Contacts of the strand formed by residues 498 - 503 (chain D) in PDB entry 1Q57
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 THR 498 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D PHE* 5.4 0.4 - - + -
299D THR* 3.8 30.7 - - + -
303D ARG* 4.3 4.2 + - - -
306D GLU* 3.9 9.0 + - - -
307D VAL 3.7 3.9 + - - +
308D ILE* 3.5 28.2 - - + +
309D MET 2.9 25.3 + - - -
497D ASP* 1.3 77.7 + - - +
499D ILE* 1.3 67.3 + - - +
500D ILE* 4.0 14.8 - - + -
518D ILE* 4.3 2.7 - - + -
520D LYS 3.2 15.0 - - - +
521D CYS* 4.1 13.1 - - + -
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Residues in contact with ILE 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D MET* 3.3 24.0 - - + +
311D THR* 5.1 7.4 - - + -
483D ILE* 5.6 8.7 - - + -
486D LEU* 6.1 7.6 - - + -
492D LEU 4.9 4.3 - - - +
493D ARG* 6.0 2.9 - - - +
496D SER* 3.2 31.9 - - - +
498D THR* 1.3 84.8 - - - +
500D ILE* 1.3 63.4 + - - +
518D ILE* 3.5 3.3 - - - +
519D LEU* 2.6 73.1 + - + -
520D LYS* 2.8 25.8 + - + +
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Residues in contact with ILE 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D PHE* 3.5 40.8 - - + -
295D ILE* 3.7 14.6 - - + -
308D ILE* 3.8 10.5 - - + -
309D MET 2.9 8.2 + - - +
310D VAL* 3.3 10.9 - - + +
311D THR* 2.9 23.9 + - - +
321D PHE* 4.5 15.9 - - + -
498D THR* 4.0 8.0 - - + -
499D ILE* 1.3 74.0 - - - +
501D ALA* 1.3 63.8 + - - +
502D LEU* 4.8 5.2 - - + -
516D VAL* 3.4 30.1 - - + -
517D ARG 3.6 4.3 - - - +
518D ILE* 3.6 19.3 - - + -
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Residues in contact with ALA 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D THR* 3.1 24.9 - - + +
481D VAL* 4.1 24.5 - - + -
499D ILE* 3.9 1.2 + - + -
500D ILE* 1.3 75.6 - - - +
502D LEU* 1.3 63.8 + - - +
503D GLU* 5.2 1.1 - - - +
516D VAL* 3.3 9.2 - - - +
517D ARG* 2.8 37.3 + - + +
519D LEU* 4.2 13.5 - - + -
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Residues in contact with LEU 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310D VAL* 3.6 23.1 - - + -
311D THR 3.0 18.5 + - - +
312D SER* 2.4 40.2 + - - +
313D GLY 4.2 1.2 + - - -
317D VAL* 4.6 10.5 - - + +
318D MET* 3.8 10.5 - - + -
321D PHE* 3.7 44.0 - - + -
481D VAL* 5.3 1.5 - - - +
500D ILE* 4.8 1.3 - - + -
501D ALA* 1.3 79.3 - - - +
503D GLU* 1.3 62.7 + - - +
504D ARG* 4.3 0.5 + - - +
514D VAL* 4.0 12.6 - - + -
515D LEU 3.1 10.5 - - - +
516D VAL* 4.6 7.0 - - + -
533D MET* 4.1 10.8 - - + -
542D LEU* 5.2 0.7 - - + -
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Residues in contact with GLU 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478D GLY* 3.5 14.6 - - - +
479D ARG 4.8 0.9 - - - +
480D PRO* 2.8 29.5 - - - +
481D VAL* 2.7 38.9 + - + +
501D ALA 5.2 1.6 - - - -
502D LEU* 1.3 78.7 - - - +
504D ARG* 1.3 61.4 + - - +
514D VAL* 3.2 7.5 - - - +
515D LEU* 2.8 51.1 + - + +
517D ARG* 2.8 29.4 + - - +
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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