Contacts of the helix formed by residues 510 - 524 (chain C) in PDB entry 5I94
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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481C SER* 5.3 1.0 - - - -
482C GLY 5.6 0.8 + - - -
485C GLY* 3.3 27.0 + - - -
486C GLY 5.5 0.4 + - - -
487C ILE* 4.3 12.4 - - - +
499C CYS 6.1 0.2 - - - -
501C SER* 2.9 27.6 + - - -
503C PRO 3.7 7.0 - - - -
504C LEU* 3.8 4.9 - - - +
508C GLY 4.2 0.2 + - - -
509C ASN* 1.3 71.7 - - - +
511C VAL* 1.3 58.7 + - - +
513C GLY* 3.2 21.9 + - - -
514C ILE* 2.8 34.5 + - - +
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Residues in contact with VAL 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C GLN* 4.0 29.2 - - + +
242C GLY* 3.7 31.0 - - - +
243C GLY* 3.8 7.6 - - - +
503C PRO* 3.2 9.0 + - + +
504C LEU 3.8 5.8 - - - -
505C ASP* 3.6 33.9 - - + +
509C ASN 3.3 0.8 + - - -
510C SER* 1.3 71.2 - - - +
512C LYS* 1.3 64.5 + - + +
514C ILE* 4.0 3.9 - - - +
515C HIS* 3.2 23.0 + - - +
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Residues in contact with LYS 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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237C ALA* 3.2 27.0 - - - +
238C LYS* 3.4 23.8 - - - +
240C GLN* 3.7 24.6 + - + +
241C SER* 5.5 2.9 + - - +
242C GLY 5.7 0.6 + - - +
257C PRO 3.6 18.6 + - - -
258C ASP* 5.0 4.2 + - - +
259C LEU 4.5 3.6 + - - -
260C TRP* 3.7 36.6 - - + +
501C SER* 3.4 30.5 + - - +
503C PRO* 4.9 4.6 - - + +
510C SER* 3.4 1.2 + - - -
511C VAL* 1.3 74.1 - - + +
513C GLY* 1.3 61.0 + - - +
515C HIS* 3.5 4.4 + - - +
516C PHE* 2.9 30.5 + - - +
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Residues in contact with GLY 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C TRP* 4.2 3.7 - - - -
487C ILE* 3.7 16.8 - - - -
499C CYS* 4.1 19.9 - - - -
510C SER* 3.2 16.4 + - - -
512C LYS* 1.3 78.7 - - - +
514C ILE* 1.3 56.1 + - - +
516C PHE* 3.0 5.0 + - - +
517C CYS* 3.0 31.2 + - - -
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Residues in contact with ILE 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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464C MET* 3.6 29.6 - - + -
467C PHE* 4.4 14.8 - - + -
471C PHE* 3.9 22.2 - - + -
487C ILE* 3.7 4.6 - - + +
505C ASP* 4.3 7.2 - - - +
509C ASN* 3.7 18.6 - - + +
510C SER 2.8 23.2 + - - +
511C VAL* 4.0 4.7 - - - +
513C GLY* 1.3 68.2 - - - +
515C HIS* 1.3 68.5 + - - +
517C CYS* 3.2 3.9 + - - +
518C HIS* 3.0 46.1 + - + +
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Residues in contact with HIS 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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233C LEU 5.6 0.4 - - - -
236C SER* 3.8 11.9 + - - -
237C ALA* 3.8 22.4 - - + -
240C GLN* 3.7 38.3 + - + +
511C VAL 3.2 15.6 + - - +
512C LYS* 3.7 5.8 - - - +
514C ILE* 1.3 81.4 - - - +
516C PHE* 1.3 64.8 + - - +
518C HIS* 3.1 9.1 + - - +
519C ASP* 3.1 43.9 + - - +
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Residues in contact with PHE 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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230C ILE* 4.0 24.7 - - + -
233C LEU* 3.5 45.0 - - + +
234C TYR 3.9 4.3 - - - -
237C ALA* 4.1 6.3 - - + -
260C TRP* 4.1 11.2 - + + -
262C VAL* 3.8 30.1 - - + -
497C MET* 3.3 27.4 - - + -
499C CYS* 3.9 15.3 - - - -
512C LYS 2.9 15.1 + - - +
513C GLY* 3.0 8.5 + - - +
515C HIS* 1.3 78.6 - - - +
517C CYS* 1.3 62.0 + - - +
519C ASP* 3.3 5.9 + - - +
520C LEU* 3.1 34.1 + - + +
