Contacts of the helix formed by residues 596 - 607 (chain A) in PDB entry 5W3R
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 SER 596 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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516A SER* 4.5 8.7 - - - -
518A MET* 3.7 23.8 + - - +
587A CYS* 4.1 10.5 - - - -
594A PHE* 3.2 8.3 - - - +
595A GLN* 1.3 80.7 - - - +
597A ILE* 1.3 65.0 + - - +
598A PHE* 3.5 7.6 + - - +
599A ASP* 2.7 34.7 + - - -
600A MET* 3.0 18.7 + - - +
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Residues in contact with ILE 597 (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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518A MET* 3.9 11.7 - - - -
522A LEU* 4.7 16.8 - - + -
527A TRP* 3.7 25.8 - - + -
528A PHE* 5.8 0.7 - - + -
554A VAL* 4.6 6.5 - - + -
564A TYR* 4.0 31.6 - - + -
579A LEU* 4.0 10.8 - - + -
587A CYS* 4.0 14.1 - - - +
596A SER* 1.3 73.4 - - - +
598A PHE* 1.3 62.4 + - - +
600A MET* 3.2 19.4 + - + +
601A LEU* 3.0 24.4 + - + +
702A IPH 3.8 21.1 + - + +
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Residues in contact with PHE 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A HIS* 3.8 31.9 - + + -
518A MET* 3.3 31.2 - - + +
525A TYR* 4.9 14.6 - + - +
527A TRP* 4.6 14.4 - + + -
596A SER* 3.2 0.8 + - - +
597A ILE* 1.3 79.8 - - - +
599A ASP* 1.3 71.1 + - - +
601A LEU* 3.2 7.2 + - + +
602A GLU* 2.9 64.7 + - + +
703A IPH 5.5 3.4 - - - -
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Residues in contact with ASP 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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517A HIS* 2.7 40.5 + - - +
594A PHE* 4.0 11.0 - - + -
595A GLN* 3.8 15.2 - - + +
596A SER* 2.7 36.0 + - - +
598A PHE* 1.3 84.3 - - - +
600A MET* 1.3 56.2 + - - +
602A GLU* 3.4 6.3 + - - +
603A HIS* 3.0 29.1 + - - +
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Residues in contact with MET 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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554A VAL* 5.1 0.9 - - + -
566A LEU* 4.1 14.4 - - + -
579A LEU* 4.0 30.5 - - + -
587A CYS* 4.7 2.7 - - - -
589A VAL* 3.8 16.8 - - + -
594A PHE* 3.5 42.1 - - + +
596A SER 3.0 10.9 + - - +
597A ILE* 3.2 16.8 + - + +
599A ASP* 1.3 76.3 - - - +
601A LEU* 1.3 88.1 + - + +
603A HIS* 3.3 3.3 + - - +
604A PHE* 3.1 44.7 + - + -
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Residues in contact with LEU 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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527A TRP* 3.5 54.1 - - + +
552A PHE* 3.8 25.6 - - + -
554A VAL* 4.1 4.0 - - + -
566A LEU* 3.9 9.0 - - + -
597A ILE* 3.0 16.7 + - + +
598A PHE* 3.2 7.6 + - + +
600A MET* 1.3 96.6 - - + +
602A GLU* 1.3 62.1 + - - +
604A PHE 3.2 2.1 + - - -
605A ARG* 2.9 23.6 + - - +
621A LEU* 3.8 19.5 - - + +
703A IPH 4.1 19.0 - - + +
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Residues in contact with GLU 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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598A PHE* 2.9 58.3 + - + +
599A ASP* 3.7