Contacts of the helix formed by residues 508 - 520 (chain C) in PDB entry 1Z5S
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 508 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466C PRO* 3.8 10.5 - - + +
507C PHE* 1.3 74.4 - - - +
509C SER* 1.3 63.8 + - - +
510C ASN* 2.8 25.6 + - - +
511C THR* 2.8 51.7 + - - +
512C PHE* 3.4 8.7 + - - +
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Residues in contact with SER 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C PHE* 3.9 28.3 - - - -
507C PHE* 3.5 10.2 + - - -
508C ASN* 1.3 72.5 + - - +
510C ASN* 1.3 74.0 + - - +
512C PHE* 3.1 11.7 + - - +
513C LEU* 3.1 21.8 + - - +
552C PRO* 4.6 7.1 - - - +
555C LEU* 4.0 17.5 - - - +
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Residues in contact with ASN 510 (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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132A GLU* 4.8 7.9 - - - +
508C ASN* 2.8 19.0 + - - +
509C SER* 1.3 78.9 + - - +
511C THR* 1.3 63.0 + - - +
512C PHE 3.0 1.6 - - - -
513C LEU* 3.4 5.1 + - - +
514C THR* 2.9 31.5 + - - +
555C LEU* 4.0 18.5 - - - +
558C LEU* 4.0 17.8 - - + +
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Residues in contact with THR 511 (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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466C PRO* 3.8 20.8 - - + +
467C GLU 5.7 0.2 - - - +
508C ASN* 2.8 41.0 + - - +
510C ASN* 1.3 72.8 - - - +
512C PHE* 1.3 60.2 + - - +
514C THR* 3.7 5.0 - - - -
515C ARG* 3.1 33.6 + - + +
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Residues in contact with PHE 512 (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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466C PRO* 3.9 14.5 - - + +
469C VAL* 3.9 16.6 - - + -
470C VAL* 3.2 44.6 - - + -
473C PHE* 4.7 10.1 - + + -
498C MET* 3.2 34.8 - - + -
502C PHE* 4.3 13.2 - + - -
507C PHE* 4.3 11.4 - + + -
508C ASN 3.4 5.8 + - - +
509C SER* 3.1 13.9 + - - +
510C ASN 3.0 0.6 - - - -
511C THR* 1.3 75.3 - - - +
513C LEU* 1.3 77.9 + - + +
514C THR 2.7 5.4 + - - -
515C ARG* 2.9 3.1 + - - +
516C LEU* 2.8 40.7 + - + +
542C LEU* 6.0 2.9 - - + -
545C MET* 5.0 4.9 - - + -
551C PHE* 5.9 1.8 - + - -
555C LEU* 5.5 1.8 - - + -
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Residues in contact with LEU 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ALA* 4.3 10.1 - - + -
509C SER 3.1 8.8 + - - +
510C ASN* 3.8 9.6 - - - +
512C PHE* 1.3 85.9 - - + +
514C THR* 1.3 60.6 + - - +
516C LEU* 3.5 9.6 - - + +
517C LEU* 3.1 55.6 + - + +
551C PHE* 6.2 1.1 - - + -
555C LEU* 4.3 22.9 - - + +
558C LEU* 3.8 30.7 - - + -
559C LEU* 3.8 34.5 - - + -
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Residues in contact with THR 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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88A PRO* 4.9 18.6 - - + +
130A GLN* 6.3 0.7 - - - -
131A ALA* 4.6 9.4 + - + +
510C ASN* 2.9 21.1 + - - +
511C THR* 3.7 7.2 - - - -
512C PHE 2.7 5.1 + - - -
513C LEU* 1.3 76.9 - - - +
515C ARG* 1.3 63.6 + - + +
516C LEU 2.7 13.9 + - - -
517C LEU* 2.8 19.4 + - - +
518C VAL* 2.8 24.8 + - + +
523C LEU* 4.5 12.8 - - + -
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Residues in contact with ARG 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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467C GLU* 2.9 49.1 + - + +
470C VAL* 3.7 11.4 - - + +
511C THR* 3.1 26.9 + - + +
512C PHE 2.9 5.3 + - - +
514C THR* 1.3 83.7 - - + +
516C LEU* 1.3 60.4 + - - +
518C VAL* 3.7 30.0 - - - +
519C HIS* 3.2 36.0 + - - -
525C SER* 3.9 4.2 - - - +
526C GLU 5.2 0.8 - - - +
527C ASP* 3.7 22.6 + - - -
529C VAL* 4.2 16.0 - - - +
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Residues in contact with LEU 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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470C VAL* 3.9 17.9 - - + +
473C PHE* 4.1 15.7 - - + -
474C LEU* 3.7 30.3 - - + -
512C PHE* 2.8 32.5 + - + +
513C LEU* 3.5 16.6 - - + +
514C THR 2.7 1.2 + - - -
515C ARG* 1.3 76.0 - - - +
517C LEU* 1.3 69.7 + - + +
519C HIS* 3.0 5.5 + - - +
520C MET* 2.9 53.6 + - - +
542C LEU* 4.5 18.8 - - + -
559C LEU* 5.4 0.9 - - + -
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Residues in contact with LEU 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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131A ALA* 4.2 7.9 - - + -
513C LEU* 3.1 35.3 + - + +
514C THR* 2.8 7.5 + - - +
516C LEU* 1.3 86.6 - - + +
518C VAL* 1.3 59.4 + - - +
520C MET* 3.3 6.6 + - - -
522C LEU* 2.9 48.1 + - + +
523C LEU* 3.3 16.3 + - + -
558C LEU 4.0 2.9 - - - +
559C LEU* 4.2 20.0 - - + -
562C PHE* 3.4 48.9 - - + -
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Residues in contact with VAL 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 THR* 2.8 26.9 + - + +
515C ARG* 3.7 25.1 - - - +
517C LEU* 1.3 78.7 - - - +
519C HIS* 1.3 61.6 + - + +
521C GLY* 3.5 9.9 + - - -
523C LEU* 3.5 36.7 - - + +
524C LYS 4.3 0.7 - - - +
525C SER* 3.2 37.2 - - - +
529C VAL* 3.5 24.1 - - + +
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Residues in contact with HIS 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C GLU* 3.2 30.8 + - - -
470C VAL* 3.6 16.6 - - + -
471C SER* 5.6 3.6 - - - -
474C LEU* 3.6 21.5 - - + +
515C ARG* 3.2 28.2 + - - +
516C LEU 3.0 6.0 + - - +
518C VAL* 1.3 74.8 - - - +
520C MET* 1.3 57.9 + - - +
521C GLY 3.0 8.2 + - - -
529C VAL* 4.4 25.3 - - + +
530C LYS 4.7 9.4 + - - -
531C ALA* 4.0 4.0 - - - -
532C ILE* 3.0 31.3 + - + +
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Residues in contact with MET 520 (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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474C LEU* 4.2 16.8 - - + -
516C LEU* 2.9 41.6 + - - +
517C LEU* 3.3 2.0 + - - +
518C VAL 3.3 0.4 - - - -
519C HIS* 1.3 76.2 - - - +
521C GLY* 1.3 50.6 - - - +
522C LEU* 2.7 49.9 + - + +
532C ILE* 3.4 17.3 - - + -
535C LEU* 3.7 35.7 - - + +
538C PRO* 3.7 24.0 - - + -
539C LEU* 4.2 13.7 - - + -
542C LEU* 4.1 15.0 - - + -
559C LEU* 6.2 0.2 - - - -
567C ASN* 4.9 0.2 + - - -
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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