Contacts of the helix formed by residues 556 - 574 (chain C) in PDB entry 2G4D
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 ASN 556 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498C PHE* 5.5 2.9 - - - -
502C LYS* 5.6 2.6 - - - +
528C ILE* 5.4 2.0 - - - +
530C LEU* 4.1 19.0 - - - +
548C TYR* 3.3 44.6 + - + +
555C ILE* 1.3 81.4 - - - +
557C ASN* 1.3 60.3 + - - +
558C GLU* 2.9 22.0 - - - +
559C ALA* 3.1 40.4 + - - +
560C CYS 3.7 2.1 + - - -
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Residues in contact with ASN 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555C ILE* 3.1 21.7 + - + +
556C ASN* 1.3 74.5 - - - +
558C GLU* 1.3 61.6 + - - +
559C ALA 3.2 0.2 - - - -
560C CYS* 3.2 12.4 + - + +
561C ARG* 3.1 44.9 + - - +
586C LEU* 4.9 7.2 - - + +
587C PHE* 3.5 8.2 - - - -
588C SER* 3.3 32.2 + - - -
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Residues in contact with GLU 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498C PHE* 5.8 0.2 - - - -
502C LYS* 4.8 11.9 - - - +
556C ASN* 3.9 15.0 - - - +
557C ASN* 1.3 77.9 - - - +
559C ALA* 1.3 64.7 + - - +
561C ARG* 2.9 24.8 + - + +
562C ILE* 2.9 41.8 + - + +
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Residues in contact with ALA 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C PHE* 3.6 29.0 - - + -
528C ILE* 4.4 4.5 - - + -
537C ALA* 5.5 1.1 - - + -
548C TYR* 4.1 13.5 - - + -
556C ASN* 3.1 33.5 + - + +
558C GLU* 1.3 80.9 - - - +
560C CYS* 1.3 60.8 + - - +
562C ILE* 3.3 6.2 + - - +
563C LEU* 3.1 28.9 + - - +
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Residues in contact with CYS 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537C ALA* 5.9 2.5 - - - -
546C ILE* 3.4 38.0 - - + +
547C THR 4.3 0.2 - - - -
548C TYR* 3.8 24.0 - - - -
556C ASN 4.2 4.0 - - - -
557C ASN* 3.2 10.4 + - - +
558C GLU 3.1 0.2 - - - -
559C ALA* 1.3 78.2 - - - +
561C ARG* 1.3 61.0 + - - +
563C LEU* 3.3 2.8 + - - +
564C LEU* 2.9 23.4 + - - +
586C LEU* 3.4 27.0 - - + +
587C PHE 3.5 19.3 - - - +
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Residues in contact with ARG 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557C ASN* 3.1 26.7 + - - +
558C GLU* 2.9 44.6 + - + +
560C CYS* 1.3 73.4 - - - +
562C ILE* 1.3 67.1 + - + +
564C LEU* 3.3 1.8 + - - +
565C GLN* 2.9 27.4 + - - +
586C LEU* 3.7 19.0 - - + +
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Residues in contact with ILE 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498C PHE* 3.9 23.8 - - + -
501C LEU* 3.7 33.6 - - + +
502C LYS* 3.6 33.4 - - + -
558C GLU* 2.9 34.0 + - + +
559C ALA 3.4 6.7 - - - +
560C CYS 3.3 0.2 - - - -
561C ARG* 1.3 77.6 - - + +
563C LEU* 1.3 57.0 + - - +
565C GLN* 3.2 7.5 + - - +
566C TYR* 2.9 25.1 + - - +
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Residues in contact with LEU 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497C PHE* 4.5 11.4 - - + -
498C PHE* 4.1 15.9 - - + -
501C LEU* 4.0 22.9 - - + -
526C VAL* 4.1 17.9 - - + -
537C ALA* 3.5 31.9 - - + -
539C VAL* 4.7 9.4 - - + +
546C ILE* 4.1 22.9 - - + -
559C ALA 3.1 15.0 + - - +
560C CYS 3.7 7.6 - - - +
561C ARG 3.2 0.2 - - - -
562C ILE* 1.3 74.6 - - - +
564C LEU* 1.3 61.1 + - - +
566C TYR* 3.2 8.7 + - + +
567C LEU* 2.9 30.8 + - - +
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Residues in contact with LEU 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546C ILE* 3.6 20.4 - - + +
560C CYS 2.9 16.5 + - - +
561C ARG* 3.3 3.1 + - - +
563C LEU* 1.3 74.0 - - - +
565C GLN* 1.3 68.4 + - - +
567C LEU* 3.3 4.1 + - + +
568C LYS* 3.1 34.2 + - - +
579C PHE* 3.6 28.0 - - + -
581C THR* 4.2 21.8 - - + -
584C TRP* 4.5 15.0 - - + +
586C LEU* 3.8 23.8 - - + -
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Residues in contact with GLN 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561C ARG 2.9 14.2 + - - +
562C ILE* 3.4 11.9 - - - +
564C LEU* 1.3 80.2 - - - +
