Contacts of the strand formed by residues 615 - 618 (chain B) in PDB entry 6M04
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 LYS 615 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810A PHE* 5.8 5.3 - - - -
591B LYS 3.8 1.4 + - - -
592B ILE* 3.2 48.7 - - + +
593B LEU 3.8 3.1 + - - +
613B LEU* 5.7 1.2 - - - +
614B THR* 1.3 85.8 - - + +
616B LEU* 1.3 59.5 + - - +
617B VAL* 3.9 10.0 + - + +
639B GLU* 3.3 28.1 - - + +
641B GLU* 2.9 42.0 + - - +
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Residues in contact with LEU 616 (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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593B LEU* 3.7 38.6 - - + +
603B PRO* 6.0 3.4 - - + -
605B ASN* 3.8 24.0 - - - +
613B LEU* 5.4 8.5 - - + -
615B LYS* 1.3 72.9 - - - +
617B VAL* 1.3 66.0 + - - +
618B ILE* 5.6 8.7 - - + +
630B SER* 6.6 0.2 - - - -
634B MET* 4.7 16.4 - - + -
637B VAL* 4.9 6.4 - - + +
639B GLU 3.4 7.5 + - - -
640B LEU* 3.3 25.5 - - + +
641B GLU* 3.0 20.5 + - - -
642B LEU* 4.6 7.1 - - + +
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Residues in contact with VAL 617 (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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566B TYR* 5.8 0.2 - - + -
592B ILE* 4.7 6.1 - - + -
593B LEU* 3.4 16.5 + - - +
594B HIS* 3.3 54.5 - - + +
595B VAL* 3.3 2.8 + - - +
615B LYS* 4.6 11.7 - - + +
616B LEU* 1.3 77.4 - - - +
618B ILE* 1.3 61.8 + - - +
641B GLU* 3.3 39.7 - - + +
643B GLN* 4.6 10.1 - - - +
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Residues in contact with ILE 618 (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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595B VAL* 3.4 18.8 - - + +
600B THR* 3.8 27.6 - - + +
601B LYS 5.1 5.2 - - - +
603B PRO* 3.9 27.8 - - + -
616B LEU* 5.6 10.3 - - + +
617B VAL* 1.3 76.1 - - - +
619B HIS* 1.3 70.0 + - - +
621B ASP* 6.4 1.8 - - + -
641B GLU 3.1 6.1 + - - +
642B LEU* 3.9 30.5 - - + -
643B GLN* 3.0 28.9 + - - +
645B CYS* 5.5 3.1 - - - -
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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