Contacts of the helix formed by residues 625 - 636 (chain A) in PDB entry 5ZF6
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 625 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621A VAL* 3.2 31.1 - - - +
622A GLY 3.2 5.3 + - - -
623A PRO 3.1 1.2 - - - -
624A GLY* 1.3 79.0 - - - +
626A TYR* 1.3 64.1 + - - +
628A LEU* 3.3 6.7 + - - +
629A LYS* 3.1 28.8 + - - +
477B LEU* 4.2 3.1 - - - -
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Residues in contact with TYR 626 (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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621A VAL 3.4 1.6 + - - -
622A GLY 4.4 0.2 - - - -
623A PRO* 3.4 26.8 + - + +
624A GLY 3.5 0.8 - - - -
625A GLY* 1.3 77.0 - - - +
627A ASN* 1.3 72.2 + - - +
629A LYS* 3.2 4.6 + - - +
630A LYS* 2.8 54.1 + - + +
373B GLU* 5.0 2.6 + - - -
376B MET* 3.4 26.0 - - - +
377B PHE* 3.7 28.5 - + - -
385B LEU* 3.7 29.5 - - + +
392B GLN* 4.9 3.6 - - - +
394B LEU* 5.0 4.0 - - + -
477B LEU* 4.3 22.0 - - + +
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Residues in contact with ASN 627 (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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619A LYS 4.2 9.8 + - - +
620A PHE 3.3 20.6 - - - +
621A VAL 3.2 6.4 + - - +
622A GLY* 3.8 12.8 - - - -
623A PRO* 4.4 4.2 - - - +
626A TYR* 1.3 92.5 - - - +
628A LEU* 1.3 63.1 + - - +
630A LYS* 3.5 23.8 - - - +
631A LEU* 3.1 22.5 + - - +
667A ILE 5.8 2.6 + - - -
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Residues in contact with LEU 628 (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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620A PHE* 3.7 31.4 - - + +
621A VAL* 3.5 41.8 + - + +
625A GLY* 3.3 9.1 + - - +
626A TYR 3.3 0.8 - - - -
627A ASN* 1.3 79.3 - - - +
629A LYS* 1.3 58.7 + - + +
631A LEU* 3.3 7.2 + - + +
632A GLN* 3.1 35.3 + - - +
639A ILE* 3.7 39.0 - - + +
640A SER* 6.2 0.7 - - - -
647A PHE* 3.9 15.7 - - + -
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Residues in contact with LYS 629 (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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624A GLY 5.2 2.5 - - - -
625A GLY* 3.1 13.7 + - - +
626A TYR 3.9 3.1 - - - +
628A LEU* 1.3 75.1 - - + +
630A LYS* 1.3 63.4 + - - +
632A GLN* 3.3 25.1 + - - +
633A ALA* 3.2 21.3 + - - +
377B PHE* 4.1 5.9 - - + -
394B LEU* 4.4 13.5 - - + -
428B GLU* 4.9 0.8 + - - +
475B GLU* 3.3 46.3 + - + +
476B VAL 5.5 3.9 + - - -
477B LEU* 3.6 29.8 - - + -
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Residues in contact with LYS 630 (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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626A TYR* 2.8 41.7 + - + +
627A ASN* 3.5 28.7 - - - +
628A LEU 3.3 0.2 - - - -
629A LYS* 1.3 76.4 - - - +
631A LEU* 1.3 66.2 + - + +
633A ALA* 3.4 2.8 + - - +
634A GLU* 3.2 49.5 + - - +
376B MET 4.4 12.8 + - - -
377B PHE* 3.4 28.0 - - + +
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Residues in contact with LEU 631 (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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620A PHE* 4.7 7.2 - - + -
627A ASN 3.1 13.8 + - - +
628A LEU* 3.6 9.6 - - + +
629A LYS 3.3 0.2 - - - -
630A LYS* 1.3 77.1 - - + +
632A GLN* 1.3 61.6 + - - +
634A GLU* 4.4 5.2 - - - +
635A THR* 2.7 59.0 + - + +
637A VAL* 3.9 10.3 - - + -
639A ILE* 3.6 27.1 - - + -
660A ALA* 4.2 9.0 - - + +
663A PHE* 3.8 28.3 - - + -
664A ILE* 4.0 20.4 - - + +
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Residues in contact with GLN 632 (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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628A LEU* 3.1 21.0 + - - +
629A LYS* 3.6 26.6 + - - +
630A LYS 3.3 0.4 - - - -
631A LEU* 1.3 76.5 - - - +
633A ALA* 1.3 57.3 + - - +
636A GLY* 3.2 26.3 + - - -
637A VAL* 3.2 31.1 + - + +
638A THR* 4.2 10.4 - - - +
639A ILE* 3.4 34.6 + - + +
475B GLU* 5.2 4.2 - - - +
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Residues in contact with ALA 633 (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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629A LYS 3.2 14.0 + - - +
630A LYS 3.4 3.8 + - - +
631A LEU 3.2 0.4 - - - -
632A GLN* 1.3 77.1 - - - +
634A GLU* 1.3 64.7 + - + +
636A GLY* 4.0 3.1 + - - -
377B PHE* 3.9 28.7 - - + -
379B THR* 3.0 17.5 + - - +
380B LEU* 4.0 24.0 - - + +
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Residues in contact with GLU 634 (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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630A LYS* 3.2 42.8 + - - +
631A LEU* 3.4 8.4 + - - +
633A ALA* 1.3 81.1 - - + +
635A THR* 1.3 66.8 + - + +
636A GLY 3.7 0.2 + - - -
663A PHE* 3.4 39.8 - - + -
377B PHE* 6.2 3.8 - - + -
378B LYS* 5.9 6.3 - - + +
379B THR* 4.3 22.1 - - + +
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Residues in contact with THR 635 (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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631A LEU* 2.7 38.1 + - + +
634A GLU* 1.3 78.6 - - - +
636A GLY* 1.3 61.1 + - - +
637A VAL* 3.2 18.9 + - - +
656A ALA* 3.4 33.7 - - - +
659A GLU* 3.7 30.1 - - + -
660A ALA* 3.8 6.0 - - - +
663A PHE* 3.9 11.2 - - + -
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Residues in contact with GLY 636 (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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632A GLN 3.2 14.3 + - - -
633A ALA 4.0 3.1 + - - -
634A GLU 3.4 3.0 + - - -
635A THR* 1.3 78.8 - - - +
637A VAL* 1.3 60.5 + - - +
638A THR* 4.8 2.3 + - - -
652A PRO* 3.2 28.5 - - - +
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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