Contacts of the strand formed by residues 501 - 506 (chain A) in PDB entry 5D3O
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 501 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A ILE* 5.0 0.9 - - - -
232A PHE* 3.8 31.2 - - + -
270A VAL* 4.1 9.0 - - + -
271A CYS 3.6 6.5 - - - +
272A THR* 3.6 17.3 - - + +
273A ALA 4.0 2.2 - - - +
440A ALA* 3.2 12.9 - - - +
497A VAL* 2.9 48.5 + - + +
500A VAL* 1.3 97.4 - - + +
502A GLY* 1.3 67.7 + - - +
503A MET* 3.2 35.4 - - + -
526A LEU* 4.1 12.6 - - + -
532A PHE* 4.7 6.1 - - + -
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Residues in contact with GLY 502 (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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270A VAL* 3.7 0.2 - - - -
271A CYS 3.0 34.0 + - - -
433A SER 3.9 4.0 - - - +
436A ALA* 3.6 6.5 - - - -
437A ALA* 3.6 24.2 - - - +
495A LEU 3.6 8.5 - - - -
501A MET* 1.3 73.6 - - - +
503A MET* 1.3 69.8 + - - +
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Residues in contact with MET 503 (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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236A ILE* 4.7 3.1 - - - -
268A VAL* 3.8 11.2 - - + -
269A SER 3.3 11.4 - - - +
270A VAL* 3.8 15.7 - - + -
433A SER* 4.2 4.9 - - - -
436A ALA* 3.5 9.2 - - - +
494A LEU* 3.9 1.6 - - - +
495A LEU* 2.8 46.8 + - + +
497A VAL* 5.8 0.2 - - + -
501A MET* 3.2 35.0 - - + -
502A GLY* 1.3 79.1 - - - +
504A MET* 1.3 62.1 + - - +
505A CYS* 3.7 19.3 - - - -
522A PHE* 3.3 36.3 - - + -
526A LEU* 4.3 6.3 - - - -
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Residues in contact with MET 504 (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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267A GLY 3.7 1.4 - - - +
268A VAL* 3.6 2.6 - - - -
269A SER 3.2 27.4 + - - -
287A PHE* 4.0 20.2 - - + -
289A LEU* 4.7 7.2 - - + -
292A CYS* 4.4 11.9 - - - -
429A CYS* 3.6 33.0 - - - +
432A ALA* 3.6 26.2 - - + -
433A SER* 3.8 2.4 - - - +
492A GLY* 4.1 0.7 - - - -
493A ILE 3.6 21.3 - - - +
494A LEU* 3.1 44.9 - - + +
503A MET* 1.3 77.4 - - - +
505A CYS* 1.3 72.9 + - - +
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Residues in contact with CYS 505 (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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266A TRP* 3.9 17.7 - - + -
267A GLY 3.3 5.2 - - - -
268A VAL* 3.9 11.0 - - + -
491A GLY 3.4 2.2 - - - +
492A GLY* 3.2 3.1 - - - -
493A ILE* 2.8 41.0 + - + +
495A LEU* 5.4 1.3 - - - -
503A MET* 3.7 30.5 - - - -
504A MET* 1.3 74.2 - - - +
506A TRP* 1.3 61.0 + - - +
507A SER 4.2 0.2 - - - -
519A GLY* 4.2 12.1 - - - -
522A PHE* 3.9 14.4 - - - -
523A CYS* 4.7 12.6 - - - -
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Residues in contact with TRP 506 (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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261A PHE* 3.8 21.5 - + - -
265A LEU* 3.4 40.4 - - + -
266A TRP* 3.2 8.5 - - - -
267A GLY 2.9 33.8 + - - -
282A ASP* 3.8 19.3 - - + -
285A VAL* 3.8 32.5 - - + -
287A PHE* 3.3 55.9 - + + +
429A CYS* 3.5 16.6 - - - -
490A ALA 3.1 25.5 + - - -
491A GLY 3.4 10.5 - - - -
505A CYS* 1.3 75.0 - - - +
507A SER* 1.3 60.6 + - - +
508A PRO* 3.9 12.3 - - + +
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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