Contacts of the strand formed by residues 678 - 681 (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 TYR 678 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B ILE 3.7 21.8 - - - -
408B LYS* 3.8 29.3 + - + +
409B GLY* 3.9 19.7 - - - -
410B LEU* 3.5 24.0 - - + +
589B ARG* 4.2 16.6 + - - -
637B VAL* 3.9 29.6 - - + -
652B CYS* 4.0 5.4 - - - -
676B VAL* 4.1 1.5 - - - +
677B ASN* 1.3 103.0 - - + +
679B MET* 1.3 61.0 + - - +
693B LEU* 3.5 2.6 - - - -
694B ALA* 2.9 32.8 + - + +
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Residues in contact with MET 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU* 3.6 5.4 - - - +
637B VAL* 6.1 0.2 - - - +
639B ARG* 3.2 36.2 + - + +
640B THR 3.4 14.4 - - - +
641B PHE* 3.4 30.3 - - + -
650B PHE* 3.3 55.0 - - + -
652B CYS* 4.1 4.2 - - - -
678B TYR* 1.3 76.4 - - - +
680B CYS* 1.3 78.3 + - - +
681B PRO* 3.7 12.3 - - + -
691B LEU* 4.0 14.4 - - + -
692B ALA 3.2 9.6 - - - +
693B LEU* 4.2 14.1 - - + -
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Residues in contact with CYS 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU* 3.3 47.6 - - - +
411B TRP* 4.3 1.3 - - - -
412B PRO* 4.3 9.2 - - + -
425B LEU* 4.2 10.5 - - - -
639B ARG* 4.7 2.9 - - - +
679B MET* 1.3 82.3 - - - +
681B PRO* 1.4 77.3 - - + +
682B LEU* 5.0 0.7 - - - -
691B LEU* 3.3 0.5 - - - -
692B ALA* 2.6 57.4 + - - +
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Residues in contact with PRO 681 (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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412B PRO* 3.4 27.4 - - + +
422B TYR* 5.3 0.9 - - - +
639B ARG* 4.7 7.6 - - - +
640B THR 3.4 20.6 - - - +
641B PHE* 4.1 7.4 - - - -
642B ARG* 4.6 13.9 - - + +
679B MET* 3.7 10.3 - - + -
680B CYS* 1.4 91.5 - - + +
682B LEU* 1.3 73.7 + - - +
690B SER 3.5 7.9 - - - +
691B LEU* 4.2 8.7 - - + -
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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