Contacts of the helix formed by residues 613 - 619 (chain B) in PDB entry 2FJU
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 PRO 613 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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611B TYR* 3.5 8.1 - - + +
612B MET* 1.3 83.3 - - + +
614B GLN* 1.3 68.4 + - - +
615B MET 3.3 2.5 - - - -
616B PHE* 2.9 19.3 + - + +
617B TRP* 3.1 47.1 + - + -
624B VAL* 3.6 26.9 - - + +
626B LEU* 4.7 7.2 - - + -
634B PRO* 3.8 20.9 - - + +
637B GLN* 3.7 17.5 - - - +
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Residues in contact with GLN 614 (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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612B MET* 3.6 6.5 - - + -
613B PRO* 1.3 80.3 - - - +
615B MET* 1.3 55.1 + - - +
617B TRP* 3.0 17.3 + - - +
618B ASN* 2.8 59.2 + - - +
637B GLN* 2.9 31.1 - - - +
704B PHE* 3.7 16.7 + - + +
705B GLY* 3.3 34.7 - - - +
744B LEU* 3.4 21.1 + - - +
746B SER* 4.8 1.0 + - - -
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Residues in contact with MET 615 (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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578B TYR* 3.4 42.2 - - + -
581B LEU* 3.7 26.4 - - + +
612B MET 4.6 4.6 + - - +
613B PRO 3.2 0.4 + - - -
614B GLN* 1.3 79.2 - - - +
616B PHE* 1.3 80.4 + - + +
618B ASN* 3.4 21.1 - - - +
619B ALA* 3.4 9.7 + - - +
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Residues in contact with PHE 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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574B GLU* 3.7 23.6 - - + -
577B ALA* 3.5 32.3 - - + -
578B TYR* 4.0 10.1 - + + -
581B LEU* 4.3 15.9 - - + -
588B PHE* 5.8 0.2 - + - -
599B ILE* 4.2 11.7 - - + -
611B TYR* 3.6 38.6 - + + -
612B MET 3.9 10.1 - - - -
613B PRO* 2.9 11.7 + - + +
615B MET* 1.3 87.6 - - + +
617B TRP* 1.3 66.2 + - - +
618B ASN 3.1 1.3 - - - -
619B ALA* 3.1 7.5 + - - +
621B CYS* 3.0 39.0 + - + +
624B VAL* 3.9 15.7 - - + -
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Residues in contact with TRP 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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322B PHE* 3.3 42.1 - + + +
323B ILE 5.6 0.4 + - - -
613B PRO* 3.1 39.6 + - + -
614B GLN* 3.0 32.3 + - - +
616B PHE* 1.3 76.1 - - - +
618B ASN* 1.3 58.5 + - - +
620B GLY 2.9 15.6 + - - -
621B CYS 3.4 18.8 - - - -
622B GLN 4.7 4.2 + - - -
624B VAL* 3.5 24.8 - - + +
637B GLN* 3.7 16.8 - - - -
638B ASN* 3.6 30.1 - - - -
641B VAL* 3.9 23.3 - - + -
642B PHE* 3.8 14.7 - + - -
657B MET* 3.3 10.6 - - - +
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Residues in contact with ASN 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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589B VAL* 5.1 3.6 - - - +
614B GLN* 2.8 42.3 + - - +
615B MET* 3.4 14.6 - - - +
616B PHE 3.1 0.2 - - - -
617B TRP* 1.3 78.4 - - - +
619B ALA* 1.3 56.6 + - - +
657B MET* 3.3 16.8 - - - +
705B GLY 3.0 21.9 + - - +
706B LEU* 3.5 34.9 - - + +
707B PRO* 3.8 15.1 - - + +
744B LEU* 5.1 3.8 - - - +
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Residues in contact with ALA 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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581B LEU* 3.8 31.0 - - + -
588B PHE* 4.9 2.5 - - + -
589B VAL* 3.7 32.4 - - + +
592B ASN* 2.8 19.0 + - - +
615B MET 3.4 7.7 + - - +
616B PHE 3.1 9.3 + - - +
617B TRP 3.1 1.2 - - - -
618B ASN* 1.3 78.6 - - - +
620B GLY* 1.3 57.6 + - - +
621B CYS* 3.4 9.6 - - - -
657B MET* 4.0 1.8 - - - -
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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