Contacts of the strand formed by residues 495 - 500 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B ILE* 4.9 1.8 - - - -
226B PHE* 4.0 29.4 - - + -
264B VAL* 3.5 23.1 - - + -
265B CYS 3.4 15.3 - - - +
266B THR* 3.8 7.9 - - + +
267B ALA 4.3 1.6 - - - +
434B ALA* 3.4 13.7 - - - +
491B VAL* 2.8 55.1 + - + +
494B VAL* 1.3 91.5 - - + +
496B GLY* 1.3 61.8 + - - +
497B MET* 3.5 26.5 - - + +
520B LEU* 4.0 13.0 - - + -
526B PHE* 4.1 7.2 - - + -
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Residues in contact with GLY 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B VAL* 3.8 0.2 - - - -
265B CYS 2.8 32.1 + - - -
427B SER 3.8 6.0 - - - +
430B ALA* 3.6 4.5 - - - -
431B ALA* 3.4 25.4 - - - +
489B LEU 3.4 7.2 - - - -
490B VAL* 4.5 0.4 - - - -
495B MET* 1.3 76.6 - - - +
497B MET* 1.3 66.4 + - - +
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Residues in contact with MET 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ILE* 4.9 1.6 - - - -
262B VAL* 4.2 4.7 - - + -
263B SER 3.3 15.0 - - - +
264B VAL* 3.5 20.2 - - + -
427B SER* 4.1 6.1 - - - -
430B ALA* 3.6 9.6 - - - +
487B ILE 4.5 0.2 - - - -
488B LEU* 3.7 2.6 - - - +
489B LEU* 2.7 59.5 + - + +
495B MET* 3.5 29.8 - - + -
496B GLY* 1.3 77.3 - - - +
498B MET* 1.3 61.2 + - - +
499B CYS* 3.7 14.6 - - - -
516B PHE* 3.2 37.5 - - + -
520B LEU* 4.1 4.7 - - - -
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Residues in contact with MET 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B GLY 3.8 0.7 - - - +
262B VAL* 3.5 2.8 - - - -
263B SER 3.1 29.0 + - - -
281B PHE* 4.0 18.6 - - + -
283B LEU* 4.3 9.9 - - + -
286B CYS* 4.3 15.5 - - - -
423B CYS* 3.5 34.3 - - - +
426B ALA* 3.7 23.8 - - + -
427B SER* 4.1 1.3 - - - +
486B GLY* 4.0 4.7 - - - -
487B ILE 3.5 18.4 - - - +
488B LEU* 3.5 32.5 - - + +
497B MET* 1.3 75.9 - - - +
499B CYS* 1.3 78.8 + - - +
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Residues in contact with CYS 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B TRP* 3.6 18.8 - - + -
261B GLY 3.3 5.6 - - - -
262B VAL* 4.4 3.4 - - - +
485B GLY 3.7 1.5 - - - +
486B GLY* 3.5 0.3 - - - -
487B ILE* 3.1 39.0 + - + +
489B LEU* 5.1 0.9 - - - -
497B MET* 3.7 27.6 - - - -
498B MET* 1.3 77.0 - - - +
500B TRP* 1.3 63.3 + - - +
513B GLY* 4.2 12.6 - - - -
516B PHE* 3.8 22.7 - - - -
517B CYS* 4.6 12.1 - - - -
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Residues in contact with TRP 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B PHE* 3.6 30.7 - + - -
259B LEU* 3.9 24.2 - - + -
260B TRP* 3.1 10.2 - - - -
261B GLY 2.8 33.7 + - - -
276B ASP* 3.7 19.1 - - + -
279B VAL* 3.5 42.0 - - + -
281B PHE* 3.4 42.3 - + + +
423B CYS* 3.6 16.2 - - - -
484B ALA 2.9 19.3 + - - -
485B GLY 3.2 19.1 - - - -
486B GLY 3.8 2.5 - - - -
499B CYS* 1.3 77.3 - - - +
501B SER* 1.3 67.2 + - - +
502B PRO* 3.8 15.4 - - + +
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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