Contacts of the helix formed by residues 611 - 620 (chain F) in PDB entry 4YJL
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 GLY 611 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577F LEU* 4.1 7.0 - - - +
609F VAL 3.3 1.6 + - - -
610F ASP* 1.3 77.1 + - - +
612F ALA* 1.3 57.6 + - - +
613F LEU 3.4 2.4 - - - +
614F ALA* 3.5 10.5 + - - +
615F PHE* 2.9 30.3 + - - +
497K ARG* 5.4 3.4 - - - -
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Residues in contact with ALA 612 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573F MET* 3.6 34.7 - - + +
577F LEU* 4.3 2.9 - - - +
606F ILE* 3.4 22.4 - - + +
609F VAL* 3.2 20.8 + - + +
610F ASP 3.3 3.0 + - - -
611F GLY* 1.3 76.1 - - - +
613F LEU* 1.3 57.9 + - + +
615F PHE* 3.3 4.3 + - - +
616F LEU* 2.8 36.0 + - - +
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Residues in contact with LEU 613 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606F ILE* 5.0 0.9 - - + -
607F CYS* 4.0 29.4 - - + +
609F VAL 4.7 0.8 + - - -
611F GLY 3.4 0.4 - - - -
612F ALA* 1.3 75.8 - - - +
614F ALA* 1.3 59.2 + - - +
616F LEU* 3.1 21.0 + - + +
617F VAL* 2.9 34.8 + - - +
639F LEU* 4.9 3.8 - - + +
642F VAL* 4.3 3.6 - - + -
646F ILE* 3.8 29.2 - - + -
652F HIS* 3.5 49.6 - - + +
655F ILE* 4.2 17.9 - - + -
656F LEU* 4.4 7.4 - - + -
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Residues in contact with ALA 614 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611F GLY* 3.5 13.0 + - - +
612F ALA 3.4 0.2 - - - -
613F LEU* 1.3 78.2 - - - +
615F PHE* 1.3 62.6 + - - +
617F VAL* 3.3 4.8 + - - +
618F GLY* 3.0 19.6 + - - -
655F ILE* 3.9 12.4 - - + +
659F ASN* 3.6 34.1 + - - +
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Residues in contact with PHE 615 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573F MET* 3.9 14.4 - - + -
576F ALA* 3.5 37.0 - - + -
577F LEU* 3.5 26.9 - - + -
579F VAL* 5.4 1.1 - - + -
585F LEU* 3.8 15.9 - - + -
589F LEU* 4.4 6.7 - - + -
611F GLY 2.9 18.6 + - - +
612F ALA 3.4 3.4 - - - +
614F ALA* 1.3 76.5 - - - +
616F LEU* 1.3 65.8 + - + +
618F GLY 3.1 5.2 + - - -
619F THR* 3.1 20.7 + - + +
801F EDO 3.0 53.4 + - - -
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Residues in contact with LEU 616 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573F MET* 4.4 16.6 - - + -
589F LEU* 4.6 7.9 - - + -
606F ILE* 4.0 20.0 - - + -
612F ALA 2.8 24.0 + - - +
613F LEU* 3.1 19.0 + - + +
615F PHE* 1.3 74.4 - - + +
617F VAL* 1.3 65.1 + - - +
619F THR* 2.7 23.8 + - + +
620F LEU* 3.7 8.9 + - - +
635F GLY* 4.3 12.1 - - - +
638F ILE* 3.9 50.0 - - + -
639F LEU* 4.7 14.1 - - + +
642F VAL* 4.9 4.3 - - + -
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Residues in contact with VAL 617 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613F LEU 2.9 19.7 + - - +
614F ALA* 3.8 5.8 - - - +
616F LEU* 1.3 75.6 - - - +
618F GLY* 1.3 63.1 + - - +
620F LEU* 3.1 30.4 + - + +
621F THR* 4.2 2.6 + - - +
639F LEU* 4.6 6.7 - - + -
656F LEU* 3.9 35.0 - - + -
659F ASN* 3.3 37.7 - - + +
661F CYS* 3.9 23.3 - - + -
664F THR* 5.7 2.0 - - - +
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Residues in contact with GLY 618 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614F ALA 3.0 13.8 + - - -
615F PHE 3.1 5.8 + - - -
617F VAL* 1.3 76.1 - - - +
619F THR* 1.3 60.8 + - - +
620F LEU 3.1 1.4 + - - -
621F THR* 3.1 21.1 + - - -
622F TYR* 3.6 5.2 + - - -
659F ASN* 5.6 1.7 - - - +
801F EDO 3.3 18.3 - - - -
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Residues in contact with THR 619 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585F LEU* 4.9 0.2 - - + -
589F LEU* 4.1 14.4 - - + -
615F PHE* 3.1 37.6 + - + +
616F LEU* 2.7 20.3 + - + +
618F GLY* 1.3 75.4 - - - +
620F LEU* 1.3 60.6 + - - +
621F THR 3.2 0.2 - - - -
622F TYR* 3.2 21.2 + - - +
631F ILE* 4.0 14.8 - - + -
632F ILE* 3.4 14.1 - - - +
635F GLY* 3.3 25.2 - - - -
801F EDO 3.7 13.9 - - - +
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Residues in contact with LEU 620 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616F LEU 3.8 9.9 - - - +
617F VAL* 3.2 28.3 - - + +
618F GLY 3.1 1.2 - - - -
619F THR* 1.3 79.1 + - - +
621F THR* 1.3 59.7 + - - +
622F TYR 3.5 0.2 - - - -
632F ILE* 3.8 13.2 - - - +
636F GLY* 3.5 35.2 - - - +
639F LEU* 3.8 26.2 - - + -
661F CYS* 4.2 8.3 - - - -
664F THR* 3.7 19.7 - - + +
665F LEU* 4.2 13.9 - - + -
668F HIS* 3.0 41.6 + - + +
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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