Contacts of the helix formed by residues 510 - 524 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481D SER* 5.5 0.8 - - - -
482D GLY 5.3 0.8 + - - -
485D GLY* 3.1 30.6 + - - -
486D GLY 5.5 0.2 + - - -
487D ILE* 4.2 10.6 - - - +
500D TRP 4.8 0.2 - - - -
501D SER* 2.9 25.4 + - - -
503D PRO 3.5 9.0 - - - -
504D LEU* 3.7 7.0 - - - +
509D ASN* 1.3 71.0 - - - +
511D VAL* 1.3 57.5 + - - +
513D GLY* 3.1 21.7 + - - -
514D ILE* 2.9 30.5 + - - +
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Residues in contact with VAL 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D GLN* 3.7 33.9 - - + +
242D GLY* 3.8 26.0 - - - +
243D GLY* 3.9 10.1 - - - +
501D SER* 6.0 0.2 - - - +
503D PRO* 3.2 8.5 + - + +
504D LEU 4.0 0.7 - - - -
505D ASP* 3.9 33.9 - - + +
509D ASN 3.1 1.9 + - - -
510D SER* 1.3 69.7 + - - +
512D LYS* 1.3 68.3 + - + +
514D ILE* 3.4 5.0 + - - +
515D HIS* 3.1 22.7 + - - +
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Residues in contact with LYS 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D ALA* 3.5 23.1 - - - +
238D LYS* 4.1 15.9 - - - +
240D GLN* 3.7 21.1 + - - +
241D SER* 5.3 4.1 - - - +
257D PRO 3.4 20.6 + - - -
258D ASP* 4.5 7.8 + - - +
259D LEU 4.2 4.2 + - - -
260D TRP* 3.6 41.1 - - + +
501D SER* 2.9 35.2 + - - +
503D PRO* 4.4 5.1 - - - +
510D SER* 3.4 1.6 + - - -
511D VAL* 1.3 73.7 - - + +
513D GLY* 1.3 66.7 + - - +
515D HIS* 3.4 7.1 + - - +
516D PHE* 2.9 24.1 + - - +
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Residues in contact with GLY 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D TRP* 4.1 2.8 - - - -
487D ILE* 3.7 17.9 - - - -
499D CYS* 4.2 19.9 - - - -
510D SER* 3.1 19.6 + - - -
512D LYS* 1.3 76.5 - - - +
514D ILE* 1.3 61.4 + - - +
516D PHE* 3.0 15.1 + - - +
517D CYS* 3.0 15.1 + - - -
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Residues in contact with ILE 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D MET* 3.5 31.9 - - + -
467D PHE* 4.5 15.0 - - + -
471D PHE* 4.1 17.5 - - + -
487D ILE* 3.7 4.4 - - + +
505D ASP* 4.4 10.1 - - - +
509D ASN* 3.8 17.3 - - + +
510D SER 2.9 21.4 + - - +
511D VAL* 3.8 5.6 - - - +
513D GLY* 1.3 71.2 - - - +
515D HIS* 1.3 66.3 + - - +
517D CYS* 3.0 13.5 + - - +
518D HIS* 3.0 37.5 + - + +
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Residues in contact with HIS 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D LEU 5.4 0.2 - - - -
236D SER* 3.8 12.5 + - - -
237D ALA* 3.9 22.9 - - + -
240D GLN* 3.5 40.6 + - + +
511D VAL 3.1 10.6 + - - +
512D LYS* 3.6 8.7 - - - +
514D ILE* 1.3 83.0 - - - +
516D PHE* 1.3 63.3 + - - +
518D HIS* 3.3 6.3 + - - +
519D ASP* 3.1 43.0 + - - +
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Residues in contact with PHE 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D ILE* 4.0 21.3 - - + -
233D LEU* 3.4 42.6 - - + -
234D TYR* 3.8 7.9 - - - -
237D ALA* 4.4 4.7 - - + +
260D TRP* 3.9 22.9 - + + -
262D VAL* 3.8 24.5 - - + -
497D MET* 3.3 35.2 - - + -
499D CYS* 3.9 8.7 - - - -
512D LYS 2.9 13.0 + - - +
513D GLY* 3.3 9.9 - - - +
515D HIS* 1.3 74.6 - - - +
517D CYS* 1.3 61.9 + - - +
519D ASP* 3.2 6.1 + - - +
520D LEU* 2.9 37.0 + - + +
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Residues in contact with CYS 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D PHE* 3.9 33.0 - - + -
