Contacts of the helix formed by residues 544 - 559 (chain A) in PDB entry 1GUX
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 ARG 544 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542A LEU 4.1 0.2 + - - -
543A THR* 1.3 73.8 - - - +
545A GLU* 1.3 86.4 + - - +
547A ILE* 3.3 10.2 + - - +
548A LYS* 3.0 46.9 + - + +
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Residues in contact with GLU 545 (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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380A ASN* 4.4 11.3 + - - -
543A THR* 3.5 14.5 + - - +
544A ARG* 1.3 117.5 + - - +
546A MET* 1.3 56.2 + - - +
548A LYS* 3.6 7.0 + - - +
549A HIS* 3.1 26.0 + - - +
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Residues in contact with MET 546 (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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382A ILE* 4.1 11.0 - - + -
493A VAL* 3.5 41.7 - - + +
496A ALA* 3.9 16.2 - - + -
497A THR* 4.7 6.5 - - - -
542A LEU* 3.9 22.9 - - + -
543A THR* 3.0 28.1 + - - +
545A GLU* 1.3 75.4 - - - +
547A ILE* 1.3 62.1 + - - +
549A HIS* 3.2 35.9 + - + +
550A LEU* 2.9 40.5 + - + +
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Residues in contact with ILE 547 (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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536A ILE* 4.3 21.3 - - + +
539A GLU 6.0 0.2 - - - +
542A LEU* 3.6 34.5 - - + +
543A THR 2.9 22.1 + - - +
544A ARG* 3.7 8.7 - - - +
546A MET* 1.3 76.6 - - - +
548A LYS* 1.3 54.0 + - + +
550A LEU* 3.3 6.6 + - - +
551A GLU* 2.8 62.9 + - + +
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Residues in contact with LYS 548 (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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544A ARG* 3.0 36.0 + - + +
545A GLU* 3.9 8.1 - - - +
547A ILE* 1.3 76.8 - - + +
549A HIS* 1.3 56.7 + - - +
551A GLU* 2.8 32.2 + - - +
552A ARG* 2.7 35.0 + - - +
555A HIS* 5.6 5.7 - - - -
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Residues in contact with HIS 549 (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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492A GLU* 2.8 31.5 + - - -
496A ALA* 3.7 15.3 - - + +
514A PHE* 4.2 7.0 - - + -
545A GLU 3.1 18.4 + - - +
546A MET* 3.2 36.3 - - + +
547A ILE 3.2 0.4 - - - -
548A LYS* 1.3 77.0 - - - +
550A LEU* 1.3 59.1 + - + +
552A ARG* 3.3 8.9 + - - +
553A CYS* 2.9 48.8 + - - -
556A ARG* 6.1 0.9 - - - -
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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
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489A CYS* 4.2 16.8 - - - -
492A GLU* 4.4 11.9 - - + -
493A VAL* 4.1 13.7 - - + -
528A PHE* 5.8 2.2 - - + -
532A ILE* 3.7 18.0 - - + +
535A PHE* 4.0 17.5 - - + -
536A ILE* 3.7 29.8 - - + -
542A LEU* 3.9 18.4 - - + -
546A MET* 2.9 39.3 + - + +
547A ILE 3.7 3.8 - - - +
549A HIS* 1.3 77.5 - - + +
551A GLU* 1.3 61.4 + - - +
553A CYS* 3.2 9.2 + - + +
554A GLU 3.0 22.5 + - - -
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Residues in contact with GLU 551 (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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532A ILE* 5.3 0.2 - - - -
536A ILE* 4.0 15.5 - - + +
547A ILE* 2.8 38.0 + - - +
548A LYS* 2.8 39.3 + - - +
550A LEU* 1.3 70.9 - - - +
552A ARG* 1.3 58.7 + - - +
554A GLU* 3.1 15.3 + - - +
555A HIS* 2.9 42.4 + - + +
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Residues in contact with ARG 552 (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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548A LYS* 2.7 23.2 + - - +
549A HIS* 3.5 9.9 - - - +
550A LEU 3.2 0.2 - - - -
551A GLU* 1.3 73.0 - - - +
