Contacts of the helix formed by residues 551 - 564 (chain B) in PDB entry 4HXG
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 551 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500B PHE* 5.5 0.6 - - - -
542B HIS* 3.4 32.7 + - + -
543B SER 5.5 1.3 + - - +
544B LEU* 3.8 26.0 - - + +
546B ASP 4.5 1.6 + - - -
550B PRO* 1.3 72.2 - - - +
552B ASP* 1.3 64.5 + - - +
554B SER* 3.0 15.9 + - - -
555B LEU* 3.0 33.2 + - + -
572B ILE* 4.0 34.1 - - + -
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Residues in contact with ASP 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B THR* 2.9 36.4 + - - +
500B PHE* 3.8 20.8 - - + +
550B PRO* 3.0 21.0 - - - +
551B LEU* 1.3 73.9 - - - +
553B GLN* 1.3 74.1 + - - +
554B SER 3.1 0.2 + - - -
555B LEU* 4.4 4.7 - - - +
556B MET* 2.6 57.1 + - + +
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Residues in contact with GLN 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B ASN* 5.0 2.5 + - - -
490B GLY 3.0 28.3 - - - +
491B ILE* 3.2 10.9 - - + -
492B SER* 2.5 52.5 + - - -
493B TYR* 2.9 20.6 + - - +
496B THR* 2.7 29.4 + - - -
497B SER* 3.5 17.1 - - - +
540B LEU* 5.7 0.2 - - - +
542B HIS* 4.8 1.6 - - + -
549B CYS* 4.4 3.4 - - - -
550B PRO* 3.5 23.8 - - + +
551B LEU 3.1 0.2 + - - -
552B ASP* 1.3 88.3 + - - +
554B SER* 1.3 59.5 + - - +
556B MET* 5.0 0.9 - - - -
557B PHE* 3.7 4.3 - - - +
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Residues in contact with SER 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B SER* 5.6 0.3 + - - -
489B ASN 4.3 3.8 + - - -
490B GLY 4.4 3.3 + - - -
540B LEU* 3.6 22.0 - - - +
541B ILE 3.7 7.6 + - - -
542B HIS* 2.5 42.7 + - - -
551B LEU* 3.0 5.7 + - - -
553B GLN* 1.3 78.1 - - - +
555B LEU* 1.3 59.9 + - - +
556B MET 3.3 0.4 - - - -
557B PHE* 3.3 4.7 + - - +
558B TYR* 2.9 27.9 + - - +
570B ILE* 4.1 12.3 - - - -
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Residues in contact with LEU 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B LEU* 3.0 35.5 + - + +
552B ASP* 4.2 3.8 - - - +
554B SER* 1.3 74.5 - - - +
556B MET* 1.3 61.5 + - + +
558B TYR* 3.2 11.2 + - + -
559B HIS* 2.9 62.2 + - + +
570B ILE* 4.0 24.0 - - + -
572B ILE* 4.7 11.2 - - + -
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Residues in contact with MET 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B SER* 4.5 5.2 - - - +
493B TYR* 4.2 20.4 - - + -
496B THR* 3.9 23.6 - - + +
528B LEU* 4.1 14.8 - - + -
552B ASP* 2.6 58.4 + - + +
553B GLN* 4.8 1.1 - - - +
555B LEU* 1.3 73.1 - - + +
557B PHE* 1.3 61.6 + - - +
559B HIS* 3.8 5.7 - - - +
560B VAL* 3.0 29.7 + - + +
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Residues in contact with PHE 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B ASN* 3.3 50.3 - - + -
476B LEU* 6.3 0.4 - - + -
477B THR* 4.4 13.2 - - + -
492B SER* 3.7 21.1 + - - -
527B PRO* 3.9 22.9 - - + -
528B LEU* 3.9 17.3 - - + -
531B ALA* 4.0 19.1 - - + -
534B VAL* 4.6 4.5 - - + -
538B LEU* 3.9 17.3 - - + -
540B LEU* 4.2 6.7 - - + -
553B GLN 3.7 2.9 - - - +
554B SER* 3.3 8.9 + - - +
556B MET* 1.3 78.9 - - - +
558B TYR* 1.3 56.5 + - - +
560B VAL* 3.7 0.3 - - - +
561B LEU* 2.9 51.5 + - + +
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Residues in contact with TYR 558 (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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540B LEU* 3.8 12.3 - - + +
554B SER 2.9 15.9 + - - +
555B LEU* 3.2 10.3 + - + +
557B PHE* 1.3 77.0 - - - +
559B HIS* 1.3 83.9 + + - +
561B LEU* 3.4 5.8 + - - +
562B LYS* 3.0 54.2 + - + +
568B VAL* 3.6 31.1 + - + -
569B TYR* 3.7 21.7 - - - -
570B ILE* 3.6 37.2 - - + -
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Residues in contact with HIS 559 (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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555B LEU* 2.9 49.6 + - + +
556B MET* 3.8 6.1 - - - +
558B TYR* 1.3 87.0 - + - +
560B VAL* 1.3 67.7 + - + +
562B LYS* 3.1 6.7 + - + +
563B ASP* 2.9 24.4 + - - +
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Residues in contact with VAL 560 (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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528B LEU* 3.7 26.5 - - + +
531B ALA* 3.8 15.0 - - + -
556B MET* 3.0 22.9 + - + +
557B PHE 3.7 3.1 - - - +
559B HIS* 1.3 75.3 - - + +
561B LEU* 1.3 63.4 + - - +
563B ASP* 3.1 9.4 + - + +
564B LEU* 3.1 40.7 + - + +
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Residues in contact with LEU 561 (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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531B ALA* 3.7 36.1 - - + +
534B VAL* 4.2 12.3 - - + -
538B LEU* 3.8 29.8 - - + -
557B PHE* 2.9 42.2 + - + +
558B TYR* 3.7 4.3 - - - +
560B VAL* 1.3 75.8 - - - +
562B LYS* 1.3 56.7 + - - +
564B LEU* 3.0 4.3 + - + -
565B GLY 3.0 20.8 + - - -
566B LYS* 3.1 33.6 + - + +
568B VAL* 3.9 23.1 - - + -
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Residues in contact with LYS 562 (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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558B TYR* 3.0 52.1 + - + +
559B HIS* 3.5 9.0 - - + +
561B LEU* 1.3 71.1 - - - +
563B ASP* 1.3 58.0 + - - +
564B LEU 3.0 4.7 - - - -
565B GLY* 2.8 20.4 + - - +
566B LYS 4.3 13.5 + - - +
567B GLU* 5.7 0.8 - - - +
568B VAL* 3.5 29.4 + - + +
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Residues in contact with ASP 563 (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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559B HIS 2.9 12.3 + - - +
560B VAL* 3.4 13.5 - - + +
562B LYS* 1.3 75.8 - - - +
564B LEU* 1.3 64.3 + - + +
565B GLY 3.3 0.8 + - - -
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Residues in contact with LEU 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B ALA* 3.8 29.2 - - + -
532B LYS* 3.9 22.4 - - + +
560B VAL* 3.4 20.6 - - + +
561B LEU* 3.0 8.0 + - - +
562B LYS 3.0 0.8 - - - -
563B ASP* 1.3 84.1 - - + +
565B GLY* 1.3 60.6 + - - +
566B LYS* 3.3 22.5 + - + -
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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