Contacts of the helix formed by residues 521 - 539 (chain C) in PDB entry 3GQL
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 THR 521 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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738A HIS* 5.4 0.7 + - - -
739A ALA* 5.6 1.8 - - - -
740A VAL* 5.0 2.6 - - - +
516C LEU* 4.8 0.2 - - - +
519C ASP 3.6 4.1 + - - -
520C ALA* 1.3 79.2 - - - +
522C GLU* 1.3 70.9 + - - +
523C LYS* 3.4 15.3 + - + +
524C ASP* 2.8 53.2 + - - +
525C LEU* 3.6 10.6 + - - +
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Residues in contact with GLU 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A ALA* 4.3 23.4 - - + +
740A VAL* 4.2 24.7 - - + +
521C THR* 1.3 79.1 + - - +
523C LYS* 1.3 62.7 + - - +
525C LEU* 3.8 5.7 - - - +
526C SER* 3.4 17.7 + - - -
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Residues in contact with LYS 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C THR* 3.1 13.6 + - + +
522C GLU* 1.3 77.3 - - - +
524C ASP* 1.3 54.3 + - - +
525C LEU 3.1 2.0 - - - -
526C SER* 2.7 29.1 + - - -
527C ASP* 2.8 34.8 + - - +
646C ARG* 5.0 3.6 - - - +
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Residues in contact with ASP 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C ALA 4.6 9.7 - - - +
489C PHE* 4.3 18.0 - - - +
516C LEU* 3.5 24.0 - - + +
519C ASP 4.9 0.5 - - - +
520C ALA* 3.9 4.9 - - - -
521C THR* 2.8 39.1 + - - +
523C LYS* 1.3 77.8 - - - +
525C LEU* 1.3 52.4 + - - +
527C ASP* 3.1 13.8 + - - +
528C LEU* 2.7 35.0 + - - +
646C ARG* 5.5 1.9 + - - -
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Residues in contact with LEU 525 (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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738A HIS* 6.1 0.7 - - - +
740A VAL* 3.6 38.6 - - + -
742A SER* 4.6 1.1 - - - +
743A GLN* 3.6 36.8 - - + +
465C LEU* 4.9 1.8 - - + -
516C LEU* 3.5 21.0 - - + +
521C THR 3.6 6.7 + - - +
522C GLU* 3.8 9.6 - - - +
523C LYS 3.1 0.2 - - - -
524C ASP* 1.3 79.4 - - - +
526C SER* 1.3 58.2 + - - +
528C LEU* 3.6 1.4 - - - +
529C ILE* 2.8 59.9 + - + +
557C LEU* 4.2 11.4 - - + -
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Residues in contact with SER 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C GLU 3.4 11.0 + - - -
523C LYS* 2.7 21.0 + - - -
525C LEU* 1.3 77.0 - - - +
527C ASP* 1.3 57.6 + - - -
529C ILE* 3.8 10.1 - - - +
530C SER* 2.9 28.4 + - - -
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Residues in contact with ASP 527 (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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523C LYS* 2.8 30.1 + - - +
524C ASP* 3.4 12.8 - - - +
526C SER* 1.3 77.1 - - - +
528C LEU* 1.3 60.3 + - - +
530C SER* 3.1 8.3 + - - -
531C GLU* 2.8 30.0 + - - +
645C ALA 4.9 8.6 - - - +
646C ARG* 2.6 33.9 + - - +
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Residues in contact with LEU 528 (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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514C LYS* 3.8 39.3 - - + +
515C MET* 4.3 3.4 - - - -
516C LEU* 3.7 34.1 - - + +
524C ASP 2.7 19.9 + - - +
525C LEU* 3.6 6.1 - - - +
527C ASP* 1.3 72.8 - - - +
529C ILE* 1.3 62.9 + - - +
531C GLU* 3.3 11.8 + - - +
532C MET* 3.0 22.0 + - - +
557C LEU* 3.4 40.6 - - + +
559C VAL* 3.8 13.2 - - + +
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Residues in contact with ILE 529 (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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465C LEU* 3.4 36.6 - - + -
525C LEU* 2.8 44.6 + - + +
526C SER* 3.8 8.3 - - - +
528C LEU* 1.3 75.5 - - - +
530C SER* 1.3 63.0 + - - +
532C MET* 3.2 20.0 + - + +
533C GLU* 3.0 31.1 + - + +
557C LEU* 4.0 19.3 - - + -
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Residues in contact with SER 530 (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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526C SER 2.9 19.6 + - - -
527C ASP* 3.3 10.3 - - - -
529C ILE* 1.3 78.8 - - - +
531C GLU* 1.3 61.7 + - - +
533C GLU* 3.1 9.6 + - - +
534C MET* 3.0 28.8 + - - +
645C ALA* 5.4 9.3 - - - +
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Residues in contact with GLU 531 (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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1C GQL 3.2 30.8 - - - +
