Contacts of the strand formed by residues 598 - 603 (chain A) in PDB entry 5ED1
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 PHE 598 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A PRO 4.3 2.0 - - - -
346A HIS* 3.8 46.7 - + + -
348A ARG* 3.6 48.7 - - + -
373A THR* 4.7 4.4 + - - -
374A GLY* 4.4 9.0 - - - -
375A THR 5.3 0.3 + - - -
596A PRO* 3.1 34.3 - - + +
597A ASN* 1.3 84.4 - - - +
599A SER* 1.3 63.0 + - - +
600A VAL* 4.2 7.9 - - + -
611A VAL* 3.7 17.5 - - + -
612A ILE 3.2 12.6 - - - +
613A ASN* 4.6 1.6 - - - +
614A ALA* 5.0 1.9 - - - +
4C U 4.7 15.5 - - - +
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Residues in contact with SER 599 (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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373A THR* 2.9 18.5 + - - -
374A GLY* 4.1 3.1 - - - -
393A CYS* 3.7 39.9 - - - +
398A ILE* 3.9 13.2 - - - +
598A PHE* 1.3 76.8 - - - +
600A VAL* 1.3 65.8 + - - +
601A ASN* 5.0 0.5 + - - -
610A GLU 3.7 1.4 - - - +
611A VAL* 3.7 0.6 - - - -
612A ILE* 2.9 37.6 + - - +
614A ALA* 4.7 3.1 - - - -
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Residues in contact with VAL 600 (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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335A PHE* 4.8 14.4 - - + -
338A LEU* 6.3 0.2 - - + -
339A THR* 6.1 0.2 - - + -
346A HIS* 4.0 34.8 - - + +
371A VAL* 5.4 2.5 - - + +
372A SER* 3.0 9.9 - - - -
373A THR* 3.0 44.7 + - + +
398A ILE* 4.2 0.3 - - - +
598A PHE* 4.2 7.2 - - + -
599A SER* 1.3 80.3 + - - +
601A ASN* 1.3 67.0 + - - +
602A TRP* 5.9 0.4 - - + -
609A ILE* 3.7 32.3 - - + -
610A GLU 3.4 2.7 - - - +
611A VAL* 4.1 12.8 - - + -
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Residues in contact with ASN 601 (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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371A VAL 3.4 6.5 - - - -
390A LEU* 5.3 0.6 - - - +
398A ILE* 3.7 22.4 - - + +
402A SER* 4.0 6.5 + - - +
405A ARG* 5.2 0.5 + - - -
599A SER* 5.0 0.4 + - - -
600A VAL* 1.3 79.1 - - - +
602A TRP* 1.3 64.7 + - - +
603A THR* 5.1 0.7 + - - -
609A ILE* 3.3 2.6 - - - +
610A GLU* 2.9 67.9 + - - +
612A ILE* 4.2 9.7 - - - +
626A ARG* 3.1 24.9 + - - -
627A LEU* 3.7 22.9 - - + +
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Residues in contact with TRP 602 (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 LYS* 3.7 37.9 - - + -
338A LEU* 3.5 43.8 - - + +
368A VAL* 4.0 16.8 - - + -
369A ILE 4.1 2.7 - - - -
370A SER* 3.2 9.4 - - - -
371A VAL* 3.0 42.5 + - + +
402A SER* 3.9 1.8 - - - -
600A VAL* 5.9 0.4 - - + -
601A ASN* 1.3 77.2 - - - +
603A THR* 1.3 66.0 + - - +
604A VAL* 3.4 36.8 - - + -
605A GLY 4.1 4.9 - - - -
606A ASP* 3.0 28.8 + - + -
607A SER 5.2 0.2 - - - -
608A ALA 3.5 22.2 - - - -
609A ILE* 4.3 4.0 - - + -
626A ARG* 4.0 4.7 - - - +
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Residues in contact with THR 603 (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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369A ILE 3.5 6.1 - - - +
370A SER* 4.5 0.4 - - - -
402A SER* 3.3 41.4 + - - +
405A ARG* 3.1 30.1 + - + +
406A PHE* 3.9 26.5 - - + +
409A THR* 6.0 0.4 - - - +
601A ASN* 5.3 0.7 + - - -
602A TRP* 1.3 78.4 - - - +
604A VAL* 1.3 78.2 + - - +
606A ASP* 3.0 27.7 + - - +
627A LEU* 5.0 0.5 - - - +
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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