Contacts of the helix formed by residues 507 - 523 (chain B) in PDB entry 4Z7I
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 SER 507 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B LYS* 5.4 3.6 - - - -
460B LYS* 5.2 2.7 - - - -
495B TYR* 3.3 23.6 + - - -
498B LEU* 3.3 49.6 + - - +
499B GLU* 4.0 4.5 + - - -
502B PHE 4.6 3.1 + - - -
503B LYS* 5.9 0.4 - - - +
505B LEU* 3.2 8.6 - - - -
506B SER* 1.3 72.0 - - - +
508B TYR* 1.3 63.9 + - - +
509B GLU 3.1 2.7 - - - -
510B ASP* 3.2 22.3 + - - +
511B PHE 3.2 9.4 + - - -
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Residues in contact with TYR 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B TYR* 5.2 3.5 + - - -
499B GLU* 5.0 21.8 - - + +
503B LYS* 6.6 0.4 - - + -
506B SER* 3.0 34.3 + - - -
507B SER* 1.3 79.9 + - - +
509B GLU* 1.3 77.2 + - + +
511B PHE* 3.4 9.8 + - - +
512B LEU* 2.9 29.4 + - + +
515B ARG* 4.8 2.3 + - - -
725B ASP* 2.6 33.4 + - - -
726B LYS* 3.6 42.6 - - + +
763B ALA* 4.9 1.3 - - + -
815B SER* 5.6 0.3 + - - -
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Residues in contact with GLU 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B LYS* 4.5 1.9 + - - -
506B SER* 3.4 23.9 - - - +
508B TYR* 1.3 101.6 + - + +
510B ASP* 1.3 69.2 + - - +
512B LEU* 3.2 7.5 + - - +
513B ASP* 3.0 24.8 + - - +
762B THR* 3.2 33.3 + - - +
763B ALA* 3.8 23.2 - - + +
815B SER* 3.5 12.1 + - - -
818B GLU* 3.5 21.4 - - - +
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Residues in contact with ASP 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B LYS* 3.8 30.7 + - - +
460B LYS* 2.6 30.7 + - - +
495B TYR* 3.5 16.5 + - + +
506B SER 4.6 0.9 - - - +
507B SER* 3.2 13.2 + - - +
509B GLU* 1.3 78.6 - - - +
511B PHE* 1.3 53.1 + - - +
513B ASP* 3.3 6.5 + - - +
514B ALA* 2.7 35.3 + - - +
818B GLU* 4.5 8.4 - - - +
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Residues in contact with PHE 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B PHE* 4.7 7.2 - + - -
495B TYR* 3.4 51.5 - + + -
507B SER 3.2 3.5 + - - +
508B TYR* 3.6 12.1 - - - +
509B GLU 3.3 0.2 - - - -
510B ASP* 1.3 79.4 - - - +
512B LEU* 1.3 52.4 + - - +
514B ALA* 3.1 5.3 + - + +
515B ARG* 2.7 71.6 + - + +
550B PHE* 4.4 9.0 - + - -
553B SER* 3.1 42.6 - - - -
554B SER* 4.4 2.9 - - - -
557B LEU* 3.9 22.7 - - + -
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Residues in contact with LEU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B TYR 2.9 14.3 + - - +
509B GLU* 3.2 9.6 + - - +
511B PHE* 1.3 75.7 - - - +
513B ASP* 1.3 52.5 + - - +
515B ARG* 3.1 33.6 + - - +
516B PHE* 2.8 56.0 + - + -
695B ASN 4.7 2.7 - - - +
696B MET* 3.8 21.8 - - + -
726B LYS* 4.1 29.6 - - + +
729B ALA* 3.8 29.2 - - + -
763B ALA* 4.8 12.6 - - + +
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Residues in contact with ASP 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B GLU 3.0 16.3 + - - +
510B ASP* 3.6 6.5 - - - +
512B LEU* 1.3 76.3 - - - +
514B ALA* 1.3 63.0 + - - +
516B PHE* 3.2 11.9 - - + +
517B LYS* 2.8 55.5 + - - +
766B THR* 6.0 2.5 - - - +
767B GLU* 4.2 4.7 - - - +
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Residues in contact with ALA 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B TYR* 4.3 2.5 - - - +
510B ASP 2.7 21.7 + - - +
511B PHE* 3.3 9.0 - - - +
513B ASP* 1.3 73.5 - - - +
515B ARG* 1.3 55.8 + - - +
517B LYS* 3.4 4.4 + - - +
518B THR* 2.3 34.1 + - - -
550B PHE* 3.5 38.4 - - + +
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Residues in contact with ARG 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B TYR 4.8 0.4 + - - -
511B PHE* 2.7 63.6 + - + +
512B LEU* 3.5 18.5 - - - +
514B ALA* 1.3 69.5 - - - +
516B PHE* 1.3 67.7 + - - +
518B THR* 3.2 8.3 + - - -
519B MET* 3.2 27.4 + - + +
550B PHE* 4.8 1.1 - - + +
554B SER* 3.1 26.8 - - - +
557B LEU* 3.4 18.4 - - - +
695B ASN 3.0 26.1 + - - -
696B MET* 3.4 33.1 - - + +
697B ASN* 3.0 17.8 + - - +
699B TYR* 5.6 3.4 - - + -
726B LYS* 4.2 14.3 - - - +
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Residues in contact with PHE 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B LEU* 2.8 49.5 + - + -
