Contacts of the strand formed by residues 611 - 615 (chain B) in PDB entry 5IYB
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 611 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367B TYR* 3.0 26.5 + - - -
371B ARG* 4.4 2.0 + - - -
380B ARG* 5.0 0.3 + - - -
565B THR* 3.6 1.5 - - - +
566B LYS* 3.4 23.1 - - + +
568B PHE* 3.1 17.0 - - + -
605B ARG* 4.2 1.1 - - - +
606B ASP* 3.0 34.8 + - + +
609B GLU* 3.9 33.0 - - + +
610B ARG* 1.3 78.3 - - - +
612B ILE* 1.3 65.8 + - - +
613B ARG* 2.8 34.6 + - - +
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Residues in contact with ILE 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565B THR* 3.9 7.0 - - + -
566B LYS 2.7 8.5 + - - -
567B ILE* 3.4 23.7 - - + +
568B PHE* 2.9 24.6 + - - +
580B PRO* 3.8 38.1 - - + +
583B LEU* 5.4 4.9 - - + -
584B MET* 4.1 21.5 - - + +
587B LEU* 5.5 3.4 - - + -
604B ILE 3.4 14.6 - - - +
605B ARG* 3.6 25.1 - - + -
611B GLU* 1.3 76.3 - - - +
613B ARG* 1.3 63.6 + - - +
614B ILE* 4.3 15.0 - - + +
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Residues in contact with ARG 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B THR* 5.5 8.0 - - - +
367B TYR* 4.0 2.0 + - - -
371B ARG* 4.0 19.0 - - - +
380B ARG* 5.0 4.8 - - - +
568B PHE* 3.6 28.4 - - + -
604B ILE* 3.1 44.2 + - + +
606B ASP* 4.4 18.8 + - + +
609B GLU* 5.8 0.2 + - - -
611B GLU* 2.8 33.7 + - - +
612B ILE* 1.3 74.6 - - - +
614B ILE* 1.3 61.8 + - - +
615B TYR* 3.4 38.3 + - + +
668B LEU* 3.9 17.8 - - + +
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Residues in contact with ILE 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541B ILE* 4.4 21.1 - - + -
545B LEU* 4.2 21.5 - - + -
567B ILE* 5.0 4.3 - - + -
568B PHE 2.9 12.7 + - - +
569B VAL* 3.4 10.0 - - + +
570B ASN 2.9 23.7 + - - -
571B GLY 4.9 0.2 + - - -
587B LEU* 4.0 27.8 - - + -
601B VAL* 4.0 18.6 - - + -
602B SER 3.2 18.6 - - - +
603B MET* 4.4 11.7 - - + -
612B ILE* 4.3 14.8 - - + +
613B ARG* 1.3 80.3 - - - +
615B TYR* 1.3 66.7 + - - +
616B THR* 5.8 0.2 - - - -
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Residues in contact with TYR 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B ASN* 4.9 2.7 - - - -
204B THR* 3.3 28.3 + - - +
392B ARG* 3.9 22.0 - - - -
570B ASN* 3.3 18.8 - - - -
571B GLY* 3.6 23.1 + - - -
600B GLU 3.6 0.9 - - - +
601B VAL* 3.6 2.9 - - - +
602B SER* 3.0 34.5 + - - +
604B ILE* 4.2 8.5 - - + -
613B ARG* 3.4 32.4 + - + -
614B ILE* 1.3 77.9 - - - +
616B THR* 1.3 61.0 + - - +
617B ASP* 3.6 17.3 - - - +
620B ARG* 3.2 16.5 + - - +
668B LEU* 3.4 32.1 - - + +
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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