Contacts of the helix formed by residues 510 - 515 (chain C) in PDB entry 5ZR1
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 SER 510 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B ASN 2.8 17.5 + - - -
285B PHE* 2.3 31.1 + - - -
287B LYS 5.2 0.3 + - - -
508C THR* 3.3 5.3 + - - +
509C LEU* 1.3 78.5 - - - +
511C GLY* 1.3 60.6 + - - +
512C ASP 3.2 2.9 - - - -
513C LEU* 2.9 24.5 + - - +
514C ASP* 2.9 17.5 + - - +
556C PHE* 3.5 21.1 - - - -
559C LYS* 5.4 0.2 - - - +
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Residues in contact with GLY 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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505C ASN* 3.2 43.3 + - - +
506C TYR* 5.5 0.2 - - - -
508C THR* 3.5 9.9 + - - +
509C LEU 3.7 1.2 - - - -
510C SER* 1.3 74.1 - - - +
512C ASP* 1.3 65.6 + - - +
514C ASP* 3.8 15.1 + - - +
515C LYS* 4.1 11.8 + - - +
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Residues in contact with ASP 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C ASN 4.4 1.2 + - - -
506C TYR* 3.7 31.3 - - - -
508C THR 5.5 0.2 + - - -
510C SER 3.2 1.0 - - - -
511C GLY* 1.3 77.9 - - - +
513C LEU* 1.3 59.5 + - - +
515C LYS* 4.5 3.5 + - - +
516C ILE* 3.6 21.7 - - - +
552C GLU* 5.0 9.8 - - + +
555C ASN* 5.9 0.7 + - - -
559C LYS* 3.5 25.0 + - - +
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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
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281B PHE* 4.3 4.3 - - + -
285B PHE* 3.6 27.4 - - + -
510C SER* 2.9 15.8 + - - +
512C ASP* 1.3 80.6 - - - +
514C ASP* 1.3 57.1 + - - +
515C LYS 3.4 1.3 - - - -
516C ILE* 3.3 4.3 + - + +
517C MET* 2.9 42.8 + - + +
549C PRO* 4.1 7.6 - - + -
552C GLU* 4.0 31.2 - - + +
553C ILE* 4.1 14.4 - - + -
556C PHE* 3.6 39.3 - - + -
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Residues in contact with ASP 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PHE* 2.8 34.6 - - - +
286B GLN* 3.3 27.2 + - + +
288B ARG* 5.5 0.5 - - - +
289B PRO* 4.1 12.2 - - + +
494C TRP* 5.1 5.0 - - - -
505C ASN* 3.9 19.1 - - - +
508C THR* 5.0 1.7 - - - +
510C SER* 2.9 23.8 + - - +
511C GLY* 3.8 10.9 + - - +
512C ASP 3.5 0.8 - - - -
513C LEU* 1.3 80.3 - - - +
515C LYS* 1.3 62.6 + - + +
517C MET 3.2 17.8 - - - +
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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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500C SER* 3.9 15.9 - - - +
501C LEU 2.8 40.7 + - - +
502C ASP* 4.4 6.1 - - - +
505C ASN* 3.9 12.6 - - - +
511C GLY 4.1 9.6 + - - +
512C ASP 4.5 2.7 + - - +
513C LEU 3.4 0.2 - - - -
514C ASP* 1.3 80.3 - - + +
516C ILE* 1.3 65.4 + - + +
517C MET 5.3 0.2 - - - -
377F LYS* 3.6 17.3 + - - -
381F ASP* 4.9 4.0 - - - +
384F ILE* 5.5 6.9 - - - +
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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