Contacts of the helix formed by residues 545 - 567 (chain B) in PDB entry 5AIM
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 ALA 545 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B ALA 3.3 7.0 + - - +
544B MET* 1.3 75.7 - - - +
546B SER* 1.3 66.5 + - - +
547B ALA* 4.3 7.9 - - + +
548B ARG* 3.0 26.1 + - + +
549B SER* 3.1 10.8 + - - -
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Residues in contact with SER 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B MET 3.7 1.4 + - - -
545B ALA* 1.3 71.9 - - - +
547B ALA* 1.3 57.7 + - - +
549B SER* 3.2 9.6 + - - -
550B LEU* 2.9 29.7 + - - +
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Residues in contact with ALA 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B ALA* 3.2 6.1 - - + +
546B SER* 1.3 78.4 - - - +
548B ARG* 1.3 58.4 + - - +
550B LEU* 3.3 10.4 + - - +
551B ARG* 2.9 48.2 + - - +
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Residues in contact with ARG 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B ALA* 4.0 12.5 + - - +
544B MET* 3.7 48.0 - - + +
545B ALA* 3.0 19.5 + - + +
547B ALA* 1.3 77.1 - - - +
549B SER* 1.3 66.3 + - - +
551B ARG* 3.2 30.4 + - - +
552B SER* 2.9 21.1 + - - -
555B ARG* 4.9 2.7 + - - +
1641B GOL 4.1 28.6 + - - +
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Residues in contact with SER 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B MET* 3.3 30.9 + - - +
545B ALA 3.1 11.0 + - - -
546B SER* 3.5 10.8 - - - -
548B ARG* 1.3 77.5 - - - +
550B LEU* 1.3 62.5 + - - +
552B SER* 3.1 7.6 + - - -
553B LEU* 2.9 30.5 + - - +
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Residues in contact with LEU 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B SER* 2.9 15.1 + - - +
547B ALA* 3.5 12.6 - - - +
548B ARG 3.2 0.2 - - - -
549B SER* 1.3 76.3 - - - +
551B ARG* 1.3 57.7 + - + +
553B LEU* 3.0 19.6 + - + +
554B GLN* 2.9 59.7 + - + +
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Residues in contact with ARG 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B ALA* 2.9 32.2 + - - +
548B ARG* 3.2 35.1 + - - +
550B LEU* 1.3 76.3 - - + +
552B SER* 1.3 57.6 + - - +
554B GLN* 3.3 7.6 + - - +
555B ARG* 2.9 48.5 + - + +
584B MET* 5.0 0.4 - - - +
1641B GOL 2.6 39.0 + - - -
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Residues in contact with SER 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B MET* 5.0 6.3 - - - -
548B ARG 2.9 13.0 + - - -
549B SER* 3.1 12.1 + - - -
551B ARG* 1.3 76.8 - - - +
553B LEU* 1.3 63.6 + - - +
555B ARG* 3.2 10.6 + - - +
556B GLN* 2.9 35.7 + - - +
598B ASP* 2.6 34.5 + - - +
601B LEU* 3.9 6.9 - - - +
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Residues in contact with LEU 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B SER* 2.9 22.2 + - - +
550B LEU* 3.0 22.2 + - + +
552B SER* 1.3 75.9 - - - +
554B GLN* 1.3 60.1 + - + +
556B GLN* 3.3 21.6 + - - +
557B ARG* 3.0 28.2 + - - +
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Residues in contact with GLN 554 (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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550B LEU* 2.9 45.7 + - + +
551B ARG* 3.8 6.3 - - - +
553B LEU* 1.3 74.8 - - - +
555B ARG* 1.3 61.2 + - - +
557B ARG* 3.4 33.2 + - - +
558B ALA* 2.9 28.6 + - - +
584B MET* 3.7 16.4 - - + +
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Residues in contact with ARG 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B ARG* 4.9 2.6 + - - +
551B ARG* 2.9 30.8 + - - +
552B SER* 3.6 16.3 - - - +
554B GLN* 1.3 76.8 - - - +
556B GLN* 1.3 58.2 + - - +
558B ALA* 3.2 1.9 + - - +
559B ILE* 2.8 38.4 + - + +
580B VAL* 5.3 2.7 - - + -
584B MET* 3.8 26.7 - - + -
590B LEU* 4.2 23.7 - - + +
594B THR* 3.3 32.7 + - - +
595B VAL* 4.9 7.4 - - - +
598B ASP* 2.7 36.0 + - + +
1641B GOL 3.1 33.1 + - - -
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Residues in contact with GLN 556 (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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552B SER* 2.9 36.9 + - - +
553B LEU* 3.6 23.3 - - + +
555B ARG* 1.3 76.6 - - - +
557B ARG* 1.3 62.8 + - - +
559B ILE* 3.3 1.7 + - - -
560B LEU* 3.0 22.9 + - + +
598B ASP* 3.9 15.3 + - + -
601B LEU* 4.0 18.8 - - - +
602B MET* 3.4 48.9 + - + +
605B SER* 5.3 0.3 + - - -
607B LYS* 4.3 17.3 + - + +
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Residues in contact with ARG 557 (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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553B LEU 3.0 14.5 + - - +
554B GLN* 3.5 31.8 + - - +
556B GLN* 1.3 76.3 - - - +
558B ALA* 1.3 63.2 + - - +
560B LEU* 3.2 12.8 + - + +
561B LYS* 2.9 49.3 + - + +
