Contacts of the helix formed by residues 511 - 525 (chain C) in PDB entry 3UO9
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 511 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482C SER* 5.6 0.4 - - - -
483C GLY 5.6 0.6 + - - -
486C GLY* 3.3 27.1 + - - -
488C ILE* 4.4 9.8 - - - +
500C CYS 6.0 0.2 - - - -
502C SER* 2.9 29.9 + - - -
504C PRO 3.4 8.9 + - - -
505C LEU* 3.9 4.8 - - - +
510C ASN* 1.3 70.6 - - - +
512C VAL* 1.3 60.4 + - - +
514C GLY* 3.4 19.9 + - - -
515C ILE* 2.9 31.7 + - - +
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Residues in contact with VAL 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C GLN* 3.5 34.8 - - + +
243C GLY* 3.5 28.3 - - - +
244C GLY* 3.7 9.9 - - - -
504C PRO* 3.2 11.1 + - + +
506C ASP* 3.5 31.9 - - + +
510C ASN 4.3 0.7 - - - -
511C SER* 1.3 71.7 - - - +
513C LYS* 1.3 64.8 + - + +
515C ILE* 3.5 4.4 + - - +
516C HIS* 3.1 23.7 + - - +
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Residues in contact with LYS 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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238C ALA* 3.4 29.2 - - - +
239C LYS* 3.7 21.1 - - - +
241C GLN* 3.6 19.5 + - - +
242C SER* 5.1 4.9 + - - +
258C PRO 3.2 21.8 + - - -
259C ASP* 4.5 6.8 + - - +
260C LEU 4.1 3.2 + - - -
261C TRP* 3.6 42.8 - - + +
502C SER* 2.9 28.3 + - - +
504C PRO* 4.3 8.3 - - + +
511C SER* 3.9 0.8 + - - -
512C VAL* 1.3 73.6 - - + +
514C GLY* 1.3 55.9 + - - +
516C HIS* 3.4 2.9 + - - -
517C PHE* 2.8 35.7 + - - +
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Residues in contact with GLY 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C TRP* 4.0 13.3 - - - -
488C ILE* 3.7 19.1 - - - -
500C CYS* 4.5 8.6 - - - -
511C SER* 3.4 15.4 + - - -
512C VAL 3.3 0.2 - - - -
513C LYS* 1.3 77.3 - - - +
515C ILE* 1.3 55.2 + - - +
517C PHE* 3.3 4.7 + - - +
518C CYS* 3.0 32.4 + - - -
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Residues in contact with ILE 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C MET* 3.7 22.0 - - + -
468C PHE* 3.9 27.8 - - + -
472C PHE* 4.1 8.3 - - + -
488C ILE* 4.3 3.1 - - + -
506C ASP* 4.3 9.6 - - - +
510C ASN* 3.6 28.3 - - + -
511C SER 2.9 21.0 + - - +
512C VAL* 4.0 4.9 - - - +
514C GLY* 1.3 70.7 - - - +
516C HIS* 1.3 66.5 + - - +
518C CYS* 3.4 4.1 + - - +
519C HIS* 3.0 48.7 + - + +
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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
----------------------------------------------------------
3C GOL 4.0 16.5 + - - -
234C LEU 5.5 0.2 + - - -
237C SER* 3.8 31.6 - - - -
238C ALA* 3.7 14.8 - - - +
241C GLN* 3.7 31.6 + - + -
512C VAL* 3.1 18.4 + - + +
513C LYS* 3.7 4.5 - - - +
515C ILE* 1.3 78.5 - - - +
517C PHE* 1.3 61.7 + - - +
519C HIS* 3.6 6.6 + - + +
520C ASP* 3.2 35.2 + - - +
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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
----------------------------------------------------------
231C ILE* 3.9 16.2 - - + -
234C LEU* 3.3 50.4 - - + +
235C TYR* 3.6 11.7 - - - -
238C ALA* 4.3 3.3 - - + +
261C TRP* 3.9 21.8 - + + -
263C VAL* 3.9 22.7 - - + -
498C MET* 3.4 33.7 - - + -
500C CYS* 4.0 9.0 - - - -
513C LYS 2.8 21.0 + - - +
514C GLY* 3.4 4.7 - - - +
516C HIS* 1.3 71.5 + - - +
518C CYS* 1.3 65.8 + - - +
520C ASP* 3.4 5.8 + - - +
521C LEU* 3.1 27.6 + - + +
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Residues in contact with CYS 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C PHE* 3.9 25.6 - - + -
