Contacts of the helix formed by residues 487 - 500 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A CYS* 4.6 0.2 - - - -
74A ILE* 3.9 3.6 - - - +
75A THR* 3.9 21.3 - - - -
307A ASN* 3.6 17.1 + - - +
308A CYS* 4.4 0.7 - - - -
485A TRP* 4.1 1.6 - - - -
486A TYR* 1.3 88.2 - - + +
488A GLN* 1.3 69.0 + - - +
489A LYS* 3.0 28.5 + - - +
490A ALA* 3.1 23.6 + - - +
491A VAL* 3.5 8.4 + - - +
1546A FSO 1.2 101.9 + - - -
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Residues in contact with GLN 488 (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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8A GLN* 2.9 50.4 + - - +
74A ILE* 3.3 14.6 - - + +
75A THR* 2.9 44.1 + - - -
148A PHE* 3.4 35.8 - - + +
151A LYS* 4.1 13.9 - - + -
152A GLY* 3.6 9.5 - - - +
487A GLU* 1.3 77.5 + - - +
489A LYS* 1.3 65.7 + - - +
490A ALA 3.2 0.2 - - - -
491A VAL* 3.1 11.8 + - + +
492A ILE 3.1 17.8 + - - -
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Residues in contact with LYS 489 (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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71A PHE* 4.3 9.0 - - - -
74A ILE* 4.4 4.9 - - + +
152A GLY* 3.9 19.0 - - - -
155A ALA* 3.9 20.6 - - + -
156A TYR* 3.5 40.4 - - + +
159A HIS* 5.3 1.9 - - + -
240A HIS* 3.2 20.3 + - + +
307A ASN* 2.9 28.3 + - - +
452A CYS* 4.1 4.7 - - - -
487A GLU* 3.0 21.2 + - - +
488A GLN* 1.3 75.1 - - - +
490A ALA* 1.3 64.1 + - - +
492A ILE* 3.2 7.1 - - - +
493A VAL* 3.0 24.1 + - - +
1546A FSO 2.9 22.5 + - - +
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Residues in contact with ALA 490 (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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398A GLY* 5.4 4.0 - - - -
399A CYS* 3.6 23.8 - - - +
452A CYS* 6.0 1.6 - - - -
483A ILE* 6.1 2.2 - - + +
484A ALA 4.8 2.0 - - - +
485A TRP* 3.6 26.4 - - + +
487A GLU 3.1 13.6 + - - +
489A LYS* 1.3 77.4 - - - +
491A VAL* 1.3 57.0 + - - +
493A VAL* 3.3 9.2 + - - +
494A LEU* 2.9 28.8 + - - +
1546A FSO 3.5 4.0 - - - -
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Residues in contact with VAL 491 (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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8A GLN 5.1 0.2 - - - +
145A LEU* 4.0 27.8 - - + +
148A PHE* 4.2 6.7 - - + -
149A GLY* 3.8 23.1 - - - +
485A TRP* 4.3 12.3 - - + -
487A GLU 3.9 11.7 - - - +
488A GLN* 3.1 17.6 + - + +
490A ALA* 1.3 78.2 - - - +
492A ILE* 1.3 56.4 + - - +
494A LEU* 3.2 11.0 + - + +
495A LEU* 3.0 29.6 + - + +
512A PRO* 5.9 0.7 - - + -
514A PHE* 3.9 23.6 - - + -
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Residues in contact with ILE 492 (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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149A GLY* 3.4 28.9 - - - +
152A GLY* 3.7 18.4 - - - -
153A MET* 3.9 9.2 - - + +
156A TYR* 3.6 25.8 - - + -
198A THR* 3.6 38.4 - - + +
199A GLY* 4.5 0.2 - - - -
202A GLY* 3.6 21.5 - - - +
206A MET* 4.9 1.3 - - + -
488A GLN 3.1 6.9 + - - -
489A LYS 3.2 14.1 - - - +
491A VAL* 1.3 76.0 - - - +
493A VAL* 1.3 57.5 + - - +
495A LEU* 3.3 5.3 + - + +
496A ALA* 2.8 29.0 + - - +
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Residues in contact with VAL 493 (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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156A TYR* 3.6 19.3 - - + +
206A MET* 4.1 15.9 - - + -
397A ALA* 6.3 0.7 - - + -
398A GLY* 6.5 0.9 - - - -
452A CYS* 3.8 15.9 - - + +
455A SER* 3.6 24.5 - - - +
483A ILE* 5.8 5.6 - - + -
489A LYS 3.0 19.4 + - - +
490A ALA* 3.6 10.5 - - - +
492A ILE* 1.3 76.4 - - - +
494A LEU* 1.3 62.7 + - - +
496A ALA* 3.3 7.3 + - - +
497A LEU* 2.9 38.5 + - + +
