Contacts of the helix formed by residues 415 - 429 (chain A) in PDB entry 1QU2
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 SER 415 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A MET* 5.5 0.9 - - - +
174A GLY 4.7 0.2 - - - -
175A LEU* 2.6 31.5 + - - +
177A TYR* 4.5 7.8 - - - -
413A PHE 4.1 0.2 - - - -
414A ALA* 1.3 67.3 - - - +
416A ILE* 1.3 63.3 + - - +
417A SER* 3.3 5.5 + - - -
418A LYS* 2.9 56.4 + - - +
419A VAL* 3.5 13.4 + - - +
450A GLU* 3.0 11.7 + - - -
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Residues in contact with ILE 416 (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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170A MET* 6.3 0.2 - - + -
414A ALA* 3.0 13.3 + - + +
415A SER* 1.3 70.3 - - - +
417A SER* 1.3 57.4 + - - +
419A VAL* 3.0 8.2 + - + +
420A ARG* 2.7 59.5 + - + +
423A ILE* 5.1 2.9 - - + -
445A VAL* 4.7 8.1 - - + +
448A ARG* 3.9 30.3 - - + +
449A GLY 3.9 20.2 - - - +
450A GLU* 3.5 4.7 + - - +
451A TRP* 3.9 19.1 - - + +
568A THR* 3.5 33.4 - - + +
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Residues in contact with SER 417 (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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415A SER* 3.5 7.4 + - - -
416A ILE* 1.3 80.9 - - - +
418A LYS* 1.3 65.9 + - - +
419A VAL 3.6 0.3 + - - -
420A ARG* 3.5 34.6 + - - +
421A GLN 5.2 0.3 + - - -
450A GLU* 3.1 20.0 + - - -
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Residues in contact with LYS 418 (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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173A LYS 5.5 0.7 - - - +
174A GLY 3.6 22.9 - - - +
175A LEU* 3.6 15.4 - - + +
177A TYR* 5.4 7.3 - - - -
415A SER* 2.9 31.2 + - - +
416A ILE 3.1 0.8 - - - -
417A SER* 1.3 86.1 + - - +
419A VAL* 1.3 61.2 + - - +
422A ASP* 4.8 4.7 - - - +
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Residues in contact with VAL 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A MET* 6.2 1.6 - - + -
175A LEU* 3.5 33.9 - - + -
415A SER 3.5 11.7 - - - +
416A ILE* 3.3 18.8 - - + +
418A LYS* 1.3 79.5 - - - +
420A ARG* 1.3 66.2 - - - +
421A GLN 3.5 2.0 - - - -
422A ASP* 2.9 28.5 + - + +
423A ILE* 2.9 30.0 + - + +
568A THR* 4.9 4.7 - - + +
571A VAL* 5.2 1.3 - - + -
572A ALA* 4.3 18.8 - - + +
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Residues in contact with ARG 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ILE* 2.7 21.8 + - + +
417A SER* 3.5 40.1 + - - +
418A LYS 3.6 1.2 - - - -
419A VAL* 1.3 75.5 - - - +
421A GLN* 1.3 63.8 + - - +
423A ILE* 2.9 7.1 + - - +
424A LEU* 2.9 34.9 + - + +
445A VAL* 2.8 48.3 + - + +
446A ARG* 3.2 23.7 + - - +
448A ARG 2.8 29.2 + - - -
449A GLY* 5.2 1.0 - - - -
450A GLU* 4.9 1.4 + - - -
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Residues in contact with GLN 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A SER 5.2 0.2 + - - -
419A VAL 3.5 0.2 - - - -
420A ARG* 1.3 80.8 - - - +
422A ASP* 1.3 60.2 + - - +
424A LEU* 3.4 25.3 + - - +
425A ASP* 2.8 69.0 + - - +
428A GLU* 4.1 3.4 + - - -
442A TYR* 5.8 0.4 + - - -
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Residues in contact with ASP 422 (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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418A LYS 4.8 3.5 - - - +