475D VAL* 4.0 10.0 - - + +
477D LEU* 5.5 0.4 - - - +
487D ILE* 4.4 16.6 - - - -
489D LEU* 4.2 24.9 - - + -
499D CYS* 4.9 7.9 - - - -
513D GLY 3.0 16.5 + - - -
514D ILE 3.0 8.5 + - - +
516D PHE* 1.3 79.2 - - - +
518D HIS* 1.3 61.8 + - - +
520D LEU* 3.6 6.3 + - - +
521D VAL* 3.4 27.5 + - - +
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Residues in contact with HIS 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D PHE* 4.1 22.5 - + - -
471D PHE* 5.1 1.8 - + - -
474D HIS* 3.8 33.9 - + + +
475D VAL* 3.9 17.1 - - + +
514D ILE* 3.0 44.3 + - + +
515D HIS* 3.7 8.1 - - - +
517D CYS* 1.3 76.1 - - - +
519D ASP* 1.3 61.8 + - - +
521D VAL* 3.1 5.2 + - - +
522D SER* 2.8 31.2 + - - +
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Residues in contact with ASP 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D LEU* 3.4 28.1 - - + +
236D SER* 3.6 22.9 + - - -
515D HIS* 3.1 29.8 + - - +
516D PHE* 3.2 9.2 + - - +
518D HIS* 1.3 77.1 - - - +
520D LEU* 1.3 66.4 + - - +
522D SER* 3.2 11.1 + - - -
523D LEU* 3.0 24.8 + - - +
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Residues in contact with LEU 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D PHE* 5.1 0.7 - - + -
230D ILE* 4.2 16.6 - - + -
233D LEU* 3.6 24.1 - - + +
477D LEU* 4.7 9.4 - - + -
489D LEU* 3.9 28.0 - - + -
491D VAL* 4.9 0.2 - - + -
495D MET* 4.1 14.1 - - + -
497D MET* 4.1 15.3 - - - -
516D PHE* 2.9 22.3 + - + +
517D CYS 3.7 6.3 - - - +
518D HIS 3.3 0.2 - - - -
519D ASP* 1.3 75.9 - - - +
521D VAL* 1.3 60.1 + - + +
523D LEU* 3.3 2.6 + - - +
524D CYS* 2.9 44.1 + - - +
526D PHE* 4.4 12.1 - - + -
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Residues in contact with VAL 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474D HIS 4.4 5.6 - - - +
475D VAL* 3.6 24.7 - - + +
477D LEU* 3.8 22.9 - - + -
517D CYS 3.4 16.1 + - - +
518D HIS* 3.1 4.9 + - - +
520D LEU* 1.3 77.9 - - + +
522D SER* 1.3 65.6 + - - +
523D LEU 3.2 1.6 - - - -
524D CYS 3.1 14.8 - - - +
526D PHE* 4.9 2.5 - - + +
527D HIS* 3.5 43.1 - - + +
538D LYS* 3.1 17.4 + - - +
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Residues in contact with SER 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518D HIS* 2.8 16.4 + - - +
519D ASP* 3.2 17.1 + - - -
521D VAL* 1.3 79.8 - - - +
523D LEU* 1.3 60.2 + - - +
538D LYS* 3.7 19.5 - - - +
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Residues in contact with LEU 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D HIS* 3.8 44.9 - - + +
232D GLU* 5.9 0.4 - - - +
233D LEU* 4.5 19.7 - - + -
519D ASP 3.0 15.7 + - - +
520D LEU 3.6 3.4 - - - +
522D SER* 1.3 78.8 - - - +
524D CYS* 1.3 70.9 + - - +
538D LYS* 3.7 3.7 - - - +
539D LEU* 2.8 37.0 + - + +
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Residues in contact with CYS 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D PHE* 4.6 5.4 - - - -
520D LEU* 2.9 21.4 + - - +
521D VAL* 3.1 21.8 - - - +
523D LEU* 1.3 98.6 - - - +
525D ASN* 1.3 53.7 + - - +
526D PHE* 2.7 53.2 + - + -
530D ASP* 3.7 1.4 - - - +
538D LYS* 3.9 4.5 - - - -
539D LEU* 3.2 14.6 - - - +
541D PRO* 4.0 14.8 - - + -
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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