Contacts of the helix formed by residues 522 - 532 (chain A) in PDB entry 3QHE
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 MET 522 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472A LEU* 4.7 0.4 - - - -
473A GLN* 3.7 35.9 - - + +
476A ALA* 3.6 32.1 - - + -
477A GLU* 3.7 21.1 - - + +
480A GLN* 4.8 4.5 - - - +
518A THR* 3.4 22.2 - - + +
519A LEU* 3.0 15.3 + - - +
521A SER* 1.3 77.3 - - - +
523A LYS* 1.3 64.9 + - - +
524A GLY 3.4 2.2 - - - -
525A CYS* 3.2 12.9 + - + +
526A MET* 3.0 24.9 + - - +
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Residues in contact with LYS 523 (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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520A CYS 3.4 19.1 - - - +
521A SER* 3.2 16.7 + - - +
522A MET* 1.3 71.6 - - - +
524A GLY* 1.3 58.5 + - - +
526A MET* 3.2 5.4 + - - +
527A ARG* 2.9 50.8 + - - +
562A THR* 3.4 33.1 + - + +
565A GLU* 5.1 5.3 + - - -
566A VAL* 4.6 4.5 - - + +
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Residues in contact with GLY 524 (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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480A GLN* 3.6 24.4 + - - +
484A GLU* 4.4 4.8 - - - +
522A MET 3.4 0.6 - - - -
523A LYS* 1.3 76.9 - - - +
525A CYS* 1.3 56.4 + - - +
527A ARG* 3.5 27.1 + - - +
528A ALA* 3.1 24.9 + - - +
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Residues in contact with CYS 525 (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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476A ALA* 3.5 36.1 - - - +
479A LEU* 4.4 8.1 - - - -
480A GLN* 3.3 28.2 + - + +
505A LEU* 5.1 1.3 - - - -
519A LEU* 4.0 12.6 - - + -
522A MET* 3.2 22.6 + - + +
524A GLY* 1.3 73.8 - - - +
526A MET* 1.3 55.5 + - - +
528A ALA* 2.9 3.6 + - - +
529A LEU* 2.8 45.0 + - - +
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Residues in contact with MET 526 (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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519A LEU* 3.6 19.7 - - - +
520A CYS* 3.7 23.6 - - - +
522A MET 3.0 18.0 + - - +
523A LYS* 3.5 8.1 - - - +
525A CYS* 1.3 75.2 - - - +
527A ARG* 1.3 62.8 + - - +
529A LEU* 3.5 12.9 + - + +
530A VAL* 3.1 28.2 + - - +
548A LEU* 4.2 11.4 - - + -
551A LEU* 3.8 22.4 - - + -
562A THR* 4.1 5.4 - - + -
563A LEU* 3.7 34.1 - - + -
566A VAL* 4.0 25.6 - - + -
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Residues in contact with ARG 527 (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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484A GLU* 5.7 1.2 + - - -
523A LYS* 2.9 34.6 + - - +
524A GLY* 3.6 27.4 + - - +
526A MET* 1.3 75.3 - - - +
528A ALA* 1.3 57.9 + - - +
530A VAL* 3.5 3.5 + - - +
531A ALA* 3.1 28.1 + - - +
566A VAL* 3.9 25.7 - - + +
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Residues in contact with ALA 528 (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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479A LEU* 4.3 1.8 - - + -
480A GLN* 4.1 18.8 - - + +
483A CYS* 3.8 27.1 - - + -
484A GLU* 5.5 4.3 - - + -
524A GLY 3.1 13.7 + - - +
525A CYS 2.9 8.3 + - - +
527A ARG* 1.3 72.1 - - - +
529A LEU* 1.3 65.8 + - - +
531A ALA* 3.2 6.8 + - - +
532A GLN* 3.1 31.6 + - - +
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Residues in contact with LEU 529 (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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479A LEU* 3.7 31.6 - - + +
505A LEU* 4.8 3.8 - - + -
519A LEU* 4.5 6.5 - - + -
525A CYS* 2.8 29.3 + - - +
526A MET* 3.6 33.4 - - + +
528A ALA* 1.3 72.0 - - - +
530A VAL* 1.3 62.1 + - - +
532A GLN* 3.1 12.6 + - - +
533A LEU 3.8 0.2 + - - -
544A ILE* 3.2 44.1 - - + +
547A VAL* 4.0 33.0 - - + -
548A LEU* 4.7 9.0 - - + -
551A LEU* 4.5 2.2 - - + -
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Residues in contact with VAL 530 (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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526A MET 3.1 16.5 + - - +
527A ARG* 3.9 4.0 - - - +
529A LEU* 1.3 78.3 - - - +
531A ALA* 1.3 64.5 + - - +
533A LEU* 3.1 25.7 + - - +
534A LYS* 4.5 2.4 + - - +
548A LEU* 4.6 12.8 - - + -
566A VAL* 3.4 29.8 - - + +
567A GLY* 4.0 3.4 - - - +
568A SER* 3.4 29.2 - - - +
571A ALA* 3.8 23.6 - - + +
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Residues in contact with ALA 531 (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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488A LEU* 3.6 16.3 - - + +
527A ARG 3.1 17.4 + - - +
528A ALA* 3.6 7.9 - - - +
530A VAL* 1.3 77.3 - - - +
532A GLN* 1.3 70.9 + - - +
534A LYS* 3.1 21.1 + - - +
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Residues in contact with GLN 532 (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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479A LEU* 5.1 0.9 - - + -
483A CYS* 3.4 36.1 + - - +
487A GLY* 5.2 2.0 + - - -
488A LEU* 4.0 14.9 - - - +
498A ARG* 2.8 26.4 + - + +
528A ALA 3.1 22.8 + - - +
529A LEU* 3.1 10.7 + - - +
531A ALA* 1.3 78.1 - - - +
533A LEU* 1.3 56.4 + - - +
534A LYS 3.0 6.1 - - - -
535A SER* 2.9 26.4 + - - -
540A LEU* 3.8 17.6 - - + +
541A GLN* 4.1 7.6 - - - +
544A ILE* 3.7 28.3 - - + -
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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