Contacts of the strand formed by residues 352 - 358 (chain A) in PDB entry 6FD3
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 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A GLN* 5.4 3.5 - - - +
314A MET 3.3 5.8 + - - +
315A ASN* 3.4 44.4 + - - +
347A TYR 4.0 0.3 - - - +
348A LEU* 3.1 4.4 - - - +
349A VAL* 2.9 49.8 + - + +
350A GLY 3.5 0.2 - - - -
351A ASP* 1.3 86.2 - - + +
353A LEU* 1.3 60.5 + - - +
354A TRP* 4.2 14.1 + - + +
604A EDO 5.1 1.6 - - - -
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Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 4.4 11.2 - - + -
274A VAL* 3.6 24.9 - - + -
312A LYS 3.5 1.0 - - - +
313A GLN* 3.5 2.1 - - - -
314A MET* 2.7 57.1 + - + +
316A LEU* 3.9 16.8 - - + +
325A ILE* 3.4 33.4 - - + -
329A ILE* 3.8 20.0 - - + -
347A TYR 3.4 14.8 - - - +
348A LEU* 3.9 15.3 - - + -
351A ASP 4.1 0.8 + - - -
352A GLU* 1.3 73.0 - - - +
354A TRP* 1.3 66.0 + - - +
355A VAL* 4.4 0.4 - - + -
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Residues in contact with TRP 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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279A PRO* 3.3 43.7 - - + -
280A LYS* 3.7 39.9 - - + +
286A PHE* 3.5 29.6 - + - -
311A ILE* 3.5 23.3 - - + -
312A LYS 3.1 4.7 - - - +
313A GLN* 3.0 44.1 - - + +
346A SER* 3.1 7.0 - - - -
347A TYR* 2.9 40.1 + - + +
349A VAL* 4.6 7.6 - - + +
352A GLU* 4.2 18.2 + - + +
353A LEU* 1.3 87.2 - - - +
355A VAL* 1.3 62.1 + - - +
356A VAL* 4.2 1.6 - - + -
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Residues in contact with VAL 355 (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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310A ALA 3.8 0.9 - - - +
311A ILE* 3.4 3.3 - - - -
312A LYS* 2.8 41.5 + - + +
314A MET* 3.8 22.2 - - + -
328A GLU* 5.6 5.2 - - + +
329A ILE* 3.9 26.7 - - + -
332A MET* 4.2 19.7 - - + -
343A TYR* 4.2 15.5 - - + -
345A ASP 3.6 8.1 - - - +
346A SER* 4.2 3.8 - - - -
353A LEU* 4.4 2.5 - - + -
354A TRP* 1.3 78.6 - - - +
356A VAL* 1.3 71.6 + - - +
357A MET* 3.9 7.8 - - + +
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Residues in contact with VAL 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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283A TYR* 3.7 33.2 - - + +
309A VAL* 3.9 30.1 - - + -
310A ALA 3.5 4.3 - - - +
311A ILE* 4.3 13.9 - - + -
343A TYR* 4.2 0.3 - - - -
344A LEU* 2.9 33.4 + - + -
345A ASP* 2.8 25.2 + - + +
347A TYR* 4.0 24.7 - - + -
354A TRP* 5.3 1.8 - - + -
355A VAL* 1.3 78.4 - - - +
357A MET* 1.3 65.2 + - - +
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Residues in contact with MET 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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297A VAL* 5.2 0.9 - - + -
309A VAL* 3.6 7.4 - - - +
310A ALA* 2.9 37.5 + - + +
311A ILE 4.9 0.2 - - - -
312A LYS* 3.8 36.6 - - + +
332A MET* 4.3 13.2 - - + +
341A VAL* 3.9 17.3 - - + -
342A ASN 3.3 16.8 - - - +
344A LEU* 3.7 8.7 - - - +
355A VAL* 3.9 19.3 - - + +
356A VAL* 1.3 75.8 - - - +
358A GLU* 1.3 69.4 + - - +
419A THR* 4.0 15.3 - - - +
603A ADP 3.6 27.6 - - + +
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Residues in contact with GLU 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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307A GLN* 5.6 4.7 - - - +
308A GLU 5.6 0.7 - - - -
309A VAL* 5.1 1.3 - - - +
341A VAL* 3.6 13.6 - - + -
342A ASN* 2.8 44.8 + - + +
344A LEU* 3.9 9.2 - - + +
357A MET* 1.3 74.8 - - - +
359A TYR* 1.3 55.1 + - - +
360A LEU* 4.1 17.8 - - + +
417A LYS* 2.8 40.7 + - - +
603A ADP 2.8 30.7 + - - -
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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