Contacts of the strand formed by residues 615 - 620 (chain B) in PDB entry 3E0D
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 LEU 615 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B ARG 3.7 7.5 + - - +
295B ILE* 5.1 3.6 - - + -
296B PRO* 3.4 30.7 - - + -
402B TYR* 3.0 44.2 - - + -
405B ILE* 3.8 24.2 - - + -
461B MET* 3.6 14.4 - - + -
579B VAL 4.0 0.2 - - - +
580B VAL* 3.3 6.7 - - - +
581B ILE* 3.1 43.0 + - + +
614B LEU* 1.3 69.8 - - - +
616B LYS* 1.3 62.7 + - - +
617B MET* 3.7 23.6 + - + +
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Residues in contact with LYS 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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402B TYR* 4.5 0.9 + - - -
461B MET* 3.8 5.8 - - - +
463B ASP* 3.0 43.4 + - - +
465B ASP* 5.2 0.2 - - - -
492B ILE* 3.2 28.0 - - + -
579B VAL 3.4 3.8 - - - -
606B MET* 3.6 24.3 - - + +
609B VAL* 4.9 0.4 - - + -
610B GLU* 3.4 44.1 + - + +
614B LEU 3.1 5.0 + - - +
615B LEU* 1.3 77.4 - - - +
617B MET* 1.3 76.3 + - - +
618B ASP* 3.8 9.2 - - - -
21F DOC 2.3 36.5 + - - -
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Residues in contact with MET 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B TYR* 3.3 39.5 - - + +
405B ILE* 4.9 1.3 - - - -
406B VAL* 3.8 13.9 - - + -
409B TYR* 3.4 28.0 - - - +
464B ILE 4.0 10.8 - - - +
465B ASP* 4.7 1.6 - - - -
579B VAL* 2.9 30.6 + - + +
581B ILE* 4.2 22.7 - - + -
615B LEU* 3.7 17.9 - - + +
616B LYS* 1.3 80.4 - - - +
618B ASP* 1.3 71.1 + - - +
619B PHE* 3.5 25.4 - - + -
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Residues in contact with ASP 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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409B TYR* 5.3 0.5 + - - -
464B ILE 4.0 3.3 + - - +
465B ASP* 3.3 23.2 + - + +
466B THR* 3.0 29.2 + - - -
575B HIS* 3.3 16.0 + - - -
577B ALA* 3.3 17.0 - - - +
616B LYS* 3.8 12.3 - - - -
617B MET* 1.3 83.5 - - - +
619B PHE* 1.3 65.9 + - - +
620B LEU* 3.6 13.9 - - + -
21F DOC 2.4 43.5 - - - +
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Residues in contact with PHE 619 (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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409B TYR* 3.5 31.9 - + - -
466B THR 3.7 3.8 - - - -
468B PHE* 3.5 20.9 - + + -
473B ARG* 3.1 37.7 + - + +
476B VAL* 3.5 31.6 - - + -
477B ILE* 4.0 17.5 - - + -
480B VAL* 4.0 19.3 - - + -
576B ALA 3.5 0.3 - - - +
577B ALA* 2.9 16.9 + - - +
579B VAL* 4.0 20.0 - - + -
581B ILE* 5.5 0.9 - - + -
617B MET* 3.5 28.9 - - + -
618B ASP* 1.3 77.4 - - - +
620B LEU* 1.3 60.2 + - - +
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Residues in contact with LEU 620 (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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424B ARG* 3.4 40.6 - - - +
465B ASP* 4.4 0.2 - - + -
466B THR 2.9 12.4 + - - +
467B ASP* 3.4 19.2 - - - +
468B PHE* 2.8 32.2 + - - +
473B ARG* 3.8 2.0 - - - -
577B ALA* 3.8 10.8 - - + -
618B ASP* 3.6 34.3 - - + +
619B PHE* 1.3 73.6 - - - +
621B GLY* 1.3 60.8 + - - +
622B LEU* 5.4 1.1 - - + -
821B TYR* 4.6 0.4 - - - +
7E G 4.3 4.7 - - - +
8E T 4.4 6.3 - - - +
9E G 4.2 10.3 - - - +
20F A 5.6 0.7 - - + -
21F DOC 3.3 25.8 - - + +
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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