513B ASP* 3.2 18.8 - - + +
515B ARG* 1.3 72.6 - - - +
517B LYS* 1.3 71.1 + - - +
519B MET* 3.2 21.7 + - + +
520B LYS* 3.5 10.4 + - - +
696B MET* 3.4 29.6 - - - -
729B ALA* 3.9 24.0 - - + -
730B ASN* 3.9 4.3 - - - -
733B ASN* 3.5 34.5 + - + +
763B ALA 5.4 1.1 - - - -
767B GLU* 3.8 33.2 - - + -
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Residues in contact with LYS 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B ASP* 2.8 41.5 + - - +
514B ALA* 3.9 4.3 - - - +
516B PHE* 1.3 77.2 - - - +
518B THR* 1.3 62.6 + - - +
519B MET 3.4 0.2 - - - -
520B LYS* 4.2 9.4 - - + +
521B LYS* 3.6 21.1 + - - +
733B ASN* 5.3 1.3 - - - +
767B GLU* 3.6 17.5 + - - -
770B PHE* 3.5 48.8 - - + +
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Residues in contact with THR 518 (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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514B ALA 2.3 30.1 + - - -
515B ARG* 3.5 8.8 - - - -
516B PHE 3.1 0.6 - - - -
517B LYS* 1.3 79.5 - - - +
519B MET* 1.3 53.0 + - - +
521B LYS* 3.3 5.5 + - - +
522B ASP* 2.8 34.3 + - - +
546B SER* 4.7 1.8 - - - +
547B LEU* 3.7 27.2 - - + +
550B PHE* 3.5 17.8 - - + +
551B LYS* 4.0 27.4 - - + +
699B TYR* 4.1 8.3 - - - +
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Residues in contact with MET 519 (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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515B ARG 3.2 15.7 - - - +
516B PHE* 3.2 10.7 + - - +
518B THR* 1.3 73.6 - - - +
520B LYS* 1.3 54.7 + - - +
521B LYS 3.0 2.0 - - - -
523B SER* 2.7 37.2 + - - -
616B PHE* 3.2 20.5 - - + -
696B MET* 4.2 28.0 - - - +
698B GLY 5.4 0.4 - - - +
699B TYR* 3.5 37.2 - - + -
700B TYR 4.6 11.2 - - - +
701B ILE* 3.9 34.3 - - + -
733B ASN* 4.3 13.2 - - - +
734B ASN* 4.9 1.1 - - - +
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Residues in contact with LYS 520 (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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516B PHE 3.5 10.2 + - - +
517B LYS* 4.0 9.6 + - + +
518B THR 3.5 0.2 - - - -
519B MET* 1.3 77.9 - - - +
521B LYS* 1.3 57.2 + - - +
523B SER* 3.1 19.9 + - - +
524B LEU* 3.4 21.1 - - + +
737B GLU* 3.5 36.5 + - - +
770B PHE* 6.2 3.6 - - + -
774B LEU* 3.9 24.8 - - + +
1009B LEU* 6.3 2.0 - - - -
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Residues in contact with LYS 521 (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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517B LYS 3.6 16.2 + - - +
518B THR* 3.3 6.0 + - - +
519B MET 3.0 0.2 - - - -
520B LYS* 1.3 77.2 - - - +
522B ASP* 1.3 62.5 + - - +
523B SER 3.3 0.6 + - - -
524B LEU* 3.9 15.1 + - + +
527B SER* 3.8 13.2 - - - -
545B ASP* 4.7 14.6 + - - +
546B SER* 6.0 8.1 - - - +
547B LEU* 4.7 23.0 - - + +
998B ARG* 6.2 1.6 - - - +
1002B GLU* 3.3 36.2 + - - +
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Residues in contact with ASP 522 (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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518B THR 2.8 12.8 + - - +
519B MET* 3.1 4.2 + - - +
521B LYS* 1.3 78.0 - - - +
523B SER* 1.3 57.2 + - - +
524B LEU 3.2 2.7 - - - +
527B SER* 2.7 38.9 + - - -
528B HIS 4.9 0.5 - - - +
547B LEU* 3.9 10.7 - - + +
551B LYS* 3.0 29.4 + - - +
614B LYS* 4.8 0.5 - - - +
615B GLY* 3.3 28.7 + - - +
616B PHE* 3.5 2.6 - - + -
699B TYR* 2.8 37.6 + - - +
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Residues in contact with SER 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B MET 2.7 14.9 + - - -
520B LYS* 3.1 21.9 + - - +
521B LYS 3.3 0.2 - - - -
522B ASP* 1.3 74.9 - - - +
524B LEU* 1.3 67.3 + - - +
615B GLY* 5.1 1.8 - - - -
616B PHE* 3.8 6.7 - - - -
634B ARG* 6.0 0.2 + - - -
635B PHE* 3.6 48.0 - - - +
636B PHE* 4.8 1.4 - - - -
637B LEU* 3.6 27.2 - - - +
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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
------------------------------------------------------------
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