Contacts of the strand formed by residues 603 - 611 (chain A) in PDB entry 5H65
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 603 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A ARG* 3.4 4.8 - - - -
364A ALA 2.8 38.2 + - - +
366A LEU* 5.3 8.5 - - + +
546A PHE* 4.4 21.8 - - + -
548A LEU* 4.1 23.3 - - + -
565A PHE* 4.3 9.2 - - + -
590A PHE* 3.9 22.7 - - + -
601A PRO 3.9 0.8 + - - -
602A TRP* 1.3 71.4 - - - +
604A GLU* 1.3 70.7 + - - +
605A CYS* 3.8 20.9 + - + -
624A ILE* 4.9 1.6 - - + -
627A THR* 4.9 0.2 - - + -
629A VAL* 3.5 31.6 - - + -
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Residues in contact with GLU 604 (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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345A ARG* 3.1 27.1 + - - -
361A ARG* 2.7 41.3 + - - +
362A ILE 3.7 1.1 - - - -
363A ARG* 3.0 33.7 + - - +
602A TRP* 3.9 6.6 + - + +
603A LEU* 1.3 75.4 - - - +
605A CYS* 1.3 64.3 + - - +
627A THR* 3.6 11.8 - - - +
628A THR 5.2 2.4 - - - +
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Residues in contact with CYS 605 (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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361A ARG* 3.5 9.9 - - - +
362A ILE* 2.8 63.9 + - - +
548A LEU* 4.8 3.8 - - - -
603A LEU* 4.3 21.8 - - + -
604A GLU* 1.3 75.9 - - - +
606A PHE* 1.3 70.1 - - - +
607A ILE* 4.2 6.1 - - - -
624A ILE* 4.5 11.0 - - + -
627A THR* 3.4 23.3 - - + +
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Residues in contact with PHE 606 (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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359A GLN* 5.9 0.7 - - + -
360A TYR 3.2 14.8 - - - -
361A ARG* 3.8 35.9 - - + -
605A CYS* 1.3 78.4 - - - +
607A ILE* 1.3 68.5 + - - +
624A ILE* 3.4 4.9 - - - +
625A PHE* 3.3 53.6 + + + +
626A ASP* 3.4 28.5 - - + -
627A THR* 3.0 7.6 + - - -
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Residues in contact with ILE 607 (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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351A ILE* 4.0 14.6 - - + -
359A GLN* 3.4 1.2 - - - -
360A TYR* 2.8 47.5 + - + +
362A ILE* 4.0 31.0 - - + -
548A LEU* 4.5 0.9 - - + -
555A LEU* 3.9 33.4 - - + -
557A ALA* 4.3 10.3 - - + -
605A CYS* 4.2 1.8 - - - -
606A PHE* 1.3 81.6 - - - +
608A LYS* 1.3 59.2 + - - +
622A TYR* 4.2 11.2 - - + -
623A GLN 3.3 13.2 - - - +
624A ILE* 3.9 20.4 - - + -
625A PHE* 3.5 5.6 - - - -
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Residues in contact with LYS 608 (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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358A GLN 3.3 9.4 - - - +
359A GLN* 4.0 11.2 - - + +
607A ILE* 1.3 73.9 - - - +
609A SER* 1.3 62.6 + - - +
610A TYR* 3.8 6.1 - - + -
622A TYR* 3.3 6.4 - - - -
623A GLN* 2.9 55.8 + - + +
625A PHE* 3.6 29.6 - - + +
314B CYS* 3.3 45.3 + - - -
316B SER* 5.7 5.7 - - - +
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Residues in contact with SER 609 (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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355A LYS 4.4 1.4 + - - -
356A ALA* 3.4 10.9 - - - +
357A PRO* 3.4 16.3 - - - +
358A GLN* 2.7 42.1 + - - +
360A TYR* 4.1 8.4 + - - -
607A ILE 4.2 0.4 + - - -
608A LYS* 1.3 78.4 - - - +
610A TYR* 1.3 64.3 + - - +
620A ILE* 3.8 10.8 - - - -
621A CYS 3.4 5.6 - - - -
622A TYR* 3.6 26.4 - - - -
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Residues in contact with TYR 610 (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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356A ALA* 3.6 10.5 - - - +
357A PRO* 4.3 7.9 - - + -
558A TYR* 3.4 19.4 - - - -
608A LYS* 3.8 8.7 - - + -
609A SER* 1.3 79.3 - - - +
611A ASN* 1.3 71.9 + - - +
612A VAL* 5.0 5.2 - - - -
620A ILE* 3.6 3.8 - - - -
621A CYS* 3.0 52.9 + - + +
622A TYR 3.8 0.9 - - - -
623A GLN* 3.7 19.3 + - + -
311B SER 5.3 0.7 - - - -
312B MET 2.6 30.9 + - - -
313B LEU* 3.5 8.9 - - - -
314B CYS* 3.6 44.4 + - + -
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Residues in contact with ASN 611 (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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356A ALA* 3.3 39.2 + - - +
357A PRO* 4.1 6.9 - - - +
610A TYR* 1.3 79.8 - - - +
612A VAL* 1.3 65.2 + - - +
613A THR 3.9 15.5 - - - +
619A GLN 4.3 4.9 - - - +
620A ILE* 3.9 11.8 - - - +
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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