566C TYR* 1.3 55.0 + - - +
568C LYS* 2.7 62.8 + - - +
569C GLN* 2.9 26.5 + - + +
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Residues in contact with TYR 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493C PHE* 3.6 17.4 - + - -
497C PHE* 3.3 37.3 - + - -
501C LEU* 4.0 18.8 - - + -
506C TYR* 3.7 32.3 - + - -
509C VAL* 4.5 5.9 + - + -
513C THR* 3.3 30.3 + - - +
518C VAL* 4.8 4.3 - - + -
524C LEU* 5.6 1.1 - - + -
562C ILE 2.9 14.2 + - - +
563C LEU* 3.2 17.0 - - + +
565C GLN* 1.3 75.6 - - - +
567C LEU* 1.3 79.0 + - + +
569C GLN* 2.9 19.2 + - - +
570C GLU* 2.9 34.3 + - + +
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Residues in contact with LEU 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518C VAL* 4.4 4.7 - - + -
519C PHE* 3.5 11.1 - - + -
524C LEU* 4.0 15.5 - - + -
539C VAL* 4.1 10.5 - - + -
541C PHE* 3.7 24.7 - - + -
546C ILE* 4.1 23.8 - - + -
563C LEU 2.9 15.9 + - - +
564C LEU* 3.6 7.4 - - + +
565C GLN 3.2 0.2 - - - -
566C TYR* 1.3 84.9 - - + +
568C LYS* 1.3 60.5 + - - +
570C GLU* 3.9 2.9 - - - -
571C SER* 3.2 26.0 + - - -
579C PHE* 3.6 36.6 - - + +
584C TRP* 4.1 13.2 - - + -
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Residues in contact with LYS 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564C LEU* 3.1 23.3 + - - +
565C GLN* 2.7 46.3 + - - +
567C LEU* 1.3 79.6 - - - +
569C GLN* 1.3 60.0 + - + -
571C SER* 3.8 2.4 + - - -
572C ILE* 3.6 27.7 + - + +
579C PHE* 3.9 24.9 + - + +
581C THR* 3.3 27.1 + - + +
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Residues in contact with GLN 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C TYR* 3.1 59.7 - - + +
507C GLN* 4.8 4.2 + - - -
565C GLN* 2.9 24.9 + - + +
566C TYR* 2.9 5.1 + - - +
568C LYS* 1.3 76.0 - - + +
570C GLU* 1.3 60.0 + - - +
572C ILE* 3.3 6.5 + - - +
573C ASP* 2.8 31.0 + - - +
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Residues in contact with GLU 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C TYR* 2.8 25.0 + - - +
513C THR* 2.5 34.4 + - - +
516C VAL 5.0 1.2 - - - +
518C VAL* 3.9 12.0 + - + +
519C PHE* 3.5 20.6 - - + -
566C TYR* 2.9 46.7 + - + +
567C LEU* 4.5 0.7 - - - -
569C GLN* 1.3 72.9 - - - +
571C SER* 1.3 53.9 + - - +
572C ILE 2.8 10.2 + - - -
573C ASP 3.0 0.3 + - - -
574C LYS* 2.7 62.8 + - - +
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Residues in contact with SER 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519C PHE* 3.2 19.9 - - - -
567C LEU 3.2 17.0 + - - -
568C LYS 4.0 2.0 - - - -
570C GLU* 1.3 78.3 - - - +
572C ILE* 1.3 53.7 + - - +
575C LYS* 3.4 7.9 + - - +
576C ARG 3.1 17.5 + - - -
577C LYS* 2.7 34.4 + - - +
579C PHE* 3.4 36.3 + - - -
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Residues in contact with ILE 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568C LYS* 3.6 14.5 + - + +
569C GLN* 3.3 10.0 + - - +
570C GLU 2.8 1.8 + - - -
571C SER* 1.3 77.6 - - - +
573C ASP* 1.3 68.5 + - + +
574C LYS 3.2 1.1 - - - -
576C ARG* 3.1 42.6 + - - +
577C LYS 3.2 19.3 - - - +
578C GLU* 4.4 24.7 - - + +
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Residues in contact with ASP 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C TYR* 3.0 30.0 - - + +
510C LYS* 3.9 23.9 + - - +
569C GLN 2.8 13.5 + - - +
570C GLU* 3.9 0.7 - - - +
572C ILE* 1.3 77.7 - - + +
574C LYS* 1.3 95.3 + - - +
576C ARG* 4.0 15.8 + - - +
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Residues in contact with LYS 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C TYR* 3.9 0.2 + - - -
510C LYS 2.6 30.1 + - - -
511C ARG* 5.7 0.2 - - - +
513C THR* 3.0 28.5 + - - +
514C LYS* 4.5 7.6 - - - +
516C VAL 5.8 1.6 - - - +
517C ASP* 5.5 4.0 - - - +
519C PHE* 5.2 3.1 - - + -
570C GLU* 2.7 53.8 + - - +
573C ASP* 1.3 94.2 + - - +
575C LYS* 1.3 69.3 + - + +
576C ARG* 3.4 4.7 - - - -
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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