Contacts of the helix formed by residues 649 - 659 (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 ASN 649 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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645F LEU 3.6 8.9 + - - +
646F ILE 2.9 13.0 + - - +
647F ALA 3.4 0.6 - - - -
648F THR* 1.3 78.4 - - - +
650F GLU* 1.3 59.0 + - - +
651F ASP* 3.1 16.0 + - - +
652F HIS* 3.0 51.0 + - + +
653F ARG* 2.9 27.7 + - - +
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Residues in contact with GLU 650 (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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648F THR 4.0 2.6 + - - -
649F ASN* 1.3 68.8 + - - +
651F ASP* 1.3 71.1 + - - +
653F ARG* 3.2 7.5 + - - +
654F GLN* 3.0 24.6 + - + +
657F ARG* 2.9 31.9 + - - -
691F ASN* 3.7 21.5 + - - -
693F LYS* 4.4 7.4 + - - -
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Residues in contact with ASP 651 (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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554B ARG* 4.6 4.9 + - - +
649F ASN* 3.1 9.6 + - - +
650F GLU* 1.3 79.2 - - - +
652F HIS* 1.3 64.7 + - + +
654F GLN* 3.4 8.4 + - - +
655F ILE* 3.1 29.8 + - + +
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Residues in contact with HIS 652 (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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607F CYS* 3.6 41.5 + - + +
608F ALA* 5.6 0.4 - - - -
613F LEU* 3.5 23.8 - - + +
645F LEU 5.9 0.4 - - - -
646F ILE* 4.0 13.4 - - + +
649F ASN* 3.0 43.2 + - + +
651F ASP* 1.3 80.8 - - + +
653F ARG* 1.3 65.4 + - - +
655F ILE* 3.3 19.0 + - + +
656F LEU* 3.1 27.0 + - - +
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Residues in contact with ARG 653 (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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646F ILE* 3.6 17.0 - - + +
647F ALA* 2.9 44.2 + - - +
649F ASN 2.9 14.9 + - - +
650F GLU* 3.5 14.4 - - - +
652F HIS* 1.3 76.4 - - - +
654F GLN* 1.3 57.1 + - - +
656F LEU* 3.1 9.1 + - - +
657F ARG* 2.9 44.7 + - - +
686F ASN 3.6 1.8 + - - -
687F LEU* 2.8 34.0 + - + +
689F ALA 3.2 24.5 + - - -
691F ASN* 3.3 32.5 - - - +
694F ASP* 2.7 33.0 + - - +
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Residues in contact with GLN 654 (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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513B VAL* 3.9 35.7 - - + +
554B ARG* 4.2 18.2 - - - +
650F GLU* 3.0 15.1 + - + +
651F ASP* 3.6 11.7 - - - +
652F HIS 3.2 0.4 - - - -
653F ARG* 1.3 73.3 - - - +
655F ILE* 1.3 64.7 + - - +
657F ARG* 3.0 42.6 + - - +
658F GLU* 3.0 35.9 + - - +
693F LYS* 4.8 5.4 + - - -
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Residues in contact with ILE 655 (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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554B ARG* 4.1 16.6 - - - +
613F LEU* 4.2 14.6 - - + -
614F ALA* 3.9 30.1 - - + +
617F VAL* 5.9 0.2 - - + -
651F ASP* 3.1 16.9 + - + +
652F HIS* 3.3 28.5 + - + +
654F GLN* 1.3 75.7 - - - +
656F LEU* 1.3 62.4 + - + +
658F GLU* 3.3 12.8 - - + +
659F ASN* 2.8 35.6 + - - +
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Residues in contact with LEU 656 (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* 4.4 16.2 - - + -
617F VAL* 3.9 19.1 - - + -
639F LEU* 4.5 7.0 - - + -
646F ILE* 4.0 37.5 - - + -
652F HIS 3.1 14.1 + - - +
653F ARG* 3.1 12.1 + - - +
655F ILE* 1.3 79.6 - - - +
657F ARG* 1.3 62.1 + - + +
659F ASN* 3.1 8.7 + - - -
661F CYS* 3.0 55.8 + - + +
662F LEU* 6.5 0.4 - - + -
683F THR* 5.5 0.7 - - + -
687F LEU* 3.8 24.0 - - + -
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Residues in contact with ARG 657 (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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556B ASP* 4.7 2.8 - - - +
650F GLU* 2.9 27.9 + - - -
653F ARG* 2.9 26.7 + - - +
654F GLN* 3.0 47.9 + - - +
656F LEU* 1.3 74.8 - - + +
658F GLU* 1.3 59.8 + - - +
659F ASN 3.0 0.2 - - - -
660F ASN* 3.0 24.9 + - - +
661F CYS 4.8 1.8 - - - +
662F LEU* 5.3 8.1 - - + +
663F GLN* 5.2 1.2 + - - +
691F ASN* 3.5 16.2 + - - +
693F LYS* 3.6 28.7 - - - +
694F ASP* 2.8 39.8 + - - +
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Residues in contact with GLU 658 (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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554B ARG* 2.4 65.8 + - - +
555B ALA 4.1 6.1 - - - +
556B ASP* 3.2 39.6 - - + +
557B VAL* 3.2 11.0 + - - +
560B LYS* 6.0 0.2 - - - +
654F GLN* 3.0 23.0 + - - +
655F ILE* 3.3 20.2 - - - +
657F ARG* 1.3 76.5 - - - +
659F ASN* 1.3 65.4 + - - +
660F ASN 3.4 0.9 - - - -
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Residues in contact with ASN 659 (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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557B VAL* 3.6 10.6 - - - +
560B LYS* 5.0 12.3 - - - +
614F ALA* 3.6 36.3 + - - +
617F VAL* 3.3 29.6 - - + +
618F GLY* 5.6 0.8 - - - +
655F ILE* 2.8 24.6 + - - +
656F LEU 3.1 2.6 + - - +
657F ARG 3.0 1.2 - - - -
658F GLU* 1.3 88.8 + - - +
660F ASN* 1.3 67.6 + - - +
661F CYS 3.3 2.8 + - - -
664F THR* 5.0 1.7 + - - -
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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