Contacts of the helix formed by residues 414 - 429 (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 ARG 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A TYR* 3.0 61.0 - - + +
412A ASN* 2.8 12.2 + - - +
413A GLU* 1.3 78.3 - - + +
415A SER* 1.3 63.7 + - - -
416A GLU 3.4 1.3 - - - -
417A TYR* 3.1 43.1 + - + +
418A VAL* 2.9 30.9 + - + +
421A ARG* 5.8 0.6 - - - +
189B LYS* 5.8 5.2 - - - +
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Residues in contact with SER 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A PHE* 3.6 11.1 - - - +
412A ASN* 2.8 23.9 + - - -
413A GLU 3.2 2.2 - - - -
414A ARG* 1.3 76.2 - - - +
416A GLU* 1.3 64.1 + - - +
418A VAL* 3.2 4.3 + - - +
419A LYS* 2.9 38.1 + - - +
440A PRO* 3.1 39.2 - - - +
188B ARG* 3.6 14.7 + - - +
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A GLU 4.8 0.2 + - - -
414A ARG 3.4 0.8 - - - -
415A SER* 1.3 76.6 - - - +
417A TYR* 1.4 57.5 + - - +
419A LYS* 3.3 29.5 + - - +
420A LEU* 3.0 27.4 + - - +
188B ARG* 3.5 23.0 - - - +
189B LYS 3.3 27.5 + - - +
190B GLY* 4.0 16.5 - - - +
191B LEU* 3.5 28.9 - - + +
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Residues in contact with TYR 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A GLU 5.5 0.4 + - - -
414A ARG* 3.1 44.8 + - + +
416A GLU* 1.4 76.5 - - - +
418A VAL* 1.3 58.3 + - - +
420A LEU* 3.2 20.2 + - + +
421A ARG* 2.8 73.5 + - + +
189B LYS* 6.4 2.0 - - - -
190B GLY* 5.8 0.4 - - - -
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Residues in contact with VAL 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 3.8 7.0 - - + +
360A TYR* 4.1 23.3 - - + +
361A TYR* 3.9 28.5 - - + -
414A ARG* 2.9 35.6 + - + +
415A SER* 3.4 11.2 - - - +
417A TYR* 1.3 76.9 - - - +
419A LYS* 1.3 60.8 + - + +
421A ARG* 3.3 5.2 + - - -
422A PHE* 2.8 28.8 + - + +
438A VAL* 4.0 15.7 - - + +
440A PRO* 4.8 10.3 - - + -
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Residues in contact with LYS 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A SER* 2.9 26.1 + - - +
416A GLU* 3.6 32.3 + - - +
418A VAL* 1.3 77.2 - - + +
420A LEU* 1.3 65.0 + - - +
422A PHE* 3.3 9.5 + - - +
423A GLU* 3.1 26.9 + - - +
438A VAL 6.1 1.1 - - - +
440A PRO* 4.4 23.5 - - + +
188B ARG* 5.9 0.6 - - - +
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Residues in contact with LEU 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A GLU 3.0 15.9 + - - +
417A TYR* 3.2 18.8 + - + +
419A LYS* 1.3 77.7 - - - +
421A ARG* 1.3 70.2 + - - +
423A GLU* 3.2 7.9 + - - +
424A GLU* 2.6 52.4 + - + +
192B LYS* 5.7 6.5 - - - +
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Residues in contact with ARG 421 (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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334A ARG* 5.3 18.6 - - - +
335A LEU* 3.8 20.6 - - + +
336A GLU* 4.9 7.9 + - - +
414A ARG* 5.8 0.4 - - - +
417A TYR* 2.8 70.6 + - + +
418A VAL* 3.9 4.7 - - - +
420A LEU* 1.3 78.8 - - - +
422A PHE* 1.3 58.5 + - - +
424A GLU* 2.9 37.1 + - - +
425A ALA* 2.9 29.7 + - - +
428A ARG* 3.5 21.8 - - - +
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Residues in contact with PHE 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 3.4 11.3 - - + +
339A ILE* 4.0 15.7 - - + -
418A VAL 2.8 18.3 + - - +
419A LYS* 3.5 9.4 - - - +
420A LEU 3.2 0.2 - - - -
421A ARG* 1.3 75.6 - - - +
423A GLU* 1.3 68.9 + - - +
425A ALA* 3.1 4.9 + - - +
426A LYS* 2.9 57.1 + - + +
431A MSE 5.9 0.2 - - - -
436A VAL* 3.4 38.4 - - + -
437A VAL* 4.8 0.7 - - - -
438A VAL* 3.6 49.4 - - + -
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Residues in contact with GLU 423 (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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419A LYS 3.1 13.8 + - - +
420A LEU* 3.6 8.7 - - - +
422A PHE* 1.3 83.8 - - - +
424A GLU* 1.3 61.7 + - + +
426A LYS* 3.1 36.9 + - - +
427A SER* 3.2 20.6 + - - -
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Residues in contact with GLU 424 (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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420A LEU* 2.6 41.9 + - + +
421A ARG* 2.9 37.8 + - - +
423A GLU* 1.3 76.1 - - + +
425A ALA* 1.3 61.7 + - - +
427A SER* 3.3 11.3 + - - -
428A ARG* 3.2 47.6 + - - +
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Residues in contact with ALA 425 (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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335A LEU* 4.9 0.4 - - + -
336A GLU* 4.2 31.4 + - + +
339A ILE* 3.7 27.6 - - + -
421A ARG* 2.9 15.8 + - - +
422A PHE* 3.4 9.2 - - - +
424A GLU* 1.3 76.2 - - - +
426A LYS* 1.3 57.6 + - - +
428A ARG* 3.1 1.6 + - - -
429A LEU* 2.9 36.3 + - + +
431A MSE 5.4 0.2 - - - -
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Residues in contact with LYS 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE* 5.6 0.2 - - - +
422A PHE* 2.9 52.6 + - + +
423A GLU* 3.1 41.5 + - - +
425A ALA* 1.3 74.4 - - - +
427A SER* 1.3 59.9 - - - +
429A LEU 2.9 21.0 - - - +
431A MSE 3.1 33.8 - - + +
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Residues in contact with SER 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLU 3.2 9.2 + - - -
424A GLU* 3.3 13.7 - - - -
425A ALA 3.2 0.2 - - - -
426A LYS* 1.3 78.0 - - - +
428A ARG* 1.3 61.9 + - - +
429A LEU 4.8 0.3 - - - +
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Residues in contact with ARG 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ARG* 5.5 3.2 - - - +
336A GLU* 3.2 39.1 + - - +
421A ARG* 3.5 17.5 - - - +
424A GLU* 3.2 38.7 + - - +
425A ALA 3.1 8.0 + - - +
427A SER* 1.3 80.3 - - - +
429A LEU* 1.3 62.0 + - + +
430A ARG 4.5 0.2 + - - -
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Residues in contact with LEU 429 (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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336A GLU* 3.5 45.8 - - + +
339A ILE* 3.7 29.6 - - + -
340A LEU* 3.9 33.0 - - + +
343A MSE 4.7 2.9 - - + -
425A ALA 2.9 16.0 + - - +
426A LYS 2.9 5.7 - - - +
427A SER 4.7 0.2 - - - -
428A ARG* 1.3 82.3 - - - +
430A ARG* 1.3 57.9 + - + +
431A MSE 2.6 34.5 + - + +
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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