Contacts of the strand formed by residues 210 - 215 (chain A) in PDB entry 4H1V
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 THR 210 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ILE* 3.3 28.8 - - + +
183A ALA* 3.9 22.9 - - + -
197A LEU* 5.0 1.6 - - + -
200A SER* 4.3 10.9 - - - -
204A ASP* 3.0 18.7 + - - +
207A GLY* 3.8 5.7 + - - -
208A ARG 3.4 2.6 - - - -
209A ARG* 1.3 79.9 - - - +
211A LEU* 1.3 64.5 + - - +
237A VAL* 3.1 41.4 - - + +
238A LYS 3.8 1.2 + - - -
239A LEU* 3.2 17.9 + - - -
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Residues in contact with LEU 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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180A ILE* 5.1 2.7 - - + -
181A ILE 2.8 10.2 + - - +
182A LEU* 3.5 24.6 - - + +
183A ALA 2.9 25.1 + - - -
209A ARG 4.2 0.2 + - - -
210A THR* 1.3 77.2 - - - +
212A ALA* 1.3 76.6 + - - +
213A VAL* 4.2 4.3 - - + -
239A LEU* 3.4 27.1 - - + +
240A GLY 3.5 13.7 - - - +
242A ILE* 4.2 20.9 - - + -
285A LEU* 4.8 1.3 - - + -
288A THR* 4.5 12.3 - - - +
289A LEU* 4.4 11.4 - - + -
292A LEU* 3.9 26.0 - - + -
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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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183A ALA* 3.5 7.6 - - - +
185A THR* 5.4 0.7 - - + -
197A LEU* 4.5 18.8 - - + -
211A LEU* 1.3 73.8 - - - +
213A VAL* 1.3 62.4 + - - +
214A ILE* 4.0 4.0 + - + -
235A ILE* 4.5 10.1 - - + -
237A VAL* 3.8 7.4 - - + +
240A GLY 3.0 8.2 + - - +
241A ILE* 3.4 28.0 - - + +
242A ILE 2.9 25.8 + - - -
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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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41A VAL* 4.1 15.7 - - + -
182A LEU* 3.6 33.2 - - + -
183A ALA 2.9 12.4 + - - +
184A VAL* 3.6 9.5 - - + +
185A THR* 3.1 27.9 + - - +
211A LEU* 4.2 2.0 - - + -
212A ALA* 1.3 73.7 - - - +
214A ILE* 1.3 63.1 + - - +
215A THR* 3.7 19.6 + - + -
242A ILE* 3.2 9.6 - - + +
244A VAL* 4.1 10.1 - - + -
285A LEU* 4.0 28.3 - - + -
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Residues in contact with ILE 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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185A THR* 3.3 27.6 - - + +
187A ALA* 3.6 31.6 - - + +
191A MET* 3.7 7.6 - - - -
212A ALA* 4.9 3.1 - - + +
213A VAL* 1.3 72.6 - - - +
215A THR* 1.3 57.1 + - - +
217A LEU* 3.9 10.3 - - + +
229A VAL* 3.1 36.3 - - + -
230A LEU* 5.8 0.9 - - + -
235A ILE* 4.1 12.3 - - + -
241A ILE* 4.0 17.3 - - + -
242A ILE 2.8 10.4 + - - +
243A GLY* 3.2 10.0 - - - -
244A VAL 2.7 33.1 + - - +
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Residues in contact with THR 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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36A SER 2.5 29.9 + - - +
37A GLY 4.2 1.1 - - - +
41A VAL* 3.6 30.5 - - + -
184A VAL* 4.0 11.2 - - + -
185A THR 3.1 5.1 + - - -
186A ALA* 3.6 8.1 - - - -
187A ALA* 2.7 28.8 + - - +
213A VAL* 4.0 2.9 - - + -
214A ILE* 1.3 76.1 - - - +
216A LYS* 1.3 69.7 + - - +
217A LEU 3.4 2.8 + - - -
244A VAL* 3.6 15.0 - - + -
246A ASN* 3.8 5.6 - - - +
801A GNP 4.1 8.1 - - - -
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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