Contacts of the strand formed by residues 556 - 560 (chain B) in PDB entry 3I8E
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 CYS 556 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B VAL* 5.8 1.1 - - - -
541B LEU* 5.3 9.0 - - - -
542B ASP 3.4 22.2 - - - -
543B ILE* 3.7 19.3 - - + -
553B SER* 5.6 0.4 - - - +
554B PRO 4.7 0.9 - - - +
555B LEU* 1.3 76.7 - - - +
557B ALA* 1.3 75.0 + - - +
568B ILE* 3.9 2.5 - - - +
569B LEU* 2.6 43.4 + - + +
570B LYS 4.0 15.2 - - - +
571B LEU* 4.4 17.7 - - + -
593B MET* 4.3 5.2 - - - -
616B LEU* 5.7 1.6 - - - -
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Residues in contact with ALA 557 (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 LEU* 4.7 1.2 - - - +
542B ASP* 4.0 16.1 + - - +
556B CYS* 1.3 91.1 - - - +
558B ILE* 1.3 64.2 + - - +
567B ARG 3.2 14.4 - - - +
568B ILE* 4.0 13.5 - - + -
569B LEU* 4.4 2.0 - - - +
591B ILE* 4.7 9.3 - - + +
593B MET* 4.1 7.9 - - + +
602B LEU* 3.9 31.2 - - + -
616B LEU* 5.0 1.6 - - + -
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Residues in contact with ILE 558 (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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516B LEU* 3.9 11.2 - - + -
534B MET* 4.2 8.3 - - - -
538B VAL* 3.5 36.6 - - + -
540B CYS 3.2 17.7 - - - +
541B LEU* 3.8 18.6 - - + -
557B ALA* 1.3 75.9 - - - +
559B GLY* 1.3 65.1 + - - +
560B LEU* 3.9 11.2 - - + -
566B ALA* 3.2 3.0 - - - +
567B ARG* 2.8 45.3 + - + +
569B LEU* 3.6 33.0 - - + -
591B ILE* 4.4 7.1 - - - +
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Residues in contact with GLY 559 (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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539B ALA* 3.2 24.4 + - - +
540B CYS* 3.4 17.6 + - - +
558B ILE* 1.3 78.4 - - - +
560B LEU* 1.3 65.8 + - - +
565B SER 2.9 13.0 - - - -
566B ALA* 4.2 3.1 - - - -
588B PRO* 4.0 10.1 - - - -
591B ILE* 4.3 8.5 - - - +
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Residues in contact with LEU 560 (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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534B MET* 4.3 9.4 - - + -
535B GLU* 4.0 10.8 - - + +
536B HIS* 3.5 34.8 - - + +
537B GLU 3.3 19.3 - - - +
538B VAL* 3.8 11.7 - - + -
539B ALA* 3.6 3.5 - - - +
558B ILE* 3.9 19.7 - - + -
559B GLY* 1.3 77.4 - - - +
561B TRP* 1.3 60.0 + - - +
563B ASP* 3.6 22.9 - - + +
564B ILE 4.6 4.3 - - - -
565B SER* 3.0 18.4 + - - +
567B ARG* 4.1 21.3 - - + +
588B PRO* 3.3 22.3 - - - +
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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