Contacts of the helix formed by residues 510 - 524 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481A SER* 5.6 0.4 - - - -
482A GLY 5.5 1.0 + - - -
485A GLY* 3.4 22.1 + - - -
486A GLY 5.6 0.4 + - - -
487A ILE* 4.1 14.9 - - - +
499A CYS 6.2 0.2 - - - -
500A TRP* 5.2 0.3 + - - -
501A SER* 3.1 32.3 + - - -
503A PRO 3.6 9.0 - - - -
504A LEU* 3.7 8.0 - - - +
509A ASN* 1.3 68.8 - - - +
511A VAL* 1.3 58.7 + - - +
513A GLY* 3.2 17.2 + - - -
514A ILE* 2.9 33.5 + - - +
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Residues in contact with VAL 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A GLN* 4.0 32.3 - - + +
242A GLY* 3.6 28.9 - - - +
243A GLY* 3.6 11.2 - - - +
503A PRO* 3.2 10.6 + - + +
505A ASP* 3.6 33.7 - - + +
509A ASN 3.0 5.7 + - - -
510A SER* 1.3 70.2 - - - +
512A LYS* 1.3 64.5 + - + +
514A ILE* 3.5 5.7 + - - +
515A HIS* 3.1 23.1 + - + +
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Residues in contact with LYS 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ALA* 3.5 26.6 - - - +
238A LYS* 4.0 15.3 - - - +
240A GLN* 3.6 22.0 + - - +
241A SER* 5.1 4.8 - - - +
257A PRO 3.1 22.4 + - - -
258A ASP* 4.4 6.3 - - - +
259A LEU 4.0 4.8 + - - -
260A TRP* 3.6 36.1 - - + +
501A SER* 2.5 43.4 + - - +
503A PRO* 4.3 5.2 + - + +
510A SER* 3.4 1.6 + - - -
511A VAL* 1.3 74.6 - - + +
513A GLY* 1.3 60.7 + - - +
515A HIS* 3.4 7.0 + - - +
516A PHE* 2.9 29.5 + - - +
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Residues in contact with GLY 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A TRP* 4.1 12.5 - - - -
487A ILE* 3.8 15.9 - - - -
499A CYS* 4.3 11.2 - - - -
510A SER* 3.2 18.6 + - - -
512A LYS* 1.3 76.6 - - - +
514A ILE* 1.3 57.7 + - - +
516A PHE* 3.0 4.7 + - - +
517A CYS* 2.9 32.0 + - - -
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Residues in contact with ILE 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A MET* 3.5 31.6 - - + -
467A PHE* 4.1 24.5 - - + -
471A PHE* 4.3 7.6 - - + -
487A ILE* 3.8 3.8 - - + +
505A ASP* 4.2 11.2 - - - +
509A ASN* 3.8 19.5 - - + -
510A SER 2.9 19.9 + - - +
511A VAL* 3.8 5.8 - - - +
513A GLY* 1.3 73.7 - - - +
515A HIS* 1.3 64.3 + - - +
517A CYS* 3.3 5.7 + - - +
518A HIS* 3.0 49.7 + - + +
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Residues in contact with HIS 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU 5.4 0.2 - - - -
236A SER* 3.7 16.8 + - - -
237A ALA* 3.8 23.3 - - + -
240A GLN* 3.1 40.9 + - + +
511A VAL 3.1 16.2 + - - +
512A LYS* 3.5 6.3 - - - +
513A GLY 3.2 0.2 - - - -
514A ILE* 1.3 80.5 - - - +
516A PHE* 1.3 61.9 + - - +
518A HIS* 3.2 8.4 + - - +
519A ASP* 3.1 37.1 + - - +
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Residues in contact with PHE 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ILE* 4.0 22.4 - - + -
233A LEU* 3.5 41.8 - - + +
234A TYR* 3.8 9.0 - - + -
237A ALA* 4.2 4.2 - - + +
260A TRP* 4.1 15.7 - + + -
262A VAL* 3.8 32.3 - - + -
497A MET* 3.5 35.2 - - + -
499A CYS* 4.0 7.6 - - - -
512A LYS 2.9 14.0 + - - +
513A GLY* 3.3 8.7 - - - +
515A HIS* 1.3 76.7 - - - +
517A CYS* 1.3 60.7 + - - +
519A ASP* 3.2 6.8 + - - +
520A LEU* 2.8 38.7 + - + +
