Contacts of the strand formed by residues 218 - 224 (chain B) in PDB entry 6GR2
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 218 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B LEU* 3.6 27.8 - - + -
215B ASP* 2.8 30.2 + - + +
216B PRO* 4.3 3.1 - - - +
217B LYS* 1.3 79.8 - - - +
219B ALA* 1.3 63.8 + - - +
220B VAL* 5.5 2.5 - - + -
295B LEU* 5.1 0.4 - - + -
300B TYR* 3.4 40.4 - - + +
339B TYR* 3.7 12.8 - - + -
355B LEU* 3.1 37.9 - - + -
356B LEU 3.5 14.1 - - - +
358B ALA* 4.4 2.0 - - - +
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Residues in contact with ALA 219 (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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218B LEU* 1.3 78.0 - - - +
220B VAL* 1.3 66.6 + - - +
355B LEU* 3.6 3.6 - - - -
356B LEU* 2.9 51.7 + - + +
358B ALA* 3.8 21.3 - - + +
361B ALA* 5.0 1.6 - - + -
380B LEU* 4.8 11.7 - - + -
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Residues in contact with VAL 220 (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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38B VAL* 4.8 0.9 - - + -
40B LEU* 4.5 10.5 - - + -
55B MET* 3.7 31.6 - - + -
213B LEU* 4.9 10.5 - - + -
218B LEU* 5.5 4.0 - - + -
219B ALA* 1.3 76.5 - - - +
221B LEU* 1.3 60.6 + - - +
222B ILE* 3.9 9.4 + - + +
353B VAL* 3.9 26.2 - - + -
354B THR 3.5 3.8 - - - +
355B LEU* 4.9 14.6 - - + -
356B LEU* 4.5 0.2 - - - -
379B TYR 3.7 0.9 - - - +
380B LEU* 3.9 5.1 - - - +
381B SER 3.4 38.4 + - - +
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Residues in contact with LEU 221 (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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220B VAL* 1.3 72.7 - - - +
222B ILE* 1.3 64.3 + - - +
223B THR* 3.9 17.2 + - - +
352B THR 3.5 2.4 - - - +
353B VAL* 3.6 0.5 - - - -
354B THR* 2.7 49.8 + - + +
356B LEU* 3.8 19.2 - - + +
361B ALA* 5.5 0.9 - - + -
364B ALA* 4.5 13.7 - - + -
365B MET* 3.7 31.0 - - + -
368B ILE* 4.2 19.3 - - + -
378B PHE* 4.2 11.7 - - + -
379B TYR 3.8 3.8 - - - +
380B LEU* 3.3 27.6 - - + -
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Residues in contact with ILE 222 (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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38B VAL* 3.9 18.8 - - + -
57B LEU* 3.1 47.8 - - + -
139B LEU* 4.1 12.1 - - + -
220B VAL* 4.6 11.2 - - + +
221B LEU* 1.3 75.7 - - - +
223B THR* 1.3 63.0 + - - +
351B CYS* 3.8 30.5 - - + -
352B THR 3.3 5.6 - - - +
353B VAL* 5.0 0.9 - - + -
377B THR 3.7 0.2 - - - +
378B PHE* 3.2 6.8 - - - +
379B TYR* 2.8 58.1 + - + +
381B SER* 4.6 4.7 - - - -
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Residues in contact with THR 223 (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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221B LEU* 3.9 12.3 + - - +
222B ILE* 1.3 72.6 - - - +
224B ASN* 1.3 61.9 - - - +
225B SER 3.6 1.0 + - - -
328B LEU* 3.7 34.0 - - + +
351B CYS* 3.1 5.2 - - - -
352B THR* 2.7 49.5 + - - -
354B THR* 5.0 2.3 + - - -
368B ILE* 4.2 8.1 - - + +
376B ALA* 4.1 8.1 - - + -
377B THR 3.3 4.7 - - - +
378B PHE* 3.3 34.4 - - + -
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Residues in contact with ASN 224 (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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134B PRO* 4.1 29.1 - - - +
137B GLY* 4.3 9.0 - - - -
222B ILE 4.1 0.8 + - - -
223B THR* 1.3 72.1 - - - +
225B SER* 1.3 63.6 + - - +
226B ASN* 2.6 47.0 + - - +
227B VAL 4.4 1.6 + - - +
350B GLY* 3.6 9.2 - - - +
351B CYS* 3.4 20.5 - - - -
376B ALA* 3.3 7.3 - - - +
377B THR* 2.6 44.5 + - - +
379B TYR* 4.3 8.9 + - + -
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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