Contacts of the helix formed by residues 502 - 519 (chain C) in PDB entry 2R17
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 ASP 502 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500C SER 3.7 1.5 + - - -
501C GLU* 1.3 77.9 - - - +
503C PRO* 1.3 70.3 - - + +
504C ASP* 4.8 5.1 + - - +
505C GLN* 3.0 59.5 + - - +
506C GLN* 3.1 7.8 + - - +
542C ARG* 5.2 1.8 - - - +
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Residues in contact with PRO 503 (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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501C GLU 4.1 1.3 - - - +
502C ASP* 1.3 87.4 - - + +
504C ASP* 1.3 62.6 + - - +
505C GLN 3.1 0.9 + - - -
506C GLN* 3.1 25.3 + - - +
507C TYR 3.7 0.5 + - - -
539C LEU* 4.2 2.0 - - + -
542C ARG* 3.1 52.5 - - + +
543C TYR* 3.6 38.6 + - + -
546C ASN* 3.8 17.0 - - - +
556C LYS* 6.1 0.4 - - + -
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Residues in contact with ASP 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C ASP* 3.5 6.5 + - - +
503C PRO* 1.3 77.8 - - - +
505C GLN* 1.3 61.0 - - - +
506C GLN 3.8 0.2 + - - -
507C TYR* 4.1 9.0 + - - +
508C LEU* 4.3 8.1 + - - +
543C TYR* 4.5 6.5 - - - -
556C LYS* 2.8 35.3 + - - +
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Residues in contact with GLN 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C GLU* 4.4 10.3 + - + +
502C ASP* 3.0 44.1 + - - +
504C ASP* 1.3 80.7 - - - +
506C GLN* 1.3 60.3 + - - +
508C LEU* 3.4 14.5 + - + +
509C ILE* 3.0 42.9 + - + +
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Residues in contact with GLN 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C LEU* 2.9 52.7 + - + +
499C ARG* 3.5 15.0 + - - +
501C GLU* 3.1 19.6 + - + +
502C ASP 3.2 9.4 - - - +
503C PRO* 3.1 19.7 + - - +
505C GLN* 1.3 74.1 - - - +
507C TYR* 1.3 56.3 + - - +
509C ILE* 3.0 4.1 + - - +
510C LEU* 2.6 39.1 + - - +
539C LEU* 3.5 34.3 - - + +
542C ARG* 4.5 7.5 - - - +
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Residues in contact with TYR 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C PRO 3.7 3.4 + - - -
504C ASP* 4.5 7.2 - - - +
505C GLN 3.5 0.8 - - - -
506C GLN* 1.3 77.6 - - - +
508C LEU* 1.3 60.7 + - + +
510C LEU* 3.5 4.6 + - + +
511C ASN* 3.0 55.6 + - + +
539C LEU* 3.8 6.4 - - - +
543C TYR* 3.4 19.3 - - - +
556C LYS 5.8 0.2 - - - -
559C LYS* 3.4 52.2 + - + +
560C ILE* 3.8 22.0 - - + -
563C PHE* 4.0 26.7 - + + +
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Residues in contact with LEU 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504C ASP 4.3 5.5 + - - +
505C GLN* 3.4 17.7 + - + +
506C GLN 3.1 0.4 - - - -
507C TYR* 1.3 82.6 - - + +
509C ILE* 1.3 67.7 + - + +
511C ASN* 3.2 6.8 + - + +
512C THR* 2.9 41.7 + - + +
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Residues in contact with ILE 509 (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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494C PHE* 3.8 25.1 - - + -
498C LEU* 4.7 7.4 - - + -
501C GLU* 4.1 24.9 - - + -
505C GLN* 3.0 37.2 - - + +
506C GLN* 3.0 7.4 + - - +
508C LEU* 1.3 80.2 - - + +
510C LEU* 1.3 58.1 + - - +
512C THR* 3.4 10.7 + - - +
513C ALA* 3.0 27.7 + - - +
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Residues in contact with LEU 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C PHE* 4.1 2.4 - - + -
498C LEU* 3.3 30.3 - - + -
506C GLN 2.6 17.4 + - - +
507C TYR* 3.7 5.8 - - + +
509C ILE* 1.3 71.4 - - - +
511C ASN* 1.3 58.0 + - - +
513C ALA* 3.5 4.2 + - - +
514C ARG* 3.1 26.7 + - - +
532C LEU* 3.6 37.4 - - + +
535C ALA* 3.6 25.8 - - + -
536C ALA* 3.8 16.8 - - - +
539C LEU* 4.3 18.6 - - + -
560C ILE* 4.4 5.8 - - + -
563C PHE* 3.8 15.5 - - + -
