Contacts of the helix formed by residues 515 - 523 (chain C) in PDB entry 6PUO
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 515 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512C GLU 4.6 3.1 - - - +
513C PHE 3.0 15.7 + - - +
514C VAL* 1.3 79.0 - - - +
516C TRP* 1.3 63.3 + - - +
517C ASP* 3.2 6.7 + - - +
518C THR* 3.0 29.6 + - - +
519C LEU* 3.5 19.2 + - - +
615C VAL* 4.9 19.5 - - + -
616C THR 3.9 9.9 - - - -
617C PHE* 4.2 18.2 - - + -
618C THR* 5.5 3.0 - - - +
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Residues in contact with TRP 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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515C THR* 1.3 75.7 - - - +
517C ASP* 1.3 78.0 + - - +
519C LEU* 3.2 11.9 + - + +
520C LEU* 3.0 37.7 + - + +
558C MET* 3.9 37.5 - - + +
577C TYR* 4.5 19.5 - + + -
578C PRO* 5.3 9.9 - - + -
616C THR* 3.1 35.9 + - + +
617C PHE* 4.8 0.9 - - - +
618C THR* 4.2 32.8 - - + +
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Residues in contact with ASP 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C THR* 3.2 5.2 + - - +
516C TRP* 1.3 92.8 - - - +
518C THR* 1.3 61.7 + - - +
520C LEU* 3.3 10.9 + - + +
521C TYR* 2.9 28.8 + - - +
614C HIS 5.4 3.6 - - - +
615C VAL* 5.7 3.1 - - - -
616C THR* 5.6 2.6 - - - +
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Residues in contact with THR 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C THR* 4.4 11.2 - - + +
513C PHE* 4.2 33.6 + - + +
514C VAL* 4.9 2.2 - - + -
515C THR* 3.0 30.6 + - - +
517C ASP* 1.3 75.5 - - - +
519C LEU* 1.3 57.3 + - - +
521C TYR* 3.3 9.0 + - + +
522C LEU* 2.9 39.6 + - + +
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Residues in contact with LEU 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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514C VAL* 4.4 14.5 - - + +
515C THR 3.5 13.8 + - - +
516C TRP* 3.2 17.6 + - + +
517C ASP 3.2 0.6 - - - -
518C THR* 1.3 79.6 - - - +
520C LEU* 1.3 55.6 + - - +
522C LEU* 3.1 12.2 + - + +
523C TYR* 3.0 46.6 + - + -
558C MET* 3.8 25.8 - - + -
577C TYR* 4.4 12.6 - - + +
618C THR* 5.6 4.0 - - + -
624C ASP* 3.9 39.0 - - + +
625C LEU* 4.8 5.4 - - + +
628C TRP* 5.2 3.6 - - + -
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Residues in contact with LEU 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C TRP* 3.0 27.4 + - + +
517C ASP* 3.3 12.8 + - - +
519C LEU* 1.3 77.5 - - - +
521C TYR* 1.3 60.8 + - - +
523C TYR* 3.4 10.1 + - + +
524C GLU* 3.5 20.8 + - - +
555C ARG* 5.0 9.4 - - - +
556C LEU* 3.7 38.1 - - + +
557C GLN* 4.6 10.8 - - - +
558C MET* 3.7 30.7 - - + +
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Residues in contact with TYR 521 (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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317C GLY 3.2 25.5 + - - -
318C GLY* 4.0 7.7 - - - -
489C THR* 4.0 28.3 - - + -
493C ILE* 4.3 3.6 - - + -
517C ASP 2.9 17.4 + - - +
518C THR* 3.6 9.9 - - + +
519C LEU 3.2 0.2 - - - -
520C LEU* 1.3 74.8 - - - +
522C LEU* 1.3 66.3 + - - +
524C GLU* 3.2 30.4 + - - +
525C ASN* 3.3 33.7 + - - -
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Residues in contact with LEU 522 (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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489C THR* 4.4 11.9 - - + -
492C LEU* 4.2 17.0 - - + -
493C ILE* 3.8 31.2 - - + -
513C PHE* 5.3 4.3 - - + -
514C VAL* 5.9 2.0 - - + -
518C THR* 2.9 33.1 + - + +
519C LEU* 3.1 11.4 + - + +
521C TYR* 1.3 77.8 - - + +
523C TYR* 1.3 60.4 + - - +
524C GLU 3.1 1.1 + - - -
525C ASN* 3.3 16.2 + - - +
526C LEU* 4.1 0.2 - - - +
625C LEU* 4.1 26.2 - - + -
628C TRP* 3.0 44.3 + - + +
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Residues in contact with TYR 523 (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 LEU* 3.0 47.7 + - + +
520C LEU* 3.4 6.9 + - - +
521C TYR 3.2 0.4 - - - -
522C LEU* 1.3 76.9 - - - +
524C GLU* 1.3 56.5 + - - +
525C ASN 3.4 0.4 - - - -
526C LEU* 3.3 31.1 - - + +
532C PHE* 4.3 16.2 - + - -
536C LEU* 4.5 6.6 - - + +
556C LEU* 3.4 22.1 - - + +
558C MET* 4.4 14.8 - - + -
561C VAL* 4.0 32.4 - - + +
565C LEU* 5.3 0.2 - - - +
577C TYR* 5.1 6.6 + - - -
624C ASP 4.1 2.2 + - - -
627C ILE* 3.7 15.6 + - - +
628C TRP* 3.4 44.0 + + + -
631C VAL* 5.1 3.3 - - + +
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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