Contacts of the strand formed by residues 353 - 360 (chain A) in PDB entry 2GTI
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 LYS 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ASN* 3.7 43.0 + - + +
76A ASN* 5.5 7.6 + - - +
191A GLU* 4.0 3.8 - - - +
349A ASN* 3.4 6.6 + - - +
350A VAL 2.7 32.2 + - - +
352A PHE* 1.3 81.4 - - - +
354A ASP* 1.3 72.5 + - - +
355A PHE* 3.3 40.5 - - + -
369A PHE* 5.5 7.0 - - - -
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Residues in contact with ASP 354 (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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191A GLU* 3.2 45.2 + - - +
192A PRO 4.5 6.8 - - - +
194A HIS 5.8 1.7 + - - -
217A ALA* 4.5 9.5 - - - +
347A ASN* 4.2 26.5 - - - +
348A VAL 3.8 2.9 - - - -
349A ASN* 2.7 37.0 + - - +
353A LYS* 1.3 83.7 + - - +
355A PHE* 1.3 61.3 + - - +
356A GLN 4.3 0.5 + - - -
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Residues in contact with PHE 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASN* 3.9 7.6 - - - -
302A SER* 3.8 26.7 - - - -
303A ILE* 3.8 24.9 - - + -
347A ASN* 4.1 2.2 - - - -
348A VAL 2.9 34.0 + - - +
350A VAL* 3.4 33.0 - - + -
353A LYS* 3.3 52.0 - - + -
354A ASP* 1.3 75.0 - - - +
356A GLN* 1.3 62.7 + - - +
357A PHE* 3.5 19.7 - - + -
366A VAL* 5.0 4.3 - - + -
367A MSE 5.7 0.9 - - - -
369A PHE* 4.4 21.3 - - + -
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Residues in contact with GLN 356 (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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194A HIS 5.1 7.5 + - - -
345A VAL* 3.9 17.5 - - + +
346A VAL 3.4 6.1 - - - +
347A ASN* 3.7 16.0 + - - +
354A ASP 4.2 0.8 + - - -
355A PHE* 1.3 72.0 - - - +
357A PHE* 1.3 60.5 + - - +
366A VAL* 4.7 0.9 - - - +
367A MSE 3.2 56.6 + - + +
368A THR 5.2 3.8 - - - +
369A PHE* 5.9 7.2 - - + +
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Residues in contact with PHE 357 (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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303A ILE* 5.4 0.2 - - + -
323A ILE* 4.1 30.5 - - + -
325A LEU* 5.1 8.5 - - + -
330A PHE* 5.3 8.7 - + - -
333A ILE* 6.2 2.9 - - + -
345A VAL* 3.5 1.6 - - - -
346A VAL* 2.7 51.6 + - + +
348A VAL* 3.7 23.6 - - + -
350A VAL* 5.0 4.9 - - + -
355A PHE* 3.5 32.5 - - + -
356A GLN* 1.3 75.6 - - - +
358A MSE 1.3 61.8 + - - +
359A LEU 3.4 0.2 + - - -
364A GLU* 3.6 21.1 - - + +
365A LYS* 3.4 5.6 - - - +
366A VAL* 3.8 35.9 - - + -
367A MSE 3.4 1.8 - - - -
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Residues in contact with MSE 358 (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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343A SER* 4.1 12.8 - - - +
344A LYS 3.4 22.4 - - - +
345A VAL* 5.7 1.8 - - + -
357A PHE* 1.3 71.2 - - - +
359A LEU* 1.3 61.0 + - - +
360A TRP* 3.5 34.3 - - + +
363A GLU 3.5 1.9 - - - +
364A GLU* 3.1 4.0 - - - +
365A LYS* 2.8 66.0 + - - +
367A MSE 3.3 35.4 - - + +
508A SO4 5.1 6.3 - - - +
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Residues in contact with LEU 359 (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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337A LEU* 3.3 35.7 - - + -
339A LEU* 3.7 31.9 - - + -
342A VAL 2.9 17.7 - - - +
344A LYS* 3.0 41.5 + - + +
346A VAL* 4.5 3.1 - - + -
357A PHE 3.4 4.9 + - - +
358A MSE 1.3 78.4 - - - +
360A TRP* 1.3 69.4 + - - +
363A GLU 3.1 20.0 - - - +
364A GLU* 3.3 22.7 - - + +
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Residues in contact with TRP 360 (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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342A VAL* 3.9 21.3 - - + -
343A SER* 3.8 30.7 - - - -
358A MSE 3.5 35.5 - - + +
359A LEU* 1.3 83.1 - - - +
361A CYS* 1.3 55.1 + - - +
362A ASN* 2.4 26.3 + - + +
363A GLU* 2.9 31.8 + - + +
365A LYS* 4.5 11.1 - - - +
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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