Contacts of the strand formed by residues 209 - 216 (chain B) in PDB entry 1GGT
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 ILE 209 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B GLU* 5.2 1.0 - - - +
207B ASN* 2.8 29.9 + - - +
208B ASP* 1.3 78.3 - - - +
210B GLY* 1.3 69.5 + - - +
211B VAL* 5.7 0.2 - - + -
224B SER* 4.3 3.1 - - - +
225B TRP 3.6 10.5 - - - +
226B SER* 5.0 0.7 - - - -
227B TYR* 3.7 7.9 - - - -
326B ARG* 4.5 0.5 + - - -
467B LYS* 4.6 5.3 - - - +
472B ASP* 5.9 0.2 - - - +
670B PRO* 3.5 30.1 - - + -
702B HIS* 4.8 4.0 - - + +
703B ARG* 3.8 25.8 - - - +
704B LYS* 4.0 55.4 - - + +
706B ILE* 5.2 2.0 - - + -
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Residues in contact with GLY 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLU* 5.9 0.2 - - - -
209B ILE* 1.3 77.6 - - - +
211B VAL* 1.3 66.3 + - - +
224B SER* 3.4 7.1 + - - -
225B TRP* 2.8 36.0 + - - -
227B TYR* 3.4 22.7 - - - -
467B LYS* 4.1 9.9 - - - -
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Residues in contact with VAL 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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209B ILE* 5.7 0.4 - - + -
210B GLY* 1.3 78.7 - - - +
212B ILE* 1.3 65.1 + - - +
213B PHE* 3.4 29.7 + - + -
222B THR* 5.0 5.6 - - - -
223B ARG 3.4 11.9 - - - +
224B SER* 4.0 13.9 - - - +
227B TYR* 4.5 5.4 + - - -
334B ILE* 5.3 6.1 - - - +
467B LYS* 3.3 44.6 + - + +
472B ASP* 4.0 29.8 - - + +
704B LYS* 5.1 0.7 - - - -
720B GLU* 5.6 0.9 - - - +
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Residues in contact with ILE 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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211B VAL* 1.3 74.9 - - - +
213B PHE* 1.3 66.0 + - - +
214B TYR* 3.7 11.9 - - + -
222B THR* 3.4 2.7 - - - -
223B ARG* 2.9 40.3 + - - +
225B TRP* 3.4 49.1 - - + -
227B TYR* 5.3 0.7 - - - +
315B TRP* 3.8 44.4 - - + +
334B ILE* 4.3 25.8 - - + -
336B THR* 5.2 0.9 - - - +
374B CYS* 4.3 11.2 - - - -
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Residues in contact with PHE 213 (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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211B VAL* 3.4 32.3 - - + -
212B ILE* 1.3 74.6 - - - +
214B TYR* 1.3 58.9 - - - +
220B ILE* 3.8 14.4 - - + -
221B LYS 3.4 2.5 - - - -
222B THR* 3.2 28.9 - - + -
336B THR* 2.9 36.5 + - - +
338B TYR* 3.5 6.5 - - - +
372B TYR* 4.3 1.6 - - - -
374B CYS* 4.7 0.2 - - - -
465B VAL* 3.7 26.7 - - + -
466B THR* 3.8 4.9 - - - -
467B LYS 3.5 21.8 - - - -
472B ASP 4.1 2.5 - - - -
473B GLY 3.5 9.9 - - - -
474B MET* 3.2 43.7 - - + -
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Residues in contact with TYR 214 (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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212B ILE* 3.7 17.3 - - + -
213B PHE* 1.3 73.5 - - - +
215B GLY* 1.3 71.6 + - - +
220B ILE* 3.6 1.2 - - - -
221B LYS* 2.8 50.3 + - + +
222B THR 3.6 30.2 + - - -
223B ARG* 3.8 11.0 - - + -
338B TYR* 2.6 20.7 + - - -
372B TYR* 3.6 32.8 - - + +
601B GLN* 4.5 4.7 - - + -
629B ILE* 6.1 2.3 - - + +
716B HIS* 3.5 36.9 + + - -
718B TYR* 3.7 21.0 - + - -
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Residues in contact with GLY 215 (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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214B TYR* 1.3 86.1 - - - +
216B GLU* 1.3 64.6 + - - +
219B ASP 4.0 8.1 - - - -
221B LYS* 4.0 9.4 - - - -
338B TYR* 3.9 2.6 - - - -
371B ASN* 3.4 22.0 + - - +
372B TYR* 3.6 12.2 - - - -
626B VAL* 4.1 17.8 - - - +
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Residues in contact with GLU 216 (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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214B TYR 3.7 1.0 + - - -
215B GLY* 1.3 76.4 - - - +
217B VAL* 1.3 59.4 + - + +
218B ASN* 3.2 37.5 + - - +
219B ASP* 2.7 61.2 + - - +
220B ILE* 3.0 3.1 + - - -
338B TYR* 3.8 11.0 - - - -
339B PHE* 5.4 7.7 - - + -
371B ASN* 4.5 14.6 - - + +
526B ASN* 5.9 0.5 - - - +
624B SER* 3.2 29.8 - - - +
625B THR* 3.8 20.9 - - - +
626B VAL* 4.2 11.0 + - + +
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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