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Residues in contact with ALA 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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554B GLN 2.9 14.7 + - - +
555B ARG 3.6 4.0 - - - +
557B ARG* 1.3 76.8 - - - +
559B ILE* 1.3 59.1 + - - +
561B LYS* 3.2 4.0 + - - +
562B VAL* 2.8 36.3 + - - +
580B VAL* 4.2 7.0 - - + +
583B TYR* 4.2 17.5 - - + -
584B MET* 3.4 35.7 - - + -
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Residues in contact with ILE 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B ARG* 2.8 25.0 + - + +
556B GLN 3.5 6.7 - - - +
558B ALA* 1.3 75.7 - - - +
560B LEU* 1.3 57.5 + - - +
562B VAL* 3.4 0.9 + - - +
563B MET* 2.9 38.6 + - + +
576B PHE* 4.1 17.0 - - + -
580B VAL* 4.0 27.1 - - + -
595B VAL* 4.1 14.1 - - + +
598B ASP* 4.2 5.4 - - + -
599B VAL* 3.8 26.0 - - + +
602B MET* 3.7 30.7 - - + -
608B LEU* 4.1 14.1 - - + -
621B ILE* 4.9 0.2 - - + -
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Residues in contact with LEU 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B GLN* 3.0 15.2 + - + +
557B ARG* 3.2 12.5 + - + +
559B ILE* 1.3 76.6 - - - +
561B LYS* 1.3 65.9 + - + +
563B MET* 3.3 5.1 + - - +
564B ASN* 2.9 24.3 + - - +
602B MET* 3.5 26.0 - - + -
607B LYS* 4.2 28.7 - - + +
608B LEU* 4.4 1.6 - - + -
623B LEU* 4.1 23.6 - - + +
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Residues in contact with LYS 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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557B ARG* 2.9 45.1 + - + +
558B ALA* 3.8 2.5 - - - +
560B LEU* 1.3 77.7 - - + +
562B VAL* 1.3 58.7 + - - +
564B ASN* 3.4 7.3 + - + +
565B THR* 2.9 32.8 + - - -
583B TYR* 3.3 37.0 - - + +
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Residues in contact with VAL 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A THR* 4.1 7.4 - - + -
558B ALA 2.8 20.4 + - - +
559B ILE 3.8 3.6 - - - +
561B LYS* 1.3 73.3 - - - +
563B MET* 1.3 68.2 + - - +
565B THR* 3.0 7.7 + - - -
566B ILE* 2.9 30.8 + - + +
576B PHE* 4.0 18.4 - - + -
579B SER* 4.0 30.1 - - - +
580B VAL* 4.1 12.3 - - + -
583B TYR* 3.5 36.1 - - + -
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Residues in contact with MET 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 ILE* 2.9 30.2 + - + +
560B LEU 3.7 3.8 - - - +
562B VAL* 1.3 76.0 - - - +
564B ASN* 1.3 60.9 + - - +
566B ILE* 3.5 5.7 + - - +
567B GLY 3.2 4.5 + - - -
568B GLY* 2.8 55.8 + - - +
569B VAL* 3.9 2.9 - - - +
570B ALA* 3.8 13.5 - - - +
576B PHE* 3.6 28.0 - - + -
608B LEU* 4.5 8.5 - - + -
621B ILE* 3.5 33.2 - - + +
622B PHE* 3.6 9.9 - - - +
623B LEU* 3.9 18.4 - - + +
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Residues in contact with ASN 564 (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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582A LYS* 3.2 60.3 - - - +
583A TYR* 5.1 0.2 - - - -
560B LEU 2.9 13.6 + - - +
561B LYS* 3.6 11.0 - - + +
563B MET* 1.3 77.8 - - - +
565B THR* 1.3 63.8 + - - +
566B ILE 3.4 0.2 + - - -
567B GLY* 3.5 8.1 + - - -
568B GLY 4.6 0.4 + - - +
623B LEU* 4.1 16.8 - - + +
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Residues in contact with THR 565 (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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562A VAL* 4.1 20.9 - - + -
565A THR* 4.8 11.7 - - + -
566A ILE* 4.9 1.6 - - + -
579A SER* 2.8 51.3 + - - +
582A LYS* 4.1 9.9 - - - +
583A TYR* 3.9 24.2 - - + +
561B LYS 2.9 16.3 + - - -
562B VAL* 3.0 10.4 + - - -
564B ASN* 1.3 77.9 - - - +
566B ILE* 1.3 65.5 + - + +
567B GLY 3.6 0.5 + - - -
583B TYR* 4.5 3.0 - - + -
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Residues in contact with ILE 566 (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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565A THR* 4.7 4.7 - - + -
566A ILE* 4.2 23.6 - - + -
575A GLN* 5.7 2.8 + - - -
579A SER* 4.5 4.5 - - - -
562B VAL* 2.9 44.8 + - + +
563B MET* 3.8 9.6 - - - +
565B THR* 1.3 78.1 - - + +
567B GLY* 1.3 57.4 + - - +
568B GLY 4.0 0.8 + - - +
569B VAL 4.5 11.1 - - - +
570B ALA* 4.1 25.6 - - + -
576B PHE* 4.1 9.6 - - + -
579B SER* 5.1 7.0 - - - +
634B TYR* 5.9 2.1 - - - -
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Residues in contact with GLY 567 (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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582A LYS* 6.3 1.6 - - - -
563B MET 3.2 2.2 + - - -
564B ASN 3.5 6.3 + - - -
565B THR 3.4 4.6 + - - -
566B ILE* 1.3 77.7 - - - +
568B GLY* 1.3 61.6 + - - +
569B VAL* 3.4 7.8 + - - +
626B VAL* 3.9 13.6 - - - +
630B ALA* 5.4 1.4 - - - +
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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
------------------------------------------------------------
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