476C VAL* 3.7 10.3 - - + +
488C ILE* 4.5 12.8 - - - -
490C LEU* 3.9 33.0 - - + -
500C CYS* 4.9 8.7 - - - -
514C GLY 3.0 24.2 + - - +
515C ILE 3.4 4.7 + - - +
517C PHE* 1.3 77.3 - - - +
519C HIS* 1.3 62.6 + - - +
521C LEU* 3.6 5.1 + - - +
522C VAL* 3.4 28.8 + - - +
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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
----------------------------------------------------------
468C PHE* 4.0 19.3 - + - -
471C GLN 5.6 0.2 - - - -
472C PHE* 5.3 0.4 - + - -
475C HIS* 3.9 33.1 - + + +
476C VAL* 3.8 19.4 - - + +
515C ILE* 3.0 41.4 + - + +
516C HIS* 3.7 10.3 - - + +
518C CYS* 1.3 74.8 - - + +
520C ASP* 1.3 61.7 + - - +
522C VAL* 3.4 3.8 + - - +
523C SER* 3.0 29.5 + - - -
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Residues in contact with ASP 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GOL 3.4 39.6 + - - -
234C LEU* 3.7 27.0 - - + +
237C SER* 3.9 11.8 + - - -
516C HIS* 3.2 26.5 + - - +
517C PHE* 3.7 7.4 - - - +
518C CYS 3.4 0.2 - - - -
519C HIS* 1.3 79.3 - - - +
521C LEU* 1.3 57.5 + - - +
523C SER* 3.1 10.7 + - - -
524C LEU* 2.9 31.2 + - - +
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Residues in contact with LEU 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C ILE* 4.1 17.0 - - + -
234C LEU* 3.7 23.9 - - + +
478C LEU* 4.8 6.7 - - + -
490C LEU* 4.1 13.5 - - + -
496C MET* 3.9 14.6 - - + -
498C MET* 3.8 28.9 - - + -
517C PHE* 3.1 18.6 + - + +
518C CYS* 3.6 7.0 - - - +
520C ASP* 1.3 75.6 - - - +
522C VAL* 1.3 58.7 + - + +
524C LEU* 3.8 1.6 - - - +
525C CYS* 2.9 42.1 + - - +
526C ASN 4.0 0.2 + - - -
527C PHE* 4.0 26.9 - - + -
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Residues in contact with VAL 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ARG* 6.1 0.4 - - - +
475C HIS 3.7 13.9 - - - +
476C VAL* 3.3 33.0 - - + +
478C LEU* 3.6 23.6 - - + -
518C CYS 3.4 17.6 + - - +
519C HIS* 3.4 3.6 + - - +
521C LEU* 1.3 78.7 - - + +
523C SER* 1.3 64.4 + - - +
525C CYS 3.8 5.0 + - - -
526C ASN* 3.8 9.6 + - - +
527C PHE* 4.5 3.6 - - + -
528C HIS* 3.8 26.7 - - + +
531C ASP* 4.6 0.6 - - - +
539C LYS* 4.0 9.2 - - - +
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Residues in contact with SER 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 HIS 3.0 14.2 + - - -
520C ASP* 3.1 17.3 + - - -
522C VAL* 1.3 79.2 - - - +
524C LEU* 1.3 65.2 + - - +
538C LYS 5.2 1.6 - - - +
539C LYS* 3.7 15.8 - - - +
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Residues in contact with LEU 524 (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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230C HIS* 3.8 40.6 - - + +
231C ILE* 6.3 0.2 - - + -
233C GLU* 5.7 1.1 - - - +
234C LEU* 4.1 26.0 - - + -
520C ASP 2.9 18.4 + - - +
521C LEU 3.8 3.6 - - - +
523C SER* 1.3 79.9 + - - +
525C CYS* 1.3 76.3 + - - +
538C LYS 5.1 0.3 - - - +
539C LYS* 4.1 2.9 - - - -
540C LEU* 3.2 31.5 + - + +
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Residues in contact with CYS 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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227C PHE* 4.2 13.2 - - - -
521C LEU* 2.9 21.7 + - - +
523C SER 3.5 1.8 - - - -
524C LEU* 1.3 100.5 - - - +
526C ASN* 1.2 69.9 + - - +
527C PHE* 3.9 32.8 - - + +
539C LYS* 3.5 3.3 - - - +
540C LEU* 2.3 48.0 + - - +
542C PRO* 4.4 3.1 - - + -
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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