Contacts of the helix formed by residues 520 - 532 (chain B) in PDB entry 1ZM9
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 ALA 520 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466B TRP* 5.4 0.3 - - - -
516B LEU* 5.3 3.8 - - + -
517B THR* 2.8 37.3 + - - +
519B ALA* 1.3 73.7 - - - +
521B PRO* 1.4 63.9 - - + +
522B GLU* 3.0 17.9 - - - +
523B ALA* 2.7 36.0 + - + +
524B ALA* 3.7 1.9 + - - +
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Residues in contact with PRO 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B ALA 3.6 2.6 - - - +
520B ALA* 1.4 84.5 - - + +
522B GLU* 1.3 78.8 + - + +
523B ALA 3.3 0.2 + - - -
524B ALA* 3.6 15.1 + - + +
525B GLY 4.2 1.7 + - - -
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Residues in contact with GLU 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B LEU* 3.7 29.1 - - + +
520B ALA* 3.0 27.4 - - - +
521B PRO* 1.3 80.4 - - + +
523B ALA* 1.3 63.9 + - - +
525B GLY* 3.1 5.0 + - - +
526B GLU* 2.9 22.9 + - + +
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Residues in contact with ALA 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B TRP* 3.9 3.1 - - + -
516B LEU* 3.9 15.8 - - + +
517B THR 3.6 9.0 - - - +
518B LEU* 3.3 36.3 - - + +
520B ALA* 2.7 23.8 + - + +
522B GLU* 1.3 73.1 + - - +
524B ALA* 1.3 67.7 + - - +
527B VAL* 2.7 30.3 + - + +
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Residues in contact with ALA 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B ILE* 4.9 9.6 - - + -
466B TRP* 3.7 21.1 - - + +
520B ALA 3.7 1.0 + - - +
521B PRO 3.6 10.9 + - - +
522B GLU 3.2 0.6 + - - -
523B ALA* 1.3 83.4 - - - +
525B GLY* 1.3 62.9 + - - +
527B VAL* 3.5 1.7 - - - +
528B GLU* 3.0 31.8 + - - +
535B LEU* 4.1 9.6 - - + -
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Residues in contact with GLY 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B PRO 4.2 2.2 + - - -
522B GLU* 3.1 7.0 + - - -
524B ALA* 1.3 80.0 - - - +
526B GLU* 1.3 56.5 + - - +
528B GLU* 3.4 14.0 + - - +
529B ARG* 2.8 26.7 + - - +
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Residues in contact with GLU 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B THR* 4.5 11.0 - - - +
516B LEU* 3.6 25.4 - - + -
522B GLU* 2.9 16.0 + - + +
523B ALA 3.8 1.1 - - - +
525B GLY* 1.3 73.5 - - - +
527B VAL* 1.3 67.2 + - + +
529B ARG* 2.9 47.0 + - - -
530B LEU* 3.0 35.1 + - + +
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Residues in contact with VAL 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B TRP* 3.5 28.0 - - + -
514B THR* 5.2 5.2 - - + -
518B LEU* 4.3 13.0 - - + -
523B ALA* 2.7 30.4 + - - +
524B ALA 3.5 3.4 - - - +
526B GLU* 1.3 71.7 - - + +
528B GLU* 1.3 65.9 + - - +
530B LEU* 3.0 13.0 + - - +
531B ILE* 2.9 32.0 + - + +
535B LEU* 3.9 22.9 - - + -
537B LEU* 4.3 13.2 - - + -
542B ILE* 4.3 17.0 - - + -
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Residues in contact with GLU 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B ILE* 5.8 0.5 - - - +
524B ALA* 3.0 23.1 + - - +
525B GLY* 3.6 13.5 - - - +
527B VAL* 1.3 74.3 - - - +
529B ARG* 1.3 65.4 + - - +
531B ILE* 3.7 3.1 - - - -
532B GLY* 3.1 20.1 + - - -
533B HIS 3.6 19.6 + - - +
534B PRO* 3.2 11.4 - - - +
535B LEU* 2.6 51.1 + - + +
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Residues in contact with ARG 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B GLY 2.8 17.9 + - - +
526B GLU* 2.9 44.3 + - - +
527B VAL 3.1 0.4 - - - -
528B GLU* 1.3 79.9 - - - +
530B LEU* 1.3 68.0 + - - +
532B GLY* 3.7 6.8 + - - -
602B SER 4.5 0.6 + - - -
603B GLN* 3.9 21.8 + - - +
604B PRO* 3.1 52.1 - - + +
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Residues in contact with LEU 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B TYR* 3.2 37.5 + - + -
513B ARG 3.5 24.5 - - - +
514B THR* 4.2 15.0 - - - -
526B GLU* 3.0 27.9 + - + +
527B VAL* 3.0 8.1 + - - +
529B ARG* 1.3 85.7 - - - +
531B ILE* 1.3 61.4 + - + +
532B GLY 3.7 0.2 + - - -
542B ILE* 4.3 10.8 - - + -
602B SER* 3.2 30.7 - - - +
603B GLN 4.0 0.9 - - - -
604B PRO* 3.5 32.6 - - + +
605B GLY 4.3 0.9 + - - -
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Residues in contact with ILE 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B TYR* 4.1 29.8 + - + -
527B VAL* 2.9 28.0 + - + +
528B GLU* 3.6 5.2 - - - +
530B LEU* 1.3 79.0 - - + +
532B GLY* 1.3 60.7 + - - +
533B HIS* 3.3 56.0 + - + +
534B PRO 4.6 0.7 - - - +
535B LEU* 4.2 11.0 - - + -
537B LEU* 4.0 32.1 - - + -
540B ASP* 4.0 14.3 - - + +
541B ALA 5.3 1.1 - - - +
542B ILE* 5.7 1.6 - - + -
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Residues in contact with GLY 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B GLU 3.1 9.8 + - - -
529B ARG 3.7 5.2 + - - -
530B LEU 3.4 3.4 + - - -
531B ILE* 1.3 77.6 - - - +
533B HIS* 1.3 64.7 + - - +
604B PRO* 5.8 0.2 - - - +
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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