Contacts of the strand formed by residues 601 - 606 (chain A) in PDB entry 1YC0
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 PRO 601 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419A HIS* 6.4 0.2 - - + -
421A TRP* 4.2 24.0 - - + +
422A LEU* 3.3 22.0 - - + -
434A GLY 4.0 0.2 - - - +
435A SER* 3.1 26.9 - - - +
520A ILE* 4.5 7.2 - - + -
536A GLN 3.6 8.0 - - - +
537A ILE* 3.8 12.5 - - - +
538A ALA* 4.3 6.6 + - + +
600A GLY* 1.3 86.5 - - - +
602A LEU* 1.3 62.6 + - - +
603A ALA* 3.6 7.3 + - + +
612A LEU* 3.4 15.3 - - + -
614A GLY 3.6 5.8 - - - +
615A ILE* 4.7 0.4 - - + -
616A ILE* 4.2 3.7 - - - +
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Residues in contact with LEU 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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535A CYS* 4.0 15.9 - - + -
536A GLN 4.0 2.0 - - - +
537A ILE* 3.5 23.1 - - + -
559A VAL* 3.6 20.4 - - + -
561A LEU* 3.9 15.7 - - + -
582A LEU* 3.9 28.3 - - + -
584A ALA* 4.0 4.7 - - + -
600A GLY 3.9 0.2 + - - -
601A PRO* 1.3 71.4 - - - +
603A ALA* 1.3 59.8 + - - +
604A CYS* 3.7 1.9 + - - -
612A LEU 4.2 0.3 - - - -
613A TYR* 3.3 27.7 + - + +
614A GLY* 2.9 23.8 + - - +
616A ILE 4.8 0.2 - - - +
631A TYR* 3.6 29.6 - - + -
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Residues in contact with ALA 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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397A ARG* 5.8 1.3 - - - +
419A HIS* 6.4 0.2 - - - +
421A TRP* 4.7 9.6 - - + +
520A ILE* 3.7 26.7 - - + -
535A CYS* 3.2 2.1 - - - +
536A GLN* 2.8 48.5 + - + +
601A PRO* 3.5 5.3 - - + -
602A LEU* 1.3 72.9 - - - +
604A CYS* 1.3 61.0 - - - +
605A GLU 4.4 0.3 + - - -
610A ALA* 4.6 10.3 - - + -
611A TYR 3.3 4.9 - - - +
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Residues in contact with CYS 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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529A PHE* 3.7 30.0 - - + -
533A HIS* 4.3 0.7 - - + -
535A CYS* 2.0 48.9 - - - +
561A LEU* 4.0 1.1 - - - -
602A LEU* 4.3 2.9 - - - -
603A ALA* 1.3 73.7 - - - +
605A GLU* 1.3 61.0 + - - +
610A ALA* 4.6 1.3 - - - -
611A TYR* 2.8 36.3 + - - +
613A TYR* 3.7 31.9 - - + -
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Residues in contact with GLU 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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397A ARG* 3.2 28.1 + - - -
529A PHE* 3.7 1.1 - - - -
533A HIS* 2.9 30.0 + - - -
534A LYS 5.0 4.8 + - - +
603A ALA 4.4 0.2 + - - -
604A CYS* 1.3 73.9 - - - +
606A LYS* 1.3 63.5 + - - +
608A GLY* 3.7 21.7 + - - +
609A VAL 3.2 27.1 - - - +
610A ALA* 4.2 3.1 + - - +
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Residues in contact with LYS 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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529A PHE* 3.9 22.0 - - + -
533A HIS* 5.6 1.3 - - + -
604A CYS 4.2 0.2 + - - -
605A GLU* 1.3 77.3 - - - +
607A ASN* 1.3 92.0 + - + +
609A VAL* 3.0 23.0 + - - +
611A TYR* 3.9 16.8 + - + -
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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