Contacts of the strand formed by residues 374 - 379 (chain A) in PDB entry 5EQX
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 VAL 374 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A ILE* 3.2 36.6 - - + -
371A ALA* 4.0 13.5 - - + +
372A SER 3.6 3.4 - - - +
373A ASN* 1.3 82.9 - - - +
375A LYS* 1.3 61.9 + - - +
376A TYR* 3.3 42.5 - - + +
390A SER 3.9 8.3 - - - +
391A LYS* 5.2 4.0 - - - +
419A ALA* 4.9 2.7 - - + -
420A ILE 3.1 18.8 - - - +
421A ASP* 4.2 3.1 - - - -
422A GLU* 3.5 12.0 - - - +
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Residues in contact with LYS 375 (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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374A VAL* 1.3 73.2 - - - +
376A TYR* 1.3 64.6 + - - +
377A VAL* 3.9 19.2 + - + +
390A SER* 3.8 22.5 - - - +
418A LEU 3.5 1.7 - - - +
419A ALA* 3.5 3.1 - - - -
420A ILE* 2.8 53.8 + - + +
422A GLU* 3.8 17.0 + - - +
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Residues in contact with TYR 376 (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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334A PHE* 4.4 5.2 - + - -
360A TYR 4.1 2.9 - - - -
361A GLN* 3.2 22.1 + - + +
362A ALA* 2.9 41.1 + - + +
371A ALA* 4.1 6.2 + - - +
374A VAL* 3.3 29.1 - - + +
375A LYS* 1.3 69.5 - - - +
377A VAL* 1.3 68.9 + - - +
388A ILE* 3.8 20.2 - - + +
389A ASP 3.3 17.7 - - - +
390A SER* 3.3 27.6 + - - -
391A LYS 3.8 25.8 - - - -
393A ALA* 3.7 19.1 - - + -
418A LEU 3.4 3.6 - - - -
419A ALA* 3.9 21.1 - - + -
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Residues in contact with VAL 377 (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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375A LYS* 4.3 22.9 - - - +
376A TYR* 1.3 83.0 - - - +
378A MET* 1.3 73.1 + - - +
388A ILE* 3.5 11.5 - - - +
390A SER* 5.6 0.2 - - - -
417A VAL* 3.5 4.3 - - - +
418A LEU* 2.6 50.7 + - + +
420A ILE* 4.2 20.9 - - + -
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Residues in contact with MET 378 (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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377A VAL* 1.3 89.9 - - - +
379A GLY* 1.3 58.2 + - - +
381A ASN* 4.2 19.5 - - + +
386A LEU* 3.7 45.5 - - + +
387A MET* 4.1 8.5 - - - -
388A ILE* 3.6 35.3 - - + +
395A ILE* 4.3 11.2 - - + -
415A ALA* 4.6 4.3 - - + -
416A GLU 3.8 11.9 - - - +
417A VAL* 3.6 26.5 - - + -
418A LEU* 3.4 4.3 - - - +
432A VAL* 5.4 0.9 - - + -
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Residues in contact with GLY 379 (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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378A MET* 1.3 76.4 - - - +
380A ARG* 1.3 69.4 + - - -
381A ASN* 3.1 4.0 + - - -
416A GLU* 2.8 40.3 + - - +
418A LEU* 3.3 18.7 - - - +
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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