Contacts of the helix formed by residues 545 - 566 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A ALA 3.5 5.6 + - - +
544A MET* 1.3 75.9 - - - +
546A SER* 1.3 66.1 + - - +
547A ALA* 4.3 7.4 - - + +
548A ARG* 3.1 23.9 + - + +
549A SER* 3.2 10.3 + - - -
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Residues in contact with SER 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A MET 3.7 1.4 + - - -
545A ALA* 1.3 73.2 - - - +
547A ALA* 1.3 61.5 + - - +
549A SER* 3.2 10.0 + - - -
550A LEU* 2.9 40.9 + - - +
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Residues in contact with ALA 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A ALA* 3.2 6.1 - - + +
546A SER* 1.3 81.9 + - - +
548A ARG* 1.3 57.1 + - - +
550A LEU* 3.3 13.6 + - + +
551A ARG* 2.9 47.3 + - - +
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Residues in contact with ARG 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ALA 4.8 4.0 + - - -
544A MET* 4.0 43.5 - - + +
545A ALA* 3.1 19.2 + - + +
547A ALA* 1.3 76.2 - - - +
549A SER* 1.3 65.8 + - - +
551A ARG* 3.1 20.9 + - - +
552A SER* 2.9 21.8 + - - -
555A ARG* 4.6 0.7 + - - -
1640A GOL 2.9 41.1 + - - +
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Residues in contact with SER 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A MET* 3.4 31.3 + - - +
545A ALA 3.2 4.6 + - - -
546A SER* 3.2 14.0 + - - -
548A ARG* 1.3 78.7 - - - +
550A LEU* 1.3 60.9 + - - +
552A SER* 3.1 9.9 + - - -
553A LEU* 3.0 28.5 + - - +
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Residues in contact with LEU 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A SER* 2.9 29.3 + - - +
547A ALA* 3.5 12.3 - - + +
549A SER* 1.3 78.5 - - - +
551A ARG* 1.3 56.8 + - + +
553A LEU* 3.2 20.6 + - + +
554A GLN* 2.9 27.4 + - - +
557A ARG* 5.0 1.2 + - - -
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Residues in contact with ARG 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ALA* 2.9 23.5 + - - +
548A ARG* 3.1 40.0 + - - +
550A LEU* 1.3 71.7 - - + +
552A SER* 1.3 66.6 + - - +
554A GLN* 3.2 19.4 + - - +
555A ARG* 2.9 44.3 + - - +
1640A GOL 2.3 50.9 + - - -
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Residues in contact with SER 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A MET* 6.1 2.7 - - - -
548A ARG 2.9 11.9 + - - -
549A SER* 3.1 13.2 + - - -
551A ARG* 1.3 76.5 - - - +
553A LEU* 1.3 56.6 + - - +
555A ARG* 3.2 21.6 + - - +
556A GLN* 2.9 41.3 + - - +
598A ASP* 2.6 25.4 + - - -
601A LEU* 3.9 7.4 - - - +
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Residues in contact with LEU 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A SER* 3.0 19.5 + - - +
550A LEU* 3.2 24.4 + - + +
552A SER* 1.3 75.2 - - - +
554A GLN* 1.3 59.4 + - - +
556A GLN* 3.2 23.6 + - + +
557A ARG* 2.9 44.3 + - + +
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Residues in contact with GLN 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A LEU 2.9 14.0 + - - +
551A ARG* 3.2 23.7 + - - +
553A LEU* 1.3 75.8 - - - +
555A ARG* 1.3 58.6 + - - +
557A ARG* 3.2 32.0 + - - +
558A ALA* 2.9 27.0 + - - +
584A MET* 3.9 22.0 - - + +
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Residues in contact with ARG 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ARG 4.6 1.4 + - - -
551A ARG* 2.9 33.5 + - + +
552A SER* 3.2 18.0 + - - +
554A GLN* 1.3 76.8 - - - +
556A GLN* 1.3 57.6 + - - +
558A ALA* 3.2 3.7 + - - +
559A ILE* 2.9 37.3 + - + +
580A VAL* 5.0 0.8 - - + +
584A MET* 3.9 27.4 - - + -
594A THR* 3.2 35.3 + - - +
595A VAL* 4.2 19.5 - - + -
598A ASP* 2.6 35.8 + - + +
1640A GOL 3.7 30.7 + - - -
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Residues in contact with GLN 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A SER* 2.9 34.5 + - - +
553A LEU* 3.6 26.2 - - + +
555A ARG* 1.3 72.2 - - - +
557A ARG* 1.3 65.1 + - + +
559A ILE* 3.3 1.2 + - - -
560A LEU* 2.9 24.9 + - - +
598A ASP* 3.8 15.8 + - + -
601A LEU* 3.9 20.2 - - - +
602A MET* 3.4 42.3 + - + +
605A SER* 5.3 0.3 + - - -
607A LYS* 4.4 14.4 + - + +
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Residues in contact with ARG 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A LEU 5.0 1.0 + - - -
