Contacts of the helix formed by residues 487 - 500 (chain B) in PDB entry 1UPX
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 GLU 487 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B ILE* 4.0 2.6 - - - +
75B THR* 3.9 20.2 - - - -
307B ASN* 3.6 11.7 + - - +
308B CYS* 4.4 0.4 - - - -
485B TRP* 4.1 1.8 - - - -
486B TYR* 1.3 87.2 - - + +
488B GLN* 1.3 70.0 + - - +
489B LYS* 3.0 32.1 + - - +
490B ALA* 3.0 23.2 + - - +
491B VAL* 3.4 8.6 + - - +
1546B FSO 1.2 105.9 + - - -
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Residues in contact with GLN 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 2.9 48.4 + - - +
74B ILE* 3.3 15.7 - - + +
75B THR* 3.0 43.9 + - - -
148B PHE* 3.4 35.6 - - + +
151B LYS* 4.1 14.4 - - + -
152B GLY* 3.5 10.7 - - - +
487B GLU* 1.3 75.7 + - - +
489B LYS* 1.3 66.1 + - - +
490B ALA 3.2 1.3 - - - -
491B VAL* 3.1 11.1 + - + +
492B ILE 3.1 17.0 + - - -
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Residues in contact with LYS 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 4.2 8.2 - - - -
74B ILE* 4.4 4.2 - - + +
152B GLY* 3.8 11.4 - - - -
155B ALA* 3.8 28.9 - - + -
156B TYR* 3.5 38.8 - - + +
159B HIS* 5.3 1.9 + - + +
240B HIS* 3.2 20.9 + - + +
307B ASN* 2.8 29.4 + - - +
452B CYS* 4.1 4.0 - - - -
487B GLU* 3.0 20.8 + - - +
488B GLN* 1.3 76.2 - - - +
490B ALA* 1.3 61.8 + - - +
492B ILE* 3.2 7.0 - - - +
493B VAL* 3.0 24.2 + - - +
1546B FSO 3.0 23.9 + - - +
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Residues in contact with ALA 490 (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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398B GLY* 5.4 3.6 - - - -
399B CYS* 3.6 20.4 - - - +
452B CYS* 6.1 1.8 - - - -
484B ALA 4.7 2.7 - - - +
485B TRP* 3.6 30.4 - - + +
487B GLU 3.0 13.3 + - - +
489B LYS* 1.3 78.6 - - - +
491B VAL* 1.3 57.8 + - - +
493B VAL* 3.3 9.0 + - - +
494B LEU* 3.0 28.4 + - - +
1546B FSO 3.5 3.8 - - - -
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Residues in contact with VAL 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN 5.1 0.4 - - - +
145B LEU* 4.1 25.4 - - + +
148B PHE* 4.3 6.3 - - + -
149B GLY* 3.8 23.8 - - - +
485B TRP* 4.2 14.6 - - + -
487B GLU 3.9 11.7 - - - +
488B GLN* 3.1 17.4 + - + +
490B ALA* 1.3 78.4 - - - +
492B ILE* 1.3 57.6 + - - +
494B LEU* 3.2 12.0 + - + +
495B LEU* 3.0 29.8 + - + +
512B PRO* 5.8 0.9 - - + -
514B PHE* 3.9 22.9 - - + -
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Residues in contact with ILE 492 (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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149B GLY* 3.4 29.6 - - - +
152B GLY* 3.6 22.2 - - - -
153B MET* 3.8 13.2 - - + +
156B TYR* 3.7 20.9 - - + -
198B THR* 3.6 35.0 - - + +
199B GLY* 4.6 0.2 - - - -
202B GLY* 3.6 21.1 - - - -
206B MET* 5.6 1.3 - - + -
488B GLN 3.1 6.9 + - - -
489B LYS 3.2 14.4 - - - +
491B VAL* 1.3 72.5 - - - +
493B VAL* 1.3 60.6 + - - +
495B LEU* 3.3 6.2 + - + +
496B ALA* 2.8 28.8 + - - +
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Residues in contact with VAL 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B TYR* 3.6 19.1 - - + +
206B MET* 4.0 17.0 - - + -
397B ALA* 6.3 0.2 - - + -
398B GLY* 6.5 1.3 - - - -
452B CYS* 3.9 15.5 - - + +
455B SER* 3.7 24.5 - - - +
483B ILE* 5.5 5.8 - - + -
489B LYS 3.0 19.8 + - - +
490B ALA* 3.7 10.5 - - - +
492B ILE* 1.3 75.0 - - - +
494B LEU* 1.3 63.7 + - - +
496B ALA* 3.3 7.3 + - - +
497B LEU* 2.9 39.1 + - + +
