Contacts of the strand formed by residues 495 - 500 (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 MET 495 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A ILE* 4.7 2.2 - - - -
226A PHE* 3.8 31.4 - - + -
230A ILE* 5.1 0.2 - - + -
264A VAL* 3.9 17.9 - - + -
265A CYS 3.5 13.9 - - - +
266A THR* 3.6 11.0 - - + +
267A ALA 4.0 2.5 - - - +
434A ALA* 3.3 13.7 - - - +
491A VAL* 2.7 64.5 + - + +
494A VAL* 1.3 86.8 - - + +
496A GLY* 1.3 61.1 + - - +
497A MET* 4.0 23.3 - - + +
520A LEU* 4.1 10.5 - - + -
526A PHE* 4.0 13.9 - - + -
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Residues in contact with GLY 496 (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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265A CYS 2.7 33.4 + - - -
427A SER 3.7 7.2 - - - -
430A ALA 3.6 5.4 - - - -
431A ALA* 3.6 25.0 - - - +
489A LEU 3.6 6.7 - - - -
490A VAL* 4.5 0.2 - - - -
491A VAL* 6.4 0.2 - - - -
495A MET* 1.3 76.2 - - - +
497A MET* 1.3 66.2 + - - +
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Residues in contact with MET 497 (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* 5.1 1.1 - - - -
262A VAL* 4.8 3.1 - - + -
263A SER 3.2 18.4 - - - +
264A VAL* 3.5 24.9 - - + -
427A SER* 4.0 5.6 - - - -
430A ALA* 3.3 12.8 - - - +
488A LEU* 3.7 1.7 - - - +
489A LEU* 2.7 58.2 + - + +
491A VAL* 6.3 0.4 - - + -
495A MET* 4.0 21.8 - - + -
496A GLY* 1.3 74.6 - - - +
498A MET* 1.3 62.3 + - - +
499A CYS* 3.5 24.2 - - - -
516A PHE* 3.5 33.4 - - + -
517A CYS* 5.4 0.2 - - - -
520A LEU* 4.2 2.9 - - - -
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Residues in contact with MET 498 (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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263A SER 3.2 26.9 + - - -
281A PHE* 4.0 26.0 - - + -
283A LEU* 4.2 14.4 - - + -
286A CYS* 4.4 10.1 - - - -
423A CYS* 3.6 35.7 - - - +
426A ALA* 3.7 27.6 - - + -
427A SER* 3.8 8.7 - - - +
486A GLY* 4.2 0.2 - - - -
487A ILE 3.4 21.8 - - - +
488A LEU* 3.8 20.6 - - + -
497A MET* 1.3 78.6 - - - +
499A CYS* 1.3 73.6 + - - +
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Residues in contact with CYS 499 (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* 3.8 18.2 - - + -
261A GLY 3.5 5.4 - - - -
262A VAL* 4.5 4.7 - - - -
485A GLY 3.5 1.3 - - - +
486A GLY* 3.3 4.0 - - - -
487A ILE* 2.9 41.6 + - + +
489A LEU* 5.4 0.4 - - - -
497A MET* 3.5 30.3 - - - -
498A MET* 1.3 75.4 - - - +
500A TRP* 1.3 63.1 + - - +
510A SER* 5.8 0.2 - - - -
513A GLY* 4.3 10.1 - - - -
516A PHE* 4.0 19.1 - - - -
517A CYS* 4.7 13.5 - - - -
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Residues in contact with TRP 500 (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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255A PHE* 3.7 24.7 - + - -
259A LEU* 3.6 37.3 - - + +
260A TRP* 3.1 10.4 + - - -
261A GLY 3.0 32.2 + - - -
276A ASP* 3.8 17.7 - - + -
279A VAL* 3.7 28.7 - - + -
281A PHE* 3.3 49.6 - + + +
423A CYS* 3.6 15.9 - - - -
484A ALA 2.9 19.1 + - - -
485A GLY 3.2 23.6 - - - -
486A GLY 3.7 3.1 - - - -
499A CYS* 1.3 78.7 - - - +
501A SER* 1.3 60.8 + - - +
502A PRO* 4.0 12.5 - - + +
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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