553A LEU* 2.9 26.7 + - + +
554A GLN* 3.2 51.1 + - - +
556A GLN* 1.3 72.9 - - - +
558A ALA* 1.3 57.9 + - - +
560A LEU* 3.3 9.9 + - + +
561A LYS* 2.9 30.4 + - - +
583A TYR* 5.3 0.9 - - - -
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Residues in contact with ALA 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A GLN 2.9 13.1 + - - +
555A ARG 3.2 8.0 + - - +
557A ARG* 1.3 74.1 - - - +
559A ILE* 1.3 65.9 + - - +
561A LYS* 3.3 1.2 + - - +
562A VAL* 2.9 30.8 + - - +
580A VAL* 4.2 6.5 - - + -
583A TYR* 3.7 22.0 - - + -
584A MET* 3.6 36.1 - - + -
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Residues in contact with ILE 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A ARG 2.9 21.4 + - - +
556A GLN 3.6 4.3 - - - +
558A ALA* 1.3 73.8 - - - +
560A LEU* 1.3 58.6 + - - +
562A VAL* 3.4 1.0 + - - +
563A MET* 2.9 37.2 + - + +
576A PHE* 4.1 15.2 - - + -
580A VAL* 4.3 23.1 - - + +
595A VAL* 4.0 12.6 - - + +
598A ASP* 4.0 12.1 - - + -
599A VAL* 3.7 38.1 - - + +
602A MET* 3.6 24.0 - - + -
608A LEU* 4.1 15.7 - - + -
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Residues in contact with LEU 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A GLN 2.9 17.4 + - - +
557A ARG* 3.6 9.0 - - + +
559A ILE* 1.3 78.0 - - - +
561A LYS* 1.3 58.1 + - - +
563A MET* 3.3 4.8 + - - +
564A ASN* 2.9 41.5 + - - +
602A MET* 4.0 16.8 - - + +
607A LYS* 4.8 14.4 - - + +
608A LEU* 5.1 1.1 - - + -
623A LEU* 3.9 24.9 - - + -
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Residues in contact with LYS 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A ARG 2.9 19.9 + - - +
558A ALA 3.3 2.9 + - - +
560A LEU* 1.3 73.3 - - - +
562A VAL* 1.3 58.0 + - - +
564A ASN* 3.3 7.6 + - + +
565A THR* 2.8 42.8 + - - +
583A TYR* 3.6 40.4 - - + +
582B LYS 3.6 11.6 + - - +
583B TYR* 3.0 35.4 + - + +
584B MET 4.9 0.4 - - - -
585B GLY* 4.4 7.1 - - - +
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Residues in contact with VAL 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558A ALA 2.9 20.8 + - - +
559A ILE 3.8 2.7 - - - +
561A LYS* 1.3 75.0 - - - +
563A MET* 1.3 64.0 + - - +
565A THR* 3.0 7.8 + - - -
566A ILE* 2.9 34.0 + - + +
576A PHE* 3.9 20.9 - - + -
579A SER* 4.0 24.5 - - - +
580A VAL* 4.1 16.4 - - + -
583A TYR* 3.6 34.1 - - + -
565B THR* 4.1 6.3 - - + -
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Residues in contact with MET 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A ILE* 2.9 23.0 + - + +
560A LEU* 3.3 4.9 + - - +
562A VAL* 1.3 77.0 - - - +
564A ASN* 1.3 60.4 + - - +
566A ILE* 3.7 5.0 - - - +
567A GLY 3.4 2.6 + - - -
568A GLY 2.9 53.9 + - - +
569A VAL* 3.9 2.2 - - - +
570A ALA* 4.0 9.9 - - - -
576A PHE* 3.5 28.9 - - + -
608A LEU* 4.2 14.4 - - + -
621A ILE* 3.5 38.4 - - + +
622A PHE* 3.6 10.1 - - - +
623A LEU* 4.0 19.1 - - + +
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Residues in contact with ASN 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A LEU* 2.9 34.9 + - - +
561A LYS* 3.6 11.6 - - + +
563A MET* 1.3 77.9 - - - +
565A THR* 1.3 64.7 + - - +
567A GLY* 3.4 10.0 + - - -
568A GLY 4.4 0.6 + - - +
623A LEU* 3.6 28.1 - - - +
582B LYS* 3.5 49.6 - - + +
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Residues in contact with THR 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561A LYS* 2.8 21.4 + - - +
562A VAL* 3.0 9.5 + - - -
564A ASN* 1.3 77.7 - - - +
566A ILE* 1.3 57.3 + - + +
567A GLY* 3.3 1.8 + - - -
562B VAL* 4.1 23.3 - - + -
565B THR* 4.8 9.0 - - + -
566B ILE* 4.7 10.3 - - + -
579B SER* 2.7 57.6 + - - +
582B LYS* 4.3 2.2 - - - -
583B TYR* 3.5 28.7 - - + -
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Residues in contact with ILE 566 (chain A).
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* 2.9 35.4 + - + +
563A MET* 3.7 11.7 - - - +
565A THR* 1.3 76.8 - - + +
567A GLY* 1.3 56.2 + - - +
568A GLY 4.5 0.9 - - - +
569A VAL 4.4 11.4 - - - +
570A ALA* 3.8 27.4 - - + -
576A PHE* 3.9 22.4 - - + -
579A SER* 4.9 9.9 - - - +
634A TYR* 6.1 0.9 - - - -
565B THR* 4.9 2.0 - - + -
566B ILE* 4.2 22.2 - - + -
575B GLN* 5.5 5.9 + - - +
579B SER* 4.6 4.0 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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