Contacts of the strand formed by residues 496 - 500 (chain B) in PDB entry 2ETM
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 TRP 496 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419B ARG* 3.3 40.2 - - - -
422B ILE* 3.8 26.7 - - + -
424B LEU* 4.5 31.2 - - + -
453B ILE* 4.0 16.4 - - + -
454B LYS 3.2 6.5 - - - +
455B THR* 3.5 30.8 - - + +
468B PHE* 4.3 0.9 - - - -
489B VAL* 3.4 4.7 - - - +
490B ILE* 2.9 47.1 + - + +
494B PRO* 3.6 30.2 + - + +
495B VAL* 1.3 86.3 - - - +
497B ILE* 1.3 64.3 - - - +
498B ILE* 4.1 15.0 - - + -
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Residues in contact with ILE 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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452B ALA 3.9 0.3 - - - +
453B ILE* 3.7 1.2 - - - -
454B LYS* 2.9 35.7 + - + +
468B PHE* 3.2 55.6 - - + +
469B LEU* 4.1 5.6 - - + -
471B GLU* 4.2 11.2 - - - +
472B ALA* 4.2 15.9 - - + +
486B LEU* 3.6 26.2 - - + -
488B GLY 3.7 4.3 - - - +
489B VAL* 4.1 12.3 - - + +
496B TRP* 1.3 75.0 - - - +
498B ILE* 1.3 64.1 + - - +
499B MET* 3.6 21.4 + - + +
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Residues in contact with ILE 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B ILE* 3.5 25.8 - - + -
422B ILE* 4.1 19.5 - - + -
441B TYR* 4.9 0.9 - - + -
451B VAL* 3.7 36.1 - - + -
452B ALA 3.5 2.7 - - - +
453B ILE* 3.6 31.4 - - + -
486B LEU* 3.6 3.6 - - - +
487B ILE* 2.7 38.9 + - + -
488B GLY 2.6 23.5 + - - +
489B VAL* 4.7 2.5 - - - +
490B ILE* 4.9 4.0 - - + -
496B TRP* 4.1 16.2 - - + -
497B ILE* 1.3 76.9 - - - +
499B MET* 1.3 57.0 + - - +
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Residues in contact with MET 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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132B 7PY 3.9 26.7 - - + -
451B VAL* 2.9 12.3 - - - +
452B ALA* 2.9 28.3 + - + +
454B LYS* 4.0 11.9 - - + +
471B GLU* 3.3 37.2 - - + +
475B MET* 3.4 32.8 - - + -
484B VAL* 4.3 6.5 - - + -
485B LYS 3.4 10.3 - - - +
486B LEU* 4.2 2.7 - - + -
487B ILE* 3.6 5.6 - - - +
497B ILE* 3.6 24.9 + - + +
498B ILE* 1.3 76.1 - - - +
500B GLU* 1.3 65.7 + - - +
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Residues in contact with GLU 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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132B 7PY 3.1 21.7 - - - -
449B LEU* 5.6 3.8 - - + -
450B ALA 4.5 0.9 - - - +
451B VAL* 4.2 4.0 - - - -
452B ALA 4.0 0.2 - - - -
483B ILE 4.2 1.2 - - - +
484B VAL* 4.0 7.9 - - + +
485B LYS* 3.0 55.7 + - + +
487B ILE* 3.7 14.3 - - + +
499B MET* 1.3 76.3 - - - +
501B LEU* 1.3 67.1 + - - +
502B CYS* 4.4 2.9 - - - -
555B SER* 4.0 6.9 + - - -
561B LYS* 2.9 41.9 + - - +
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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