Contacts of the strand formed by residues 207 - 213 (chain G) in PDB entry 4D1Q
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 LEU 207 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162G ILE* 3.9 27.6 - - + -
166G ILE* 4.0 14.8 - - + -
195G THR* 3.3 12.8 - - - +
196G LEU* 3.0 39.9 + - + +
198G TYR* 5.3 5.2 - - + +
205G ARG* 4.8 5.8 - - + -
206G ASP* 1.3 79.5 - - - +
208G ILE* 1.3 70.0 + - - +
209G LEU* 4.1 10.1 - - + -
599G PHE* 4.8 9.0 - - + -
602G SER* 3.5 13.7 - - - +
603G PHE* 4.8 3.4 - - - +
606G ASN* 3.3 37.0 - - + +
607G PHE* 4.4 13.5 - - + -
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Residues in contact with ILE 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194G VAL 3.8 3.8 - - - +
195G THR* 4.3 3.1 - - + +
206G ASP* 5.1 2.0 - - - +
207G LEU* 1.3 79.2 - - - +
209G LEU* 1.3 63.3 + - - +
210G GLY* 4.1 13.7 - - - +
570G ALA 5.8 0.7 - - - +
574G THR* 3.7 42.6 - - + +
577G LEU* 4.1 24.9 - - + -
598G LEU* 4.3 28.9 - - + +
599G PHE* 3.3 23.3 - - - +
602G SER* 3.2 21.3 + - - +
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Residues in contact with LEU 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G LYS* 4.4 7.1 - - - +
166G ILE* 4.0 19.7 - - + -
194G VAL* 2.7 29.7 + - + +
196G LEU* 3.5 35.7 - - + -
207G LEU* 4.1 10.5 - - + -
208G ILE* 1.3 73.9 - - - +
210G GLY* 1.3 55.2 + - - +
231G ILE* 3.8 11.2 - - + +
232G PHE* 3.4 41.5 - - + -
234G GLN* 4.2 6.9 - - - +
235G PHE* 3.3 43.0 - - + -
595G ASP* 4.5 0.5 - - - +
599G PHE* 4.5 2.1 - - - -
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Residues in contact with GLY 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G LEU 3.7 2.0 - - - +
193G GLY* 3.6 1.9 - - - -
194G VAL 3.0 26.7 + - - +
208G ILE* 3.3 13.2 - - - +
209G LEU* 1.3 82.2 - - - +
211G LEU* 1.3 60.7 + - - +
212G LYS* 3.9 1.8 - - - -
231G ILE* 4.2 13.0 - - - +
234G GLN* 5.4 0.4 - - - -
574G THR* 4.9 1.2 - - - +
595G ASP* 3.4 14.8 - - - -
598G LEU* 6.5 0.2 - - - -
599G PHE* 5.7 2.5 - - - -
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Residues in contact with LEU 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182G TRP* 4.7 2.0 - - + -
191G PHE* 3.7 42.6 - - + -
192G LEU 3.3 13.9 - - - +
193G GLY* 3.7 4.7 - - - -
210G GLY* 1.3 73.2 - - - +
212G LYS* 1.3 61.7 + - - +
574G THR* 4.5 8.7 - - + +
575G PHE* 3.7 28.5 - - + -
578G ALA* 3.5 32.3 - - + -
591G GLN* 4.6 5.7 - - - +
594G VAL* 4.9 5.0 - - + +
595G ASP* 2.9 24.5 + - - +
598G LEU* 3.5 22.6 - - + +
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Residues in contact with LYS 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191G PHE* 3.5 3.8 - - - -
192G LEU* 2.9 36.5 + - + +
210G GLY 3.9 0.4 - - - -
211G LEU* 1.3 73.3 - - - +
213G SER* 1.3 63.0 + - - +
214G LEU 3.9 0.2 + - - -
227G LYS* 4.1 32.1 - - + +
230G ALA* 4.9 10.7 + - - +
231G ILE* 4.5 21.1 - - + +
234G GLN* 4.3 30.1 - - - +
591G GLN* 5.9 2.5 - - + +
592G GLN* 5.8 6.7 - - - +
595G ASP* 3.8 20.9 - - + +
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Residues in contact with SER 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189G ARG* 4.7 11.4 - - - -
190G ASN 3.0 12.1 - - - -
191G PHE* 3.4 21.8 - - - -
212G LYS* 1.3 73.2 - - - +
214G LEU* 1.3 60.1 + - - +
215G ASP* 3.0 21.9 + - - +
216G PHE* 5.7 1.8 - - - -
227G LYS* 3.3 21.8 - - - -
591G GLN* 3.6 29.2 + - - +
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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