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Residues in contact with CYS 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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471C PHE* 4.1 24.9 - - + -
475C VAL* 3.6 8.8 - - + +
487C ILE* 4.6 15.5 - - - -
489C LEU* 4.1 30.7 - - + -
499C CYS* 4.8 9.2 - - - -
513C GLY 3.0 19.3 + - - -
514C ILE* 3.2 8.0 + - - +
516C PHE* 1.3 76.4 - - - +
518C HIS* 1.3 65.6 + - - +
520C LEU* 3.6 6.9 - - - +
521C VAL* 3.5 26.0 + - - +
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Residues in contact with HIS 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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467C PHE* 4.0 24.2 - + - -
471C PHE* 4.6 1.8 - + - -
474C HIS* 4.1 27.6 - + + +
475C VAL* 3.6 23.5 - - + +
514C ILE* 3.0 42.8 + - + +
515C HIS* 3.1 10.5 + - - +
517C CYS* 1.3 78.5 - - - +
519C ASP* 1.3 67.7 + - - +
521C VAL* 3.4 4.3 + - - +
522C SER* 3.0 26.5 + - - +
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Residues in contact with ASP 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C LEU* 3.8 27.4 - - + +
236C SER* 3.6 22.0 + - - -
515C HIS* 3.1 29.4 + - + +
516C PHE* 3.3 8.9 + - - +
518C HIS* 1.3 77.1 - - - +
520C LEU* 1.3 66.5 + - - +
522C SER* 3.1 11.5 + - - -
523C LEU* 3.0 23.7 + - - +
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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
----------------------------------------------------------
226C PHE* 5.3 1.1 - - + -
230C ILE* 4.3 19.1 - - + -
233C LEU* 3.6 22.7 - - + +
477C LEU* 4.7 11.0 - - + -
489C LEU* 4.0 26.7 - - + -
491C VAL* 4.8 0.7 - - + -
495C MET* 4.0 23.1 - - + -
497C MET* 4.3 5.2 - - - -
516C PHE* 3.1 22.1 + - + +
517C CYS* 3.6 7.6 - - - +
519C ASP* 1.3 75.1 - - - +
521C VAL* 1.3 58.3 + - + +
523C LEU* 3.2 5.0 + - + +
524C CYS* 2.8 42.6 + - - +
526C PHE* 4.3 13.0 - - + -
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Residues in contact with VAL 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C HIS 4.2 11.4 - - - +
475C VAL* 3.6 39.3 - - + +
477C LEU* 3.7 17.9 - - + -
517C CYS 3.5 6.9 + - - +
518C HIS* 3.4 4.3 + - - +
519C ASP 3.3 0.4 - - - -
520C LEU* 1.3 78.6 - - + +
522C SER* 1.3 59.1 + - - +
523C LEU 3.2 0.4 - - - -
524C CYS 3.3 7.7 - - - +
526C PHE* 4.7 2.7 - - + -
527C HIS* 3.5 39.7 - - + +
538C LYS* 2.6 36.9 + - - +
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Residues in contact with SER 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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518C HIS* 3.0 17.2 + - - +
519C ASP* 3.1 15.7 + - - -
521C VAL* 1.3 77.6 - - - +
523C LEU* 1.3 61.0 + - - +
538C LYS* 3.8 19.1 - - - +
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Residues in contact with LEU 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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226C PHE* 6.3 0.2 - - + -
229C HIS* 3.7 42.6 - - + +
233C LEU* 4.3 20.4 - - + -
519C ASP 3.0 11.2 + - - +
520C LEU* 3.5 6.1 - - + +
522C SER* 1.3 79.0 - - - +
524C CYS* 1.3 76.8 + - - +
538C LYS* 3.7 4.9 - - - -
539C LEU* 2.9 41.7 + - + +
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Residues in contact with CYS 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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226C PHE* 4.7 5.6 - - - -
520C LEU* 2.8 21.0 + - - +
521C VAL* 3.3 20.3 - - - +
523C LEU* 1.3 99.5 - - - +
525C ASN* 1.3 54.2 + - - +
526C PHE* 2.6 50.4 + - + -
538C LYS* 3.8 5.1 + - - -
539C LEU* 3.2 12.6 - - - +
541C PRO* 3.9 20.2 - - + -
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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