Contacts of the strand formed by residues 218 - 224 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A LEU* 3.5 29.8 - - + -
215A ASP* 2.7 36.0 + - + +
216A PRO* 4.3 2.6 - - - +
217A LYS* 1.3 74.5 - - - +
219A ALA* 1.3 61.4 + - - +
220A VAL* 5.4 1.6 - - + -
295A LEU* 5.1 0.4 - - + -
300A TYR* 3.5 40.6 - - + +
339A TYR* 4.0 16.6 - - + -
355A LEU* 3.5 36.8 - - + -
356A LEU 3.6 14.1 - - - +
358A ALA* 4.4 2.4 - - - +
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Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A LEU* 1.3 74.8 - - - +
220A VAL* 1.3 64.2 + - - +
221A LEU 4.0 0.4 - - - -
354A THR 3.7 0.3 - - - +
355A LEU* 3.7 6.1 - - - +
356A LEU* 2.9 54.5 + - + +
358A ALA* 3.8 14.8 - - + +
361A ALA* 4.8 1.6 - - + -
380A LEU* 4.4 16.6 - - + -
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Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A VAL* 4.9 0.4 - - + -
40A LEU* 4.6 6.7 - - + -
55A MET* 3.8 31.4 - - + -
213A LEU* 4.9 9.2 - - + -
218A LEU* 5.4 2.5 - - + -
219A ALA* 1.3 73.8 - - - +
221A LEU* 1.3 60.9 + - - +
222A ILE* 3.8 10.1 + - + +
353A VAL* 3.8 27.1 - - + -
354A THR 3.5 3.6 - - - +
355A LEU* 3.7 24.7 - - + -
379A TYR 3.6 2.1 - - - +
380A LEU* 3.9 4.9 - - - +
381A SER 3.4 38.4 + - - +
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ALA 4.0 0.8 - - - -
220A VAL* 1.3 71.8 - - - +
222A ILE* 1.3 62.7 + - - +
223A THR* 4.2 10.2 + - - +
352A THR 3.4 2.8 - - - +
353A VAL* 3.5 0.7 - - - -
354A THR* 2.7 52.9 + - - +
356A LEU* 4.1 14.4 - - + -
361A ALA* 4.8 1.6 - - + +
364A ALA* 4.0 27.6 - - + -
365A MET* 3.9 27.8 - - + -
368A ILE* 4.3 16.6 - - + -
378A PHE* 4.1 13.2 - - + -
379A TYR 4.0 6.3 - - - +
380A LEU* 3.7 25.8 - - + -
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Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A VAL* 3.9 20.0 - - + -
57A LEU* 3.3 44.6 - - + -
139A LEU* 4.1 11.4 - - + -
220A VAL* 4.3 12.3 - - + +
221A LEU* 1.3 75.4 - - - +
223A THR* 1.3 61.6 + - - +
351A CYS* 3.9 26.7 - - + -
352A THR 3.2 6.3 - - - +
353A VAL* 4.8 0.9 - - + -
377A THR 3.7 0.2 - - - +
378A PHE* 3.4 7.8 - - - +
379A TYR* 3.0 54.4 + - + +
381A SER* 4.4 9.4 - - - -
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Residues in contact with THR 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A LEU* 4.2 8.1 + - - +
222A ILE* 1.3 72.6 - - - +
224A ASN* 1.3 61.4 + - - +
225A SER 3.6 1.2 + - - -
328A LEU* 3.7 28.4 - - + +
351A CYS* 3.0 4.4 - - - -
352A THR* 2.6 56.4 + - + +
354A THR* 5.1 0.5 + - - -
368A ILE* 4.3 9.9 - - + +
376A ALA* 4.1 12.6 - - + -
377A THR 3.4 5.4 - - - +
378A PHE* 3.3 34.1 - - + -
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Residues in contact with ASN 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A PRO* 3.8 32.3 - - - +
137A GLY* 4.3 9.3 - - - -
222A ILE* 4.1 1.0 - - - +
223A THR* 1.3 72.0 - - - +
225A SER* 1.3 62.0 + - - +
226A ASN* 2.6 47.0 + - - +
227A VAL 4.4 0.9 + - - +
350A GLY* 3.5 7.8 - - - +
351A CYS* 3.6 20.5 - - - -
376A ALA* 3.6 5.4 - - - +
377A THR* 2.8 42.6 + - - +
379A TYR* 4.3 9.8 + - + -
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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