Contacts of the strand formed by residues 211 - 216 (chain G) in PDB entry 3GUT
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 GLU 211 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200G ASN* 4.6 5.9 + - - +
201G ARG* 4.3 9.9 + - - +
210G ASP* 1.3 70.9 - - - +
212G ILE* 1.3 72.7 + - - +
213G PHE* 3.5 27.9 + - + -
251G VAL* 3.9 17.7 - - + +
252G PHE 3.4 5.2 - - - +
253G ARG* 3.3 40.0 + - - +
552H ARG* 3.6 20.9 + - - -
553H MET 5.4 0.7 - - - +
554H ASP* 4.9 6.8 - - + +
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Residues in contact with ILE 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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199G VAL* 3.9 26.7 - - + -
200G ASN* 3.8 1.3 - - - +
201G ARG* 3.5 40.6 - - + +
210G ASP* 3.7 15.5 - - + +
211G GLU* 1.3 87.0 - - - +
213G PHE* 1.3 67.6 + - - +
214G LEU* 4.9 0.4 - - + -
250G ILE 3.4 0.2 - - - +
251G VAL* 3.3 5.4 - - - -
252G PHE* 2.6 68.7 + - + +
254G THR* 3.9 19.3 - - + -
270G MET* 5.4 2.0 - - - -
286G PHE* 4.7 4.7 - - + -
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Residues in contact with PHE 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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199G VAL* 3.4 4.9 - - - -
200G ASN* 2.7 43.9 + - - +
211G GLU* 3.5 27.4 - - + -
212G ILE* 1.3 76.3 - - - +
214G LEU* 1.3 60.6 + - - +
215G LEU* 5.7 0.9 - - + -
250G ILE 3.9 2.5 - - - -
251G VAL* 3.6 23.1 - - + -
552H ARG* 3.6 25.6 - - + -
553H MET* 3.6 3.6 - - - -
554H ASP* 3.0 44.2 - - + -
567H TYR* 3.3 39.6 - + + -
568H LEU 4.7 0.4 - - - -
569H LEU* 4.4 17.0 - - + -
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Residues in contact with LEU 214 (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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196G ILE* 4.0 22.2 - - + -
198G ARG 3.9 3.6 - - - -
199G VAL* 4.1 11.9 - - + -
212G ILE* 4.9 0.2 - - + -
213G PHE* 1.3 75.2 - - - +
215G LEU* 1.3 67.1 + - - +
216G CYS* 3.4 28.7 - - + -
226G VAL* 4.8 6.3 - - + -
249G ALA* 3.0 4.5 - - - +
250G ILE* 2.7 57.0 + - + +
251G VAL* 5.3 0.2 - - - +
252G PHE* 4.0 25.8 - - + -
270G MET* 5.6 4.3 - - + -
272G LEU* 3.8 26.9 - - + -
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Residues in contact with LEU 215 (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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196G ILE* 3.9 0.3 - - - +
197G CYS 3.0 20.3 + - - -
198G ARG* 3.4 22.5 + - + +
213G PHE* 5.2 1.1 - - + -
214G LEU* 1.3 84.3 - - - +
216G CYS* 1.3 60.4 + - - +
248G VAL 3.5 3.8 - - - +
249G ALA* 3.6 22.0 - - + -
567H TYR* 3.7 33.9 - - + -
569H LEU* 4.4 4.0 - - + -
604H HIS* 3.2 39.5 - - + +
608H ALA* 4.2 14.6 - - + -
610H VAL* 3.8 20.2 - - + -
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Residues in contact with CYS 216 (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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195G LYS 3.3 17.3 - - - +
196G ILE* 4.4 0.2 - - - -
197G CYS* 4.1 4.9 - - - -
214G LEU* 3.4 25.6 - - + -
215G LEU* 1.3 72.6 - - - +
217G ASP* 1.3 73.2 + - - +
219G VAL* 4.8 7.9 - - + -
248G VAL* 3.1 32.4 + - - +
249G ALA 3.8 2.9 - - - -
250G ILE* 4.1 11.7 - - - -
272G LEU* 4.3 9.2 - - + -
604H HIS* 2.7 29.9 + - - -
605H ARG* 4.3 2.8 - - - +
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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