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Residues in contact with LEU 494 (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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145B LEU* 6.0 3.6 - - + -
483B ILE* 5.3 3.8 - - + -
490B ALA 3.0 14.5 + - - +
491B VAL* 3.5 13.9 - - + +
493B VAL* 1.3 78.6 - - - +
495B LEU* 1.3 64.1 + - + +
497B LEU* 3.2 8.2 + - + +
498B LEU* 2.9 49.0 + - + +
505B ILE* 4.0 35.2 - - + -
507B LEU* 3.9 33.4 - - + -
512B PRO* 5.7 4.3 - - + -
515B LEU* 6.5 0.7 - - + -
523B LEU* 6.2 3.1 - - + -
529B ILE* 5.0 11.9 - - + -
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Residues in contact with LEU 495 (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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145B LEU* 4.3 21.8 - - + +
146B ILE* 5.3 0.4 - - - -
149B GLY* 4.2 15.7 - - - -
195B THR* 3.7 33.4 - - + +
196B LEU* 5.3 3.1 - - + +
198B THR* 4.1 24.5 - - + -
199B GLY* 3.4 21.5 - - - +
491B VAL* 3.0 25.5 + - + +
492B ILE* 3.3 4.9 + - + +
494B LEU* 1.3 80.8 - - + +
496B ALA* 1.3 58.6 + - - +
498B LEU* 3.3 20.9 + - + +
499B SER* 2.9 24.6 + - - -
523B LEU* 6.0 1.3 - - + -
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Residues in contact with ALA 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B GLY* 3.4 16.7 - - - +
202B GLY 4.3 2.7 - - - -
203B VAL* 3.7 23.8 - - + +
206B MET* 4.3 14.8 - - + -
492B ILE 2.8 17.7 + - - +
493B VAL* 3.4 8.3 - - - +
495B LEU* 1.3 77.3 - - - +
497B LEU* 1.3 62.1 + - + +
499B SER* 2.7 18.1 + - - -
500B LEU* 3.0 15.6 + - + +
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Residues in contact with LEU 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B MET* 6.2 3.1 - - + -
395B VAL* 5.9 0.2 - - + -
455B SER* 5.4 6.1 - - - +
459B ALA* 4.6 14.1 - - + -
481B TYR* 4.9 12.6 - - + -
483B ILE* 3.8 29.6 - - + -
493B VAL* 2.9 30.9 + - + +
494B LEU* 3.6 9.4 - - + +
496B ALA* 1.3 76.7 - - + +
498B LEU* 1.3 62.1 + - - +
500B LEU* 3.2 20.7 + - + +
501B GLY 3.3 0.3 + - - -
502B VAL* 3.1 40.5 + - + +
505B ILE* 4.0 22.0 - - + -
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Residues in contact with LEU 498 (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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196B LEU* 4.4 9.2 - - + +
494B LEU* 2.9 35.1 + - + +
495B LEU* 3.6 22.0 - - + +
497B LEU* 1.3 75.9 - - - +
499B SER* 1.3 58.7 + - - +
501B GLY* 3.0 18.7 + - - -
502B VAL 3.7 20.0 - - - +
505B ILE* 4.0 14.1 - - + -
523B LEU* 4.5 13.7 - - + -
527B PHE* 3.7 56.6 - - + +
529B ILE* 4.1 12.6 - - + -
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Residues in contact with SER 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 3.8 19.4 - - - +
199B GLY 3.4 12.7 + - - -
200B LYS* 3.5 25.1 + - - -
203B VAL* 3.6 8.7 - - - +
495B LEU 2.9 14.3 + - - -
496B ALA 2.7 16.8 + - - -
498B LEU* 1.3 75.9 - - - +
500B LEU* 1.3 59.6 + - - +
501B GLY* 3.2 1.5 + - - -
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Residues in contact with LEU 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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203B VAL* 4.0 30.1 - - + -
206B MET* 6.2 2.0 - - + -
459B ALA* 3.9 27.6 - - + -
463B LEU* 4.6 26.2 - - + +
474B VAL* 4.4 11.8 - - + +
496B ALA* 3.0 21.6 + - + +
497B LEU* 3.2 16.3 + - + +
499B SER* 1.3 76.9 + - - +
501B GLY* 1.3 59.0 + - - +
502B VAL* 3.5 7.3 + - + -
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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