Contacts of the helix formed by residues 399 - 409 (chain A) in PDB entry 1U2X
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 GLY 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A GLY 3.0 11.2 + - - +
131A LYS* 4.3 6.5 - - - -
397A ILE* 3.6 5.4 - - - +
398A ARG* 1.3 77.8 - - - +
400A PRO* 1.3 76.3 - - - +
401A ASP* 3.2 3.4 - - - -
402A ASP* 3.0 22.3 + - - +
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Residues in contact with PRO 400 (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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24A ILE* 3.3 29.7 - - + +
129A GLY 3.6 7.4 - - - +
130A LEU* 3.6 17.3 - - + +
131A LYS* 3.7 28.0 - - + +
399A GLY* 1.3 84.2 - - - +
401A ASP* 1.3 68.5 + - - +
402A ASP 3.1 1.2 + - - -
403A TYR* 3.1 22.7 + - - +
404A LYS* 4.4 1.4 + - - +
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Residues in contact with ASP 401 (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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399A GLY 3.2 1.9 + - - -
400A PRO* 1.3 82.6 - - - +
402A ASP* 1.3 63.0 + - - +
404A LYS* 2.9 46.7 + - + +
405A VAL* 4.1 1.2 + - - +
398B ARG* 3.7 19.9 + - - +
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Residues in contact with ASP 402 (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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390A ALA* 3.4 9.1 - - - +
394A LEU* 3.7 16.6 - - + +
397A ILE* 4.2 13.2 - - + -
398A ARG* 2.7 48.8 + - - +
399A GLY 3.0 16.9 + - - +
401A ASP* 1.3 78.6 - - - +
403A TYR* 1.3 60.9 + - - +
405A VAL* 3.1 23.2 + - - +
398B ARG* 2.8 40.3 + - - +
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Residues in contact with TYR 403 (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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23A MSE 3.8 39.9 - - + +
24A ILE* 4.6 4.5 - - + -
130A LEU* 4.4 13.1 - - + +
382A GLU 4.2 0.3 + - - -
383A PHE* 3.5 60.1 + + - -
386A THR* 3.4 36.4 + - + +
387A LEU* 4.0 20.0 - - + -
390A ALA* 3.9 8.0 - - - +
397A ILE* 5.0 2.0 - - - +
399A GLY 4.4 0.6 + - - -
400A PRO 3.1 16.0 + - - +
402A ASP* 1.3 74.8 - - - +
404A LYS* 1.3 68.2 + - + +
406A GLY* 3.0 21.8 + - - -
407A LEU* 4.6 8.7 - - + +
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Residues in contact with LYS 404 (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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400A PRO 5.2 0.9 - - - +
401A ASP* 2.9 43.4 + - + +
403A TYR* 1.3 81.5 - - + +
405A VAL* 1.3 64.6 + - + +
406A GLY 3.1 0.2 - - - -
407A LEU* 3.1 38.5 + - + +
408A LYS* 3.9 11.0 + - - +
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Residues in contact with VAL 405 (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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390A ALA* 4.4 2.9 - - + +
393A SER* 4.4 6.3 - - - -
394A LEU* 4.2 22.7 - - + -
401A ASP 4.6 0.9 - - - +
402A ASP* 3.1 20.6 + - - +
404A LYS* 1.3 79.0 - - + +
406A GLY* 1.3 63.2 + - - +
408A LYS* 3.1 26.4 + - + +
409A VAL* 4.0 6.6 + - - +
393B SER 3.7 23.6 - - - +
394B LEU* 3.8 29.6 - - + +
398B ARG* 4.5 9.2 - - - +
448B VAL* 4.1 9.8 - - + +
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Residues in contact with GLY 406 (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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386A THR* 3.5 29.4 - - - -
389A ALA* 4.2 4.2 - - - +
390A ALA* 3.5 14.6 - - - +
403A TYR 3.0 8.6 + - - -
405A VAL* 1.3 79.7 - - - +
407A LEU* 1.3 54.8 + - - +
408A LYS 3.0 0.2 - - - -
409A VAL* 3.0 20.4 + - - +
442A ARG* 3.4 16.6 - - - -
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Residues in contact with LEU 407 (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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23A MSE 4.9 13.5 - - + -
386A THR* 3.7 18.5 - - + +
403A TYR* 4.6 13.0 - - + +
404A LYS* 3.1 34.6 + - + +
406A GLY* 1.3 74.4 - - - +
408A LYS* 1.3 60.1 + - + +
409A VAL 3.2 0.9 + - - -
410A PRO* 5.5 0.3 - - - +
442A ARG* 3.6 36.8 + - - +
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Residues in contact with LYS 408 (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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404A LYS* 4.0 11.4 - - - +
405A VAL* 3.4 20.2 - - - +
406A GLY 3.0 1.0 - - - -
407A LEU* 1.3 78.2 - - + +
409A VAL* 1.3 61.5 + - - +
410A PRO* 3.6 8.1 - - - +
113B GLU* 4.9 9.9 + - - -
394B LEU 3.6 25.4 - - - +
395B GLY* 4.3 18.4 + - - -
396B ASP* 5.4 4.0 - - - +
448B VAL* 4.1 27.2 - - + +
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Residues in contact with VAL 409 (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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389A ALA* 3.9 13.2 - - + +
393A SER* 3.8 22.2 - - - +
405A VAL 4.1 4.5 - - - +
406A GLY 3.0 11.6 + - - +
407A LEU 4.5 0.4 - - - -
408A LYS* 1.3 79.4 - - - +
410A PRO* 1.3 67.5 - - + +
442A ARG* 2.9 46.6 + - - +
443A LEU 3.6 24.2 - - - +
444A VAL* 3.8 11.2 - - + -
448B VAL* 4.0 12.8 - - + -
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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