Contacts of the strand formed by residues 200 - 206 (chain A) in PDB entry 4HXG
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 TRP 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A PHE 5.1 3.6 + - - -
186A SER* 4.3 5.0 + - - -
187A VAL 3.2 32.3 - - - +
188A PRO* 3.8 12.1 - - + +
189A HIS* 4.1 1.1 - - - +
195A ARG 5.8 0.2 - - - -
197A PHE* 3.6 40.2 - + - -
198A LYS 3.8 11.4 - - - -
199A TYR* 1.3 77.4 - - - +
201A ASP* 1.3 72.1 + - - +
202A ILE* 4.6 4.3 - - + -
216A LYS 3.3 2.1 + - - -
217A VAL* 2.7 45.6 + - - +
218A SER 3.4 26.2 - - - -
219A PHE 3.8 13.5 - - - +
220A TYR* 3.5 47.3 - + + +
232A TYR 5.4 0.2 - - - -
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Residues in contact with ASP 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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185A VAL 3.7 1.4 - - - +
186A SER* 3.7 0.9 - - - -
187A VAL* 2.7 36.5 + - + +
188A PRO 4.6 2.1 - - - +
189A HIS* 3.0 39.1 + - - +
190A ARG 5.1 0.7 + - - -
200A TRP* 1.3 74.4 - - - +
202A ILE* 1.3 61.0 + - - +
203A TYR* 3.5 32.2 + - + +
212A LYS* 4.7 2.7 + - - -
214A PHE 3.5 9.4 - - - +
215A GLU* 3.9 12.0 - - - +
216A LYS 3.1 17.3 + - - -
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Residues in contact with ILE 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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184A VAL* 3.8 27.1 - - + -
185A VAL 3.4 5.8 - - - +
186A SER* 4.5 7.9 - - - +
200A TRP* 4.6 4.7 - - + -
201A ASP* 1.3 77.5 - - - +
203A TYR* 1.3 57.4 + - - +
212A LYS* 3.7 3.6 - - - +
213A LEU* 2.7 41.5 + - + -
214A PHE* 3.2 37.7 + - + -
217A VAL* 4.3 8.3 - - + -
219A PHE* 3.5 26.7 - - + +
220A TYR* 4.0 13.7 - - - -
221A ALA* 4.5 2.2 - - + +
229A ILE* 6.4 0.2 - - + -
231A LEU* 4.3 14.8 - - + -
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Residues in contact with TYR 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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170A LYS* 4.8 6.1 - - - -
184A VAL* 3.4 9.4 - - - +
185A VAL* 2.9 49.9 + - + +
187A VAL* 4.0 20.3 - - + +
201A ASP* 3.5 37.0 + - + +
202A ILE* 1.3 76.7 - - - +
204A LEU* 1.3 60.3 + - - +
205A TRP 4.0 0.2 - - - -
210A GLU* 3.8 36.6 - - + +
211A GLU 3.5 3.4 - - - +
212A LYS* 3.5 48.3 + - + -
213A LEU* 3.9 4.4 - - - +
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Residues in contact with LEU 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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179A HIS* 4.5 15.5 - - + -
182A SER* 4.3 22.7 - - - +
183A ILE 4.1 4.9 - - - +
184A VAL* 4.0 26.2 - - + -
203A TYR* 1.3 73.1 - - - +
205A TRP* 1.3 61.3 + - - +
206A LYS 4.0 0.3 + - - -
209A GLU 3.8 0.3 - - - +
210A GLU* 3.1 23.2 - - - -
211A GLU* 2.9 21.4 + - + +
213A LEU* 3.8 27.6 - - + -
229A ILE* 4.9 2.0 - - + -
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Residues in contact with TRP 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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156A VAL* 5.3 1.3 - - + -
166A GLU* 3.3 36.1 - - + -
167A GLN 5.2 1.6 - - - -
168A PHE* 3.3 58.8 - + + +
170A LYS* 5.0 1.7 - - - +
182A SER* 3.3 3.0 - - - -
183A ILE* 2.7 63.1 + - + +
185A VAL* 4.1 11.7 - - + -
203A TYR 5.5 0.2 - - - -
204A LEU* 1.3 74.2 - - - +
206A LYS* 1.3 66.3 + - - +
207A ASP 3.7 12.3 - - - -
208A GLY* 3.3 33.8 + - - -
209A GLU 3.6 3.8 - - - -
210A GLU* 3.4 29.2 - - + +
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Residues in contact with LYS 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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181A ASP* 4.1 28.3 - - - +
182A SER* 3.4 22.0 - - - +
204A LEU 4.0 0.8 + - - -
205A TRP* 1.3 82.1 - - - +
207A ASP* 1.3 95.9 + - - +
208A GLY 3.0 2.7 - - - -
209A GLU* 2.8 26.4 + - - +
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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