419A VAL* 2.9 25.6 + - + +
421A GLN* 1.3 80.3 - - - +
423A ILE* 1.3 61.8 + - - +
425A ASP* 3.6 7.3 + - - +
426A ALA* 3.2 21.8 + - - +
571A VAL* 3.7 20.9 - - + +
575A GLY 5.6 0.5 - - - +
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Residues in contact with ILE 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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416A ILE* 5.1 5.2 - - + -
419A VAL* 2.9 25.8 + - + +
420A ARG* 2.9 7.6 + - - +
422A ASP* 1.3 73.0 - - - +
424A LEU* 1.3 67.3 + - - +
426A ALA* 3.1 2.8 + - - +
427A ILE* 3.0 31.5 + - + +
445A VAL* 3.8 29.8 - - + -
567A ILE* 3.8 29.8 - - + -
568A THR* 3.5 40.6 - - + +
571A VAL* 4.1 20.9 - - + -
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Residues in contact with LEU 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 ARG* 2.9 31.1 + - + +
421A GLN* 3.6 33.0 - - - +
423A ILE* 1.3 76.1 - - - +
425A ASP* 1.3 62.9 + - - +
427A ILE* 3.2 9.5 + - + +
428A GLU* 3.0 27.6 + - - +
442A TYR* 3.8 53.9 - - + +
445A VAL* 3.8 23.3 - - + -
446A ARG* 4.0 13.5 - - + +
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Residues in contact with ASP 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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421A GLN* 2.8 44.2 + - - +
422A ASP* 4.0 7.1 - - - +
423A ILE 3.2 0.2 - - - -
424A LEU* 1.3 77.7 - - - +
426A ALA* 1.3 60.5 + - - +
428A GLU* 2.9 28.5 + - - +
429A ASN* 3.1 32.2 + - - +
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Residues in contact with ALA 426 (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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422A ASP 3.2 14.0 + - - +
423A ILE 3.1 9.6 + - - +
425A ASP* 1.3 77.1 - - - +
427A ILE* 1.3 54.8 + - - +
429A ASN* 3.4 7.7 + - - +
430A THR* 2.6 31.7 + - - -
567A ILE* 4.4 5.4 - - + -
571A VAL* 3.9 20.9 - - + -
575A GLY 5.1 3.8 - - - +
576A VAL* 4.7 3.6 - - - -
577A SER* 4.2 16.9 - - - +
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Residues in contact with ILE 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ILE* 3.0 22.7 + - + +
424A LEU* 3.3 11.4 - - - +
426A ALA* 1.3 76.1 - - - +
428A GLU* 1.3 60.4 + - - +
429A ASN 3.1 0.2 - - - -
430A THR* 2.8 29.2 + - - +
432A PHE* 3.9 5.3 - - + -
438A LYS* 3.3 28.2 - - + +
441A ILE* 3.9 50.3 - - + +
442A TYR* 4.2 15.0 - - + -
445A VAL* 4.0 18.6 - - + -
567A ILE* 3.8 16.6 - - + -
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Residues in contact with GLU 428 (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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421A GLN* 4.1 5.2 + - - -
424A LEU* 3.0 24.9 + - - +
425A ASP* 2.9 34.0 + - - +
427A ILE* 1.3 74.9 - - - +
429A ASN* 1.3 61.4 + - - +
430A THR 3.4 0.3 + - - +
438A LYS* 2.7 33.7 + - - +
442A TYR* 4.2 22.3 + - + -
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Residues in contact with ASN 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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425A ASP* 3.1 26.7 + - - +
426A ALA* 3.7 8.2 - - - +
427A ILE 3.1 1.0 - - - -
428A GLU* 1.3 78.7 - - - +
430A THR* 1.3 58.6 + - - +
431A ASN* 4.0 7.0 + - - +
580A LYS* 5.1 0.9 - - - +
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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