9 + - - +
219A LEU 4.1 0.2 - - - +
220A GLN* 3.2 5.7 - - - +
221A TYR* 2.9 43.5 + + + +
223A HIS* 3.5 28.3 - + - -
231A ILE* 4.5 20.9 - - + -
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Residues in contact with LYS 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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201A GLN 3.6 1.2 - - - +
202A VAL* 3.4 2.9 - - - -
203A LEU* 2.8 70.4 + - + +
205A GLU* 2.9 31.2 + - - +
208A HIS* 3.9 8.7 + - + -
209A PHE* 1.3 73.7 - - - +
211A VAL* 1.3 62.9 + - - +
212A ALA* 4.2 0.8 + - + -
217A HIS* 3.8 25.4 - - + +
219A LEU 3.7 2.7 - - - -
220A GLN* 4.2 13.5 - - + +
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PHE* 4.0 24.5 - - + -
159A PHE* 4.0 27.4 - - + -
200A ILE* 4.2 11.7 - - + -
201A GLN 3.4 7.4 - - - +
202A VAL* 4.3 12.3 - - + -
209A PHE 4.8 0.9 - - - +
210A LYS* 1.3 78.5 - - - +
212A ALA* 1.3 70.2 + - - +
213A VAL* 4.4 1.1 - - + -
217A HIS* 3.9 4.3 + - - -
218A LEU* 2.9 30.6 + - + +
219A LEU* 2.9 39.7 + - + +
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Residues in contact with ALA 212 (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 LYS 3.8 0.3 - - - +
200A ILE* 3.6 2.3 - - - -
201A GLN* 2.9 52.8 + - + +
210A LYS* 4.2 1.1 + - + -
211A VAL* 1.3 74.0 - - - +
213A VAL* 1.3 64.2 + - - +
214A ASN 4.2 0.2 - - - -
215A ASP* 4.6 3.4 - - - -
216A ALA 3.3 24.0 - - - +
217A HIS* 4.2 4.3 - - - +
218A LEU 4.2 0.2 - - - +
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Residues in contact with VAL 213 (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 PHE* 4.9 0.2 - - + -
191A PRO* 3.8 28.9 - - + +
192A PHE* 3.9 37.0 - - + -
198A PHE* 4.8 1.8 - - + -
199A LYS 3.2 10.3 - - - +
200A ILE* 4.3 8.3 - - + -
211A VAL* 4.4 5.6 - - + -
212A ALA* 1.3 75.6 - - - +
214A ASN* 1.3 87.9 + - - +
215A ASP 3.1 1.3 - - - -
216A ALA* 3.0 24.3 + - - +
218A LEU* 3.9 24.1 - - + +
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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