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Residues in contact with LEU 494 (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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145A LEU* 5.9 4.5 - - + -
483A ILE* 5.9 4.9 - - + -
490A ALA 2.9 17.8 + - - +
491A VAL* 3.2 11.9 + - + +
493A VAL* 1.3 77.2 - - - +
495A LEU* 1.3 68.0 + - + +
497A LEU* 3.2 8.5 + - + +
498A LEU* 2.9 39.7 + - + +
505A ILE* 4.0 35.0 - - + -
507A LEU* 3.9 32.8 - - + -
512A PRO* 5.7 4.3 - - + -
515A LEU* 6.3 2.2 - - + -
523A LEU* 5.9 3.8 - - + -
529A ILE* 4.4 15.7 - - + -
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Residues in contact with LEU 495 (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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145A LEU* 4.3 25.4 - - + +
146A ILE* 5.2 0.7 - - - -
149A GLY* 4.2 15.5 - - - -
195A THR* 3.7 39.5 - - + +
196A LEU* 5.1 3.6 - - + +
198A THR* 4.1 18.8 - - + -
199A GLY* 3.3 21.9 - - - +
491A VAL* 3.0 24.7 + - + +
492A ILE* 3.8 4.7 - - + +
494A LEU* 1.3 81.7 - - + +
496A ALA* 1.3 57.2 + - - +
498A LEU* 3.3 20.0 + - + +
499A SER* 2.9 24.3 + - - -
523A LEU* 6.3 0.7 - - + -
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Residues in contact with ALA 496 (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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199A GLY* 3.4 16.9 - - - +
202A GLY 4.4 0.2 - - - -
203A VAL* 3.7 16.8 - - + +
206A MET* 3.7 25.4 - - + -
492A ILE 2.8 17.9 + - - +
493A VAL* 3.4 5.2 - - + +
495A LEU* 1.3 76.5 - - - +
497A LEU* 1.3 63.1 + - + +
499A SER* 2.7 18.2 + - - -
500A LEU* 3.1 14.8 + - + +
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Residues in contact with LEU 497 (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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395A VAL* 5.8 1.8 - - + -
455A SER* 5.3 6.5 - - - +
458A LEU* 6.5 0.4 - - + -
459A ALA* 4.5 23.3 - - + +
481A TYR* 5.0 11.7 - - + -
483A ILE* 3.7 29.8 - - + -
493A VAL* 2.9 32.6 + - + +
494A LEU* 3.6 8.3 - - - +
496A ALA* 1.3 76.7 - - + +
498A LEU* 1.3 62.2 + - - +
500A LEU* 3.1 12.9 + - + +
501A GLY 3.3 0.2 + - - -
502A VAL* 3.1 41.4 + - + +
505A ILE* 4.0 18.6 - - + -
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Residues in contact with LEU 498 (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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195A THR* 6.3 0.4 - - + -
196A LEU* 4.4 11.4 - - + +
494A LEU* 2.9 27.3 + - + +
495A LEU* 3.7 21.1 - - + +
497A LEU* 1.3 75.9 - - - +
499A SER* 1.3 58.4 + - - +
501A GLY* 3.0 18.7 + - - -
502A VAL 3.7 19.3 - - - +
505A ILE* 4.1 12.6 - - + -
523A LEU* 4.1 19.5 - - + -
527A PHE* 3.6 43.3 - - + -
529A ILE* 3.9 27.6 - - + -
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Residues in contact with SER 499 (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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196A LEU* 3.7 20.1 - - - +
199A GLY 3.4 12.5 + - - -
200A LYS* 3.5 26.8 + - - -
203A VAL* 3.8 5.9 - - - +
495A LEU 2.9 14.9 + - - -
496A ALA 2.7 17.2 + - - -
498A LEU* 1.3 76.3 - - - +
500A LEU* 1.3 60.1 + - - +
501A GLY* 3.2 1.3 + - - -
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Residues in contact with LEU 500 (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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203A VAL* 4.0 30.7 - - + -
459A ALA* 3.8 30.3 - - + -
463A LEU* 4.5 28.3 - - + +
474A VAL* 4.3 11.4 - - - +
496A ALA* 3.1 19.7 + - + +
497A LEU* 3.1 14.7 + - + +
499A SER* 1.3 76.7 - - - +
501A GLY* 1.3 60.1 + - - +
502A VAL* 3.4 7.4 + - + -
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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