Contacts of the strand formed by residues 202 - 207 (chain A) in PDB entry 4MJV
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 VAL 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A GLY 3.6 0.9 - - - +
194A VAL* 3.2 3.7 - - - -
195A THR* 2.9 52.4 + - + +
196A GLY* 4.6 4.6 - - - +
200A LYS 3.7 2.4 + - - +
201A ALA* 1.3 73.7 - - - +
203A ALA* 1.3 66.5 + - - +
204A VAL* 4.0 10.2 + - + +
214A VAL* 3.8 26.2 - - + -
215A VAL 3.8 1.8 - - - +
216A ASN* 3.4 20.2 - - - +
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Residues in contact with ALA 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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192A VAL* 4.0 9.0 - - + -
193A GLY 3.0 4.7 - - - +
194A VAL* 3.6 23.3 - - + +
202A VAL* 1.3 73.1 - - - +
204A VAL* 1.3 63.3 + - - +
205A ILE* 4.4 1.3 - - + +
214A VAL* 3.3 6.9 - - - +
215A VAL* 2.8 50.2 + - + +
223A LEU* 4.1 3.5 - - + +
241A MET* 3.9 18.8 - - + -
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Residues in contact with VAL 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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176A VAL* 5.6 2.7 - - + +
192A VAL* 3.2 4.0 - - - -
193A GLY 2.5 42.6 + - - +
195A THR* 5.5 5.8 - - + -
202A VAL* 4.7 15.5 - - + +
203A ALA* 1.3 73.9 - - - +
205A ILE* 1.3 63.5 + - - +
206A HIS* 3.3 30.3 - - + +
211A PRO* 4.0 21.8 - - + -
213A ASP 3.9 5.6 - - - +
214A VAL* 4.3 13.0 - - + -
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Residues in contact with ILE 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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190A MET* 3.9 23.1 - - + -
191A THR 3.5 9.2 - - - +
192A VAL* 3.8 20.4 - - + -
203A ALA* 4.4 1.6 - - + +
204A VAL* 1.3 74.4 - - - +
206A HIS* 1.3 57.1 + - - +
211A PRO* 3.5 0.7 - - - +
212A THR* 2.7 40.2 + - - +
213A ASP* 2.8 30.4 + - + +
214A VAL* 4.0 3.1 - - - +
215A VAL* 4.0 14.1 - - + +
239A TRP* 4.4 10.5 - - + -
260A GLY* 3.6 20.9 - - - +
262A ILE* 3.6 35.0 - - + -
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Residues in contact with HIS 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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173A PHE* 5.3 3.4 - + - -
174A GLU 2.9 24.7 + - - +
175A ALA* 3.3 23.9 - - + +
176A VAL 4.8 2.3 + - - -
189A TRP 4.4 0.2 - - - -
190A MET* 3.2 10.0 - - - +
191A THR* 3.0 42.2 + - + +
204A VAL* 3.3 39.6 - - + +
205A ILE* 1.3 74.7 - - - +
207A TYR* 1.3 63.2 + - - +
209A GLY* 4.9 6.7 + - - +
210A VAL* 3.2 14.1 + - - +
211A PRO* 4.3 16.5 - - + +
212A THR* 4.1 0.2 - - - -
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Residues in contact with TYR 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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84A TYR* 4.7 2.1 + - - -
185A ASP* 3.4 35.3 + - - -
187A LYS* 4.1 9.2 - - - +
188A LYS* 3.6 43.8 + - + +
189A TRP 3.3 12.6 - - - -
190A MET* 3.9 12.3 - - + -
206A HIS* 1.3 76.1 - - - +
208A GLY* 1.3 65.4 + - - +
209A GLY 3.1 0.4 + - - -
210A VAL* 2.8 26.7 + - - +
212A THR* 3.7 9.9 - - + +
259A GLN* 3.3 54.8 - - + +
260A GLY* 3.6 17.7 - - - -
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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