Contacts of the strand formed by residues 207 - 212 (chain B) in PDB entry 2YZ2
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 ARG 207 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL 5.0 7.6 + - - -
34B GLU* 3.5 32.5 + - + +
35B CYS 3.5 4.2 + - - +
36B LEU* 3.6 20.3 - - + +
37B LEU 2.9 24.6 + - - -
205B VAL* 3.5 7.6 - - - +
206B ASP* 1.3 88.2 - - + +
208B VAL* 1.3 64.7 + - - +
219B ASP* 2.7 32.1 + - - -
220B GLY* 3.1 28.4 - - - +
221B THR* 3.9 22.6 - - + +
222B ARG 4.1 0.4 - - - +
224B GLU* 5.1 1.2 + - - -
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 3.2 26.5 - - + +
39B ALA* 4.4 3.1 - - + -
202B ILE* 3.9 20.9 - - + -
205B VAL* 4.2 8.5 - - + -
207B ARG* 1.3 79.5 - - - +
209B VAL* 1.3 71.0 + - - +
210B VAL* 4.1 6.5 - - + -
218B PHE* 3.4 6.1 - - - -
219B ASP* 3.5 1.4 - - - +
220B GLY 2.9 30.0 + - - +
222B ARG* 4.3 4.0 - - - -
225B PHE* 3.8 51.8 - - + -
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 4.3 19.7 - - + -
36B LEU* 3.6 22.9 - - + -
37B LEU 2.9 7.2 + - - +
38B VAL* 3.2 12.8 - - + +
39B ALA* 2.7 33.1 + - - +
208B VAL* 1.3 77.2 - - - +
210B VAL* 1.3 65.1 + - - +
211B LEU* 4.1 13.0 - - + -
216B LYS* 3.8 19.7 - - + -
218B PHE 3.2 10.8 - - - +
219B ASP* 3.9 25.4 - - - +
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ALA* 3.4 13.0 - - + +
40B GLY* 4.3 7.0 - - - -
208B VAL* 4.1 5.8 - - + -
209B VAL* 1.3 78.9 - - - +
211B LEU* 1.3 71.0 + - - +
212B GLU* 5.3 0.7 - - + +
216B LYS* 3.6 4.3 - - - -
217B VAL* 2.9 38.2 + - + -
218B PHE* 3.1 30.7 + - + +
225B PHE* 3.9 26.0 - - + -
229B TYR* 3.5 28.0 - - + +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 3.8 20.0 - - + -
26B VAL* 4.3 14.1 - - + -
38B VAL* 4.3 9.0 - - + -
39B ALA 2.9 7.7 + - - +
40B GLY* 3.3 22.3 - - - -
41B ASN 4.4 0.9 + - - -
44B SER* 3.5 19.4 - - - +
46B LYS* 3.6 34.1 - - + +
49B LEU* 4.0 13.9 - - + -
209B VAL* 4.1 8.7 - - + -
210B VAL* 1.3 82.2 - - - +
212B GLU* 1.3 64.6 + - - +
215B LYS* 3.1 6.7 - - - +
216B LYS* 3.6 31.6 - - + +
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ASN* 4.0 24.1 + - - +
42B THR 5.8 0.2 - - - +
44B SER* 4.2 3.4 - - - -
210B VAL* 5.3 0.2 - - + -
211B LEU* 1.3 79.3 - - - +
213B LYS* 1.3 96.5 + - + +
215B LYS* 3.1 21.9 + - - +
217B VAL* 4.0 26.2 - - + +
229B TYR* 4.8 8.0 + - - -
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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