Contacts of the strand formed by residues 210 - 216 (chain A) in PDB entry 3V4R
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A LYS* 6.0 5.2 - - - +
203A PHE* 4.1 8.0 - - - -
204A PRO* 3.5 20.3 - - + +
208A ASP* 2.4 52.8 + - + +
209A GLU* 1.4 69.6 - - - +
211A CYS* 1.3 65.2 + - - +
226A GLU* 3.6 22.7 + - + +
227A VAL 3.6 7.4 + - - -
228A ASP* 5.4 1.3 - - - +
235A LEU* 3.6 38.9 - - + +
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Residues in contact with CYS 211 (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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188A PHE* 4.3 20.4 - - - -
201A GLU* 4.8 9.2 - - - -
202A ILE 3.0 18.8 - - - +
203A PHE* 3.8 17.5 - - + -
204A PRO* 4.2 2.5 - - - -
210A HIS* 1.3 76.5 - - - +
212A VAL* 1.3 62.9 + - - +
213A ARG* 6.3 0.4 - - - -
225A ARG 3.9 0.2 - - - +
226A GLU* 3.7 3.9 - - - +
227A VAL* 2.9 54.4 + - - +
229A ALA* 4.9 9.6 - - - -
107B THR* 6.0 1.1 - - - -
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Residues in contact with VAL 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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200A VAL 3.8 1.7 - - - +
201A GLU* 3.4 3.4 - - - +
202A ILE* 2.8 45.2 + - + +
204A PRO* 5.2 7.6 - - + -
211A CYS* 1.3 74.0 - - - +
213A ARG* 1.4 60.2 + - - +
214A VAL* 3.9 20.2 - - + -
224A ILE* 4.0 10.8 - - + -
225A ARG 3.9 6.3 - - - +
226A GLU* 4.8 9.4 - - + +
241A VAL* 3.9 34.8 - - + -
243A ILE* 3.8 21.8 - - + -
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Residues in contact with ARG 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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199A VAL* 3.9 31.4 - - + -
200A VAL 3.7 2.2 - - - -
201A GLU* 3.9 28.8 + - + +
211A CYS* 3.9 0.9 + - - -
212A VAL* 1.4 73.3 - - - +
214A VAL* 1.3 62.8 + - - +
215A GLU* 3.8 2.9 + - + +
223A ARG 3.6 2.6 - - - +
224A ILE* 3.5 4.0 - - - -
225A ARG* 3.0 62.2 + - + +
227A VAL* 3.7 35.2 - - + +
232A GLY 5.4 2.2 + - - -
234A ILE* 5.7 4.4 - - - +
105B THR* 5.7 5.5 - - - +
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Residues in contact with VAL 214 (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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161A LEU* 4.0 15.9 - - + -
172A LEU* 5.1 2.2 - - + -
199A VAL* 3.3 6.4 - - - +
200A VAL* 2.8 46.1 + - + +
202A ILE* 3.9 24.5 - - + -
212A VAL* 3.9 11.7 - - + -
213A ARG* 1.3 73.6 - - - +
215A GLU* 1.3 60.3 + - - +
216A PHE* 4.0 27.9 + - + -
221A ILE* 3.8 27.8 - - + -
223A ARG 3.6 3.1 - - - -
224A ILE* 4.7 9.2 - - + +
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Residues in contact with GLU 215 (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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198A ASP 3.7 4.9 - - - +
199A VAL* 3.7 16.4 - - + -
213A ARG* 3.8 4.4 + - + +
214A VAL* 1.3 70.6 - - - +
216A PHE* 1.3 55.3 + - - +
221A ILE* 3.6 4.9 - - - +
222A GLU* 2.8 32.3 + - + -
223A ARG* 2.8 30.3 + - + +
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Residues in contact with PHE 216 (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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167A ILE* 4.0 20.9 - - + -
169A ARG* 3.9 32.1 - - + -
172A LEU* 4.2 19.1 - - + -
198A ASP* 2.7 45.0 + - + +
200A VAL* 3.7 29.8 - - + -
214A VAL* 4.0 18.6 - - + -
215A GLU* 1.3 73.2 - - - +
217A PHE* 1.4 60.2 - - - +
218A GLY* 4.5 7.9 - - - +
219A ASP* 4.8 1.8 - - - -
220A GLU 3.5 17.0 - - - -
221A ILE* 3.3 26.9 - - + -
222A GLU* 4.1 2.9 - - - -
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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