Contacts of the helix formed by residues 598 - 604 (chain A) in PDB entry 4ZTZ
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 VAL 598 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485A LEU* 6.5 0.7 - - + -
488A LEU* 6.2 2.0 - - + -
572A TRP* 4.2 34.3 - - + +
575A LYS* 6.2 4.0 - - + -
576A LEU* 5.3 8.3 - - + -
596A MET* 4.4 9.1 - - + +
597A ARG* 1.3 80.1 - - + +
599A THR* 1.3 67.9 + - + +
601A LYS* 3.3 7.3 + - - +
602A LEU* 2.9 27.5 + - + +
13T C 4.4 10.3 + - - +
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Residues in contact with THR 599 (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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463A LEU* 3.8 15.9 - - - +
576A LEU* 4.7 11.4 - - + -
592A LEU* 3.5 28.5 - - + -
593A SER 2.3 39.6 + - - +
594A LEU* 3.8 3.8 + - - +
596A MET* 4.4 6.3 - - + -
598A VAL* 1.3 79.2 - - + +
600A PRO* 1.4 70.3 - - - +
602A LEU* 3.2 27.2 + - + +
603A MET* 3.4 16.5 - - - +
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Residues in contact with PRO 600 (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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593A SER 4.4 0.2 - - - +
594A LEU* 5.3 4.5 - - + +
596A MET 3.3 25.6 - - - +
597A ARG* 3.5 11.7 - - + +
598A VAL 3.4 3.6 - - - -
599A THR* 1.4 98.5 - - - +
601A LYS* 1.3 56.8 + - - +
603A MET* 4.0 4.0 - - + +
604A ALA* 3.1 35.6 + - + +
612A LEU* 4.9 0.5 - - - +
618A HIS* 4.6 2.2 - - - +
766A PHE* 3.5 52.8 - - + -
768A LYS* 5.2 2.0 - - - +
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Residues in contact with LYS 601 (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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483A PRO 5.1 2.5 - - - -
484A TRP* 3.0 69.4 - - + +
485A LEU* 4.8 0.9 - - - -
486A TRP* 5.0 1.7 - - - +
487A ASP* 2.2 36.0 + - - +
597A ARG 4.3 9.6 - - - +
598A VAL* 3.3 7.7 + - - +
599A THR 3.3 0.2 - - - -
600A PRO* 1.3 81.5 - - + +
602A LEU* 1.3 61.6 + - - +
603A MET 3.3 0.7 + - - -
604A ALA 4.4 0.6 + - - -
611A PRO* 5.5 1.6 - - - -
612A LEU* 3.2 37.5 - - + +
613A HIS* 3.1 26.6 + - - +
618A HIS* 5.2 6.1 - - + +
766A PHE* 5.0 0.4 - - - -
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Residues in contact with LEU 602 (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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463A LEU* 4.8 4.0 - - + +
466A LEU* 3.6 35.1 - - + +
467A ALA* 4.0 14.6 - - + +
470A ALA* 5.2 5.6 - - + +
484A TRP* 5.0 3.9 - - - +
485A LEU* 3.8 27.9 - - + +
572A TRP* 3.5 36.8 - - + -
576A LEU* 5.3 0.2 - - + -
598A VAL* 2.9 18.4 + - + +
599A THR* 3.2 29.4 - - + +
600A PRO 3.1 0.6 - - - -
601A LYS* 1.3 78.4 - - - +
603A MET* 1.3 63.6 + - + +
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Residues in contact with MET 603 (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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463A LEU* 4.6 21.3 - - - -
466A LEU* 4.5 24.0 - - + -
484A TRP* 5.4 4.5 - - - -
594A LEU* 6.1 2.2 - - - -
599A THR 3.4 17.0 - - - +
600A PRO* 4.0 4.7 - - + +
601A LYS 3.2 1.0 - - - -
602A LEU* 1.3 89.7 - - + +
604A ALA* 1.3 68.4 + - + +
605A LEU* 4.4 0.2 - - - +
781A ALA* 4.0 23.8 - - + -
782A GLY 2.8 33.4 + - - +
783A PRO* 4.4 16.4 - - - +
787A SER* 4.6 15.0 - - - +
788A GLY* 5.2 6.3 - - - +
791A ALA* 5.8 5.6 - - + -
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Residues in contact with ALA 604 (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 TRP* 2.9 27.1 + - - -
600A PRO* 3.1 20.2 + - + +
601A LYS 4.4 0.2 + - - -
603A MET* 1.3 82.5 - - + +
605A LEU* 1.3 69.1 + - - +
606A THR* 3.8 3.2 - - - +
612A LEU* 4.9 4.1 - - + +
766A PHE* 4.7 16.2 - - + -
774A MET* 5.9 1.3 - - + -
779A LEU* 4.9 5.4 - - + -
780A GLN 4.6 1.3 - - - +
781A ALA* 4.1 15.5 - - + -
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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