Contacts of the helix formed by residues 623 - 630 (chain A) in PDB entry 4EZJ
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 ASP 623 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587A LYS* 3.4 25.3 + - - +
621A ALA 3.5 6.5 + - - +
622A LEU* 1.3 76.0 - - - +
624A VAL* 1.3 54.3 + - - +
625A GLY* 3.4 7.6 + - - -
626A LEU* 3.1 36.9 + - + +
627A THR* 2.6 42.2 + - - -
647A LYS* 4.9 1.2 - - - +
1026A LEU* 5.8 1.4 - - - +
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Residues in contact with VAL 624 (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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622A LEU* 4.1 8.0 - - + +
623A ASP* 1.3 69.7 + - - +
625A GLY* 1.3 53.4 + - - +
627A THR* 3.3 6.6 + - - -
628A MET* 2.8 54.7 + - + +
648A LEU* 5.3 3.8 - - + -
651A LEU* 4.0 31.6 - - + -
655A ASP* 6.1 0.2 - - - -
659A TYR* 3.9 52.0 - - + +
1026A LEU* 4.5 5.6 - - + -
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Residues in contact with GLY 625 (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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623A ASP* 3.3 7.4 + - - -
624A VAL* 1.3 79.0 - - - +
626A LEU* 1.3 61.1 + - - +
628A MET 3.2 0.3 + - - -
629A GLN* 3.1 30.5 + - - +
1025A ASN* 5.3 1.6 - - - -
1026A LEU* 3.7 39.9 - - - +
1029A ILE* 3.6 8.5 - - - +
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Residues in contact with LEU 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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586A PRO* 3.4 34.1 - - + +
587A LYS* 3.8 29.5 - - + +
590A PRO* 3.6 33.9 - - + -
617A TRP* 3.7 20.4 - - + -
623A ASP* 3.1 29.1 + - + +
625A GLY* 1.3 70.8 - - - +
627A THR* 1.3 66.0 + - - +
629A GLN* 3.1 32.0 + - - +
630A LEU* 3.5 8.8 + - - +
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Residues in contact with THR 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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617A TRP* 4.8 9.3 - - - -
622A LEU* 4.2 2.0 - - + +
623A ASP 2.6 30.5 + - - -
624A VAL* 3.5 8.1 - - - -
626A LEU* 1.3 71.6 - - - +
628A MET* 1.3 60.9 + - - +
630A LEU* 3.5 6.5 + - - -
631A LEU* 3.6 6.3 - - + +
644A ALA* 3.0 53.9 - - + +
647A LYS* 4.1 17.3 - - + +
648A LEU* 3.7 25.6 - - + -
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Residues in contact with MET 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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624A VAL* 2.8 41.7 + - + +
625A GLY 3.8 3.4 - - - +
627A THR* 1.3 75.9 - - + +
629A GLN* 1.4 58.0 + - - +
630A LEU 3.1 1.8 - - - -
631A LEU* 2.9 26.3 + - + +
632A ASP 3.4 0.7 + - - -
648A LEU* 5.3 1.6 - - + -
659A TYR* 4.7 6.7 - - - -
662A GLN* 3.7 41.5 - - + +
663A LEU* 4.0 22.0 - - + +
666A ALA* 4.5 4.3 - - + -
1026A LEU* 5.8 0.4 - - - -
1029A ILE* 4.2 13.2 - - + -
1030A LEU* 4.7 11.4 - - - -
1033A MET* 3.1 44.1 - - + +
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Residues in contact with GLN 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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563A PRO* 3.3 38.8 - - - +
587A LYS* 5.5 3.0 + - - +
590A PRO* 3.6 29.5 - - + +
591A LYS* 4.9 3.5 + - - +
625A GLY 3.1 14.3 + - - +
626A LEU* 3.1 28.0 + - - +
628A MET* 1.4 75.2 - - - +
630A LEU* 1.4 57.1 + - - +
632A ASP* 3.2 16.7 - - - +
635A PHE* 3.0 21.7 - - - -
1025A ASN* 4.3 13.5 + - - +
1029A ILE* 3.8 28.0 - - + +
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Residues in contact with LEU 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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589A TYR* 4.1 13.7 - - + -
590A PRO* 3.8 33.7 - - + -
593A PHE* 4.3 3.1 - - + -
617A TRP* 3.7 35.2 - - + -
626A LEU 3.5 10.4 + - - +
627A THR 3.8 7.2 - - - +
628A MET 3.1 0.6 - - - -
629A GLN* 1.4 76.7 - - - +
631A LEU* 1.3 59.0 + - - +
632A ASP 3.6 0.9 - - - -
635A PHE* 3.7 21.9 - - + +
640A VAL* 3.9 24.0 - - + +
641A ARG* 3.7 22.9 + - - +
643A ILE* 4.5 13.5 - - + -
644A ALA* 4.0 10.1 - - + -
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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