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Residues in contact with ASN 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C TYR* 3.0 49.3 + - + +
508C LEU* 3.2 10.0 + - + +
510C LEU* 1.3 77.0 - - - +
512C THR* 1.3 61.3 + - + +
514C ARG* 3.1 15.2 + - - +
515C LYS* 2.9 45.0 + - - +
563C PHE* 4.0 19.1 - - - -
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Residues in contact with THR 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508C LEU* 2.9 33.8 + - + +
509C ILE* 3.4 10.8 + - - +
511C ASN* 1.3 73.8 - - + +
513C ALA* 1.3 63.5 + - - +
515C LYS* 3.7 11.5 - - + +
516C HIS* 2.8 31.2 + - - +
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Residues in contact with ALA 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C PHE* 3.4 43.3 - - + -
509C ILE 3.0 10.0 + - - +
510C LEU 3.7 5.4 - - - +
511C ASN 3.2 0.2 - - - -
512C THR* 1.3 77.1 + - - +
514C ARG* 1.3 58.3 + - - +
516C HIS* 3.5 5.7 + - - +
517C PHE* 2.9 42.3 + - + -
532C LEU* 4.0 9.6 - - + -
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Residues in contact with ARG 514 (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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510C LEU 3.1 14.6 + - - +
511C ASN* 3.2 19.1 - - - +
512C THR 3.1 0.2 - - - -
513C ALA* 1.3 74.0 - - - +
515C LYS* 1.3 62.7 + - - +
517C PHE* 3.1 1.9 + - - +
518C GLY* 2.4 40.0 + - - -
529C LEU* 4.6 14.7 - - + +
532C LEU* 3.8 12.1 - - + +
563C PHE* 3.4 27.8 + - + -
566C GLN* 3.3 48.8 + - - +
567C THR* 3.2 23.8 + - - +
570C ALA* 4.8 8.6 - - - +
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Residues in contact with LYS 515 (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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511C ASN* 2.9 34.9 + - - +
512C THR* 3.8 11.0 - - + +
514C ARG* 1.3 83.5 - - + +
516C HIS* 1.3 64.5 + - - +
518C GLY* 3.1 10.3 + - - +
519C ALA* 3.2 14.0 + - - +
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Residues in contact with HIS 516 (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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487C GLU* 4.7 7.9 - - - -
490C LEU* 6.5 0.2 - - + -
512C THR 2.8 22.3 + - - +
513C ALA* 3.6 8.1 - - - +
515C LYS* 1.3 76.0 - - - +
517C PHE* 1.3 82.9 + + - +
519C ALA* 3.4 11.9 + - - +
520C GLY* 3.9 4.9 + - - -
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Residues in contact with PHE 517 (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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487C GLU* 3.8 29.2 - - + -
490C LEU* 4.0 20.0 - - + -
491C VAL* 3.5 32.8 - - + -
494C PHE* 5.1 6.7 - + + -
513C ALA* 2.9 32.8 + - + +
514C ARG 3.9 1.6 - - - +
516C HIS* 1.3 89.8 - + + +
518C GLY* 1.3 60.2 + - - +
519C ALA 3.2 0.2 - - - -
520C GLY* 2.8 22.8 + - - +
524C ARG* 5.7 0.2 - - - +
525C ILE* 3.6 13.4 + - - +
528C THR* 3.0 40.5 - - + +
529C LEU* 4.2 4.5 - - + -
532C LEU* 4.0 16.4 - - + -
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Residues in contact with GLY 518 (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 ARG* 2.4 23.8 + - - -
515C LYS* 3.5 4.9 - - - -
516C HIS 3.1 0.4 - - - -
517C PHE* 1.3 70.2 - - - +
519C ALA* 1.3 56.0 + - - +
520C GLY 3.0 8.2 + - - -
521C GLY 4.1 10.9 + - - +
525C ILE* 4.5 7.8 - - - +
529C LEU* 5.2 5.8 - - - -
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Residues in contact with ALA 519 (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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515C LYS 3.2 9.8 + - - +
516C HIS* 3.4 9.8 + - - +
517C PHE 3.2 0.6 - - - -
518C GLY* 1.3 75.5 - - - +
520C GLY* 1.3 61.8 + - - +
521C GLY* 3.4 2.0 + - - -
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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
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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