553A CYS* 1.3 55.7 - - - +
555A HIS* 3.2 18.8 + - - +
556A ARG* 2.9 60.6 + - - +
559A GLU* 3.0 38.2 + - - -
661B ARG* 3.5 14.3 - - - +
733B HIS* 3.7 35.3 + - - +
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Residues in contact with CYS 553 (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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492A GLU* 4.5 5.2 - - - -
514A PHE* 3.4 51.7 - - + -
528A PHE* 4.9 1.8 - - + -
532A ILE* 4.6 7.2 - - + -
549A HIS* 2.9 47.7 + - - -
550A LEU* 3.2 13.0 + - + +
552A ARG* 1.3 74.2 - - - +
554A GLU* 1.3 62.5 + - - +
556A ARG* 3.3 6.7 + - - +
557A ILE* 3.1 28.6 + - - +
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Residues in contact with GLU 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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529A TYR* 3.8 25.4 - - + +
532A ILE* 3.8 25.4 - - + +
533A GLU* 4.5 11.2 + - - +
550A LEU 3.0 12.3 + - - +
551A GLU* 3.1 16.1 + - - +
553A CYS* 1.3 76.5 - - - +
555A HIS* 1.3 66.0 + - - +
557A ILE* 3.1 7.4 + - - +
558A MET* 2.9 40.3 + - - +
653B LYS* 2.9 38.4 + - - +
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Residues in contact with HIS 555 (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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548A LYS* 5.6 4.9 - - - -
551A GLU* 2.9 29.4 + - + +
552A ARG* 3.6 25.2 + - - +
554A GLU* 1.3 82.5 + - - +
556A ARG* 1.3 61.1 + - - +
558A MET* 3.8 26.0 - - + +
559A GLU* 2.8 35.9 + - - +
657B LEU* 4.1 30.0 - - + +
661B ARG* 4.2 3.2 + - - +
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Residues in contact with ARG 556 (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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514A PHE* 3.1 43.5 - - + +
515A PRO* 4.2 10.0 - - - +
549A HIS* 6.1 0.8 - - - -
552A ARG* 2.9 60.5 + - - +
553A CYS* 3.6 10.0 - - - +
554A GLU 3.2 0.2 - - - -
555A HIS* 1.3 75.3 - - - +
557A ILE* 1.3 58.7 + - - +
559A GLU* 3.7 10.1 - - - +
560A SER* 3.1 26.5 + - - +
561A LEU* 3.2 25.1 + - + +
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Residues in contact with ILE 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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514A PHE* 4.1 13.7 - - + -
525A ALA* 3.6 42.0 - - + +
526A PHE 4.2 0.2 - - - +
528A PHE* 3.7 25.1 - - + -
529A TYR* 3.7 26.0 - - + -
532A ILE* 4.0 7.0 - - + -
553A CYS 3.1 17.1 + - - +
554A GLU* 3.1 6.3 + - - +
556A ARG* 1.3 77.8 - - - +
558A MET* 1.3 62.1 + - - +
559A GLU 3.4 0.3 + - - -
560A SER 3.6 0.5 + - - -
561A LEU* 3.6 10.3 + - + -
562A ALA* 2.8 45.5 + - + +
650B PHE* 5.3 0.4 - - + -
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Residues in contact with MET 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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529A TYR* 4.8 5.4 - - + -
554A GLU* 2.9 42.1 + - - +
555A HIS* 3.8 13.2 - - + +
557A ILE* 1.3 75.6 - - - +
559A GLU* 1.3 54.9 + - - +
563A TRP* 2.6 26.9 + - - -
650B PHE* 3.8 28.9 - - + -
653B LYS* 3.2 46.2 - - + +
654B VAL* 3.9 15.9 - - + +
657B LEU* 3.7 28.9 - - + -
700B LEU* 4.5 5.5 - - + +
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Residues in contact with GLU 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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552A ARG* 3.0 29.1 + - - -
555A HIS 2.8 22.1 + - - +
556A ARG* 3.5 12.9 - - - +
558A MET* 1.3 75.4 - - - +
560A SER* 1.3 64.0 + - - +
563A TRP* 4.0 2.2 - - - -
657B LEU* 4.6 1.1 - - + -
661B ARG* 2.8 48.9 + - - +
695B MET* 3.8 2.9 - - - +
698B ARG 3.7 1.2 - - - +
699B HIS* 3.2 33.0 + - + +
700B LEU* 2.9 39.2 + - + +
733B HIS* 3.9 2.1 + - - -
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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