514C LYS* 2.6 33.1 + - - +
527C ASP 2.8 15.1 + - - +
528C LEU* 3.5 14.1 - - + +
530C SER* 1.3 71.3 - - - +
532C MET* 1.3 65.2 + - - +
534C MET* 3.2 5.3 + - - +
535C MET* 3.2 42.3 + - + +
559C VAL* 6.1 0.4 - - - -
641C ASP* 6.0 0.2 - - - -
643C GLY* 3.1 29.6 - - - +
644C LEU* 3.2 20.1 - - + +
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Residues in contact with MET 532 (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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465C LEU* 5.9 1.3 - - + -
528C LEU 3.0 13.3 + - - +
529C ILE* 3.4 23.3 - - + +
531C GLU* 1.3 78.3 - - - +
533C GLU* 1.3 79.5 + - - +
535C MET* 3.5 11.7 + - - +
536C LYS* 3.3 40.9 + - - +
547C LEU* 3.5 14.2 - - + +
550C ALA* 3.8 27.6 - - - -
552C THR* 4.1 20.2 - - + -
557C LEU* 4.4 11.2 - - + -
559C VAL* 4.3 15.7 - - + +
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Residues in contact with GLU 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529C ILE* 3.0 22.2 + - + +
530C SER* 3.1 9.4 + - - +
532C MET* 1.3 87.9 - - - +
534C MET* 1.3 60.5 + - - +
536C LYS* 3.0 39.1 + - - +
537C MET* 2.9 28.9 + - - +
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Residues in contact with MET 534 (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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530C SER* 3.0 20.1 + - - +
531C GLU* 3.4 10.8 - - - +
533C GLU* 1.3 75.8 - - - +
535C MET* 1.3 57.4 + - - +
537C MET* 3.1 8.6 + - - +
538C ILE* 2.7 58.0 + - + +
619C CYS* 5.0 9.4 - - + -
642C PHE 4.6 4.0 - - - +
643C GLY* 4.4 28.3 - - - +
644C LEU 5.1 4.9 - - - +
645C ALA* 6.1 5.8 - - + -
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Residues in contact with MET 535 (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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1C GQL 4.0 24.5 - - + +
471C TRP* 5.6 1.0 - - - -
531C GLU* 3.2 46.1 + - + +
532C MET* 3.8 5.4 - - - +
533C GLU 3.3 0.2 - - - -
534C MET* 1.3 74.9 - - + +
536C LYS* 1.3 65.1 + - - +
538C ILE* 4.1 7.5 - - - +
539C GLY* 3.2 22.5 + - - +
545C ILE 4.6 3.4 - - - +
547C LEU* 4.1 23.1 - - + +
559C VAL* 4.0 27.4 - - + -
561C VAL* 4.2 15.7 - - + -
642C PHE* 4.1 22.7 - - + -
643C GLY* 5.2 2.7 - - - -
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Residues in contact with LYS 536 (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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468C ASP* 3.3 30.1 + - - +
470C ARG* 4.5 8.5 - - - +
471C TRP* 3.2 52.2 - - + +
532C MET* 3.3 32.6 + - - +
533C GLU* 3.0 40.2 + - - +
535C MET* 1.3 81.0 - - - +
537C MET* 1.3 64.3 + - - +
539C GLY* 3.4 8.3 + - - -
547C LEU* 3.7 9.4 - - + -
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Residues in contact with MET 537 (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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533C GLU 2.9 11.9 + - - +
534C MET* 3.4 12.8 - - - +
536C LYS* 1.3 78.3 - - - +
538C ILE* 1.3 65.3 + - + +
539C GLY* 3.2 2.1 + - - -
617C LYS* 3.8 11.7 + - - -
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Residues in contact with ILE 538 (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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534C MET* 2.7 53.4 + - + +
535C MET* 4.1 4.9 - - - +
537C MET* 1.3 75.1 - - + +
539C GLY* 1.3 66.3 + - - +
544C ILE* 4.7 3.6 - - + -
613C TYR* 2.8 23.9 + - + -
614C LEU* 4.0 21.8 - - + -
617C LYS* 3.3 36.7 - - + +
619C CYS* 4.4 15.0 - - + -
642C PHE* 4.2 24.7 - - + +
643C GLY* 5.0 0.7 - - - -
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Residues in contact with GLY 539 (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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535C MET 3.2 17.4 + - - +
536C LYS 3.4 7.1 + - - -
537C MET 3.2 4.5 + - - -
538C ILE* 1.3 82.9 - - - +
540C LYS* 1.3 64.1 + - - -
544C ILE* 3.7 12.3 - - - +
546C ASN* 4.1 0.9 - - - +
613C TYR* 3.5 12.0 - - - -
617C LYS* 5.3 1.1 - - - -
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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
------------------------------------------------------------
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