Contacts of the strand formed by residues 565 - 570 (chain C) in PDB entry 3EI4
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 SER 565 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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558C ILE 3.7 1.0 - - - +
559C GLY* 3.2 3.5 - - - -
560C LEU* 2.8 31.3 + - - +
563C ASP* 2.6 22.8 + - - -
564C ILE* 1.3 75.5 - - - +
566C ALA* 1.3 60.9 + - - +
567C ARG* 2.9 34.4 + - - -
579C LYS* 4.8 0.4 - - - -
580C GLU 3.3 19.1 - - - -
581C MET* 4.5 8.1 - - - -
582C LEU* 4.4 6.0 - - - +
588C PRO* 4.7 1.1 - - - +
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Residues in contact with ALA 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558C ILE 3.4 5.2 - - - -
559C GLY* 4.3 0.9 - - - -
565C SER* 1.3 71.7 - - - +
567C ARG* 1.3 59.6 + - - +
568C ILE* 5.7 0.9 - - - -
580C GLU* 3.1 31.8 + - + +
582C LEU* 4.1 13.1 - - + +
591C ILE* 3.9 14.1 - - + -
602C LEU* 4.6 7.6 - - + -
604C CYS* 3.8 31.0 - - + -
614C PHE* 5.3 2.0 - - + -
623C LEU* 4.1 8.2 - - - +
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Residues in contact with ARG 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534C MET* 3.9 12.2 - - + +
535C GLU* 3.7 27.1 + - - +
557C ALA* 3.8 0.9 - - - -
558C ILE* 2.9 52.2 + - + +
560C LEU* 3.4 25.6 - - + +
563C ASP* 3.8 12.5 + - - -
565C SER* 2.9 30.4 + - - +
566C ALA* 1.3 74.1 - - - +
568C ILE* 1.3 64.3 + - - +
569C LEU* 4.7 1.3 - - + -
576C LEU* 3.6 30.3 - - + +
578C HIS 3.3 14.1 - - - +
579C LYS* 3.3 36.3 - - - +
581C MET* 5.6 0.8 - - - -
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Residues in contact with ILE 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555C LEU* 3.8 37.2 - - + -
556C CYS 3.7 1.8 - - - +
557C ALA* 3.8 27.1 - - + +
566C ALA 5.5 0.2 - - - +
567C ARG* 1.3 75.8 - - - +
569C LEU* 1.3 65.4 + - - +
576C LEU* 3.7 4.2 - - - +
577C LEU* 2.9 26.0 + - + -
578C HIS* 3.0 13.1 + - + +
591C ILE* 5.6 0.4 - - + -
593C MET* 4.8 1.1 - - - -
602C LEU* 4.1 17.0 - - + -
616C LEU* 3.7 28.3 - - + -
621C GLY* 4.1 21.1 - - - +
623C LEU* 4.3 13.5 - - + -
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Residues in contact with LEU 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516C LEU* 4.0 14.4 - - + -
534C MET* 4.2 18.4 - - + -
555C LEU* 3.4 3.3 - - - +
556C CYS* 2.7 49.9 + - + +
558C ILE* 3.6 28.0 - - + -
567C ARG* 4.7 1.6 - - + -
568C ILE* 1.3 79.8 - - - +
570C LYS* 1.3 62.8 + - - +
571C LEU 3.2 0.2 + - - -
574C PHE* 3.7 42.0 - - + +
575C GLU 3.7 2.2 - - - -
576C LEU* 3.7 34.8 - - + -
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Residues in contact with LYS 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554C PRO* 3.8 28.1 + - - +
555C LEU* 4.7 2.7 - - + +
569C LEU* 1.3 67.6 - - - +
571C LEU* 1.3 56.2 + - - +
572C PRO* 4.0 21.3 - - + +
573C SER* 3.7 14.8 - - - +
574C PHE* 2.6 36.4 + - - -
575C GLU* 2.8 31.4 + - + +
577C LEU* 3.7 29.0 - - + +
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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