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Residues in contact with CYS 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A PHE* 4.0 27.4 - - + -
475A VAL* 3.7 19.1 - - + +
487A ILE* 4.3 16.4 - - - -
489A LEU* 4.0 28.5 - - + -
499A CYS* 4.7 10.5 - - - -
513A GLY 2.9 20.6 + - - +
514A ILE* 3.3 8.0 + - - +
516A PHE* 1.3 74.6 - - - +
518A HIS* 1.3 60.2 + - - +
520A LEU* 3.7 9.8 - - - +
521A VAL* 3.5 15.1 + - - +
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Residues in contact with HIS 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A PHE* 4.0 21.6 - + - -
471A PHE* 5.2 0.7 - + - -
474A HIS* 3.8 31.8 - + + +
475A VAL* 4.0 19.6 - - + +
514A ILE* 3.0 43.5 + - + +
515A HIS* 3.2 10.1 + - - +
517A CYS* 1.3 76.7 - - - +
519A ASP* 1.3 64.3 + - - +
521A VAL* 3.6 2.9 + - - +
522A SER* 2.8 33.1 + - - +
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Residues in contact with ASP 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU* 3.6 26.9 - - + +
236A SER* 3.4 23.4 + - - -
515A HIS* 3.1 27.5 + - + +
516A PHE* 3.6 8.5 - - - +
518A HIS* 1.3 80.0 - - - +
520A LEU* 1.3 65.1 + - - +
522A SER* 3.1 9.6 + - - -
523A LEU* 2.9 27.0 + - - +
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Residues in contact with LEU 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A PHE* 5.4 1.1 - - + -
230A ILE* 4.3 18.4 - - + -
233A LEU* 3.7 23.5 - - + +
477A LEU* 4.7 9.6 - - + -
489A LEU* 3.8 28.9 - - + -
495A MET* 4.1 22.9 - - + -
497A MET* 4.2 7.0 - - - -
516A PHE* 2.8 23.9 + - + +
517A CYS* 3.7 8.3 - - - +
519A ASP* 1.3 78.1 - - - +
521A VAL* 1.3 60.0 + - + +
523A LEU* 3.6 2.5 - - + +
524A CYS* 2.9 40.9 + - - +
526A PHE* 4.5 10.3 - - + -
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Residues in contact with VAL 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A HIS 4.1 6.3 - - - +
475A VAL* 3.3 33.4 - - + +
477A LEU* 3.6 24.9 - - + -
517A CYS 3.5 8.2 + - - +
518A HIS* 4.2 2.5 - - - +
520A LEU* 1.3 75.6 - - + +
522A SER* 1.3 58.9 + - - +
524A CYS 2.8 11.9 - - - +
526A PHE* 4.8 3.8 - - + +
527A HIS* 3.5 41.5 - - + +
538A LYS* 2.5 36.2 + - - +
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Residues in contact with SER 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A HIS* 2.8 26.0 + - - +
519A ASP* 3.1 14.3 + - - -
521A VAL* 1.3 76.4 - - - +
523A LEU* 1.3 59.3 + - - +
537A LYS 5.7 0.3 - - - +
538A LYS* 3.8 17.8 - - - +
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Residues in contact with LEU 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A HIS* 3.9 43.3 - - + +
233A LEU* 3.9 29.8 - - + -
519A ASP 2.9 14.5 + - - +
520A LEU 3.6 0.7 - - - +
522A SER* 1.3 79.1 - - - +
524A CYS* 1.3 73.0 + - - +
538A LYS* 3.8 5.8 - - - -
539A LEU* 3.0 35.6 + - + +
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Residues in contact with CYS 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A PHE* 4.7 5.2 - - - -
520A LEU* 2.9 25.1 + - - +
521A VAL* 2.8 22.3 - - - +
523A LEU* 1.3 94.0 - - - +
525A ASN* 1.3 58.5 + - - +
526A PHE* 3.1 43.4 + - + -
530A ASP* 3.7 0.2 - - - +
538A LYS* 3.4 8.2 + - - -
539A LEU* 3.3 15.5 - - - +
541A PRO* 4.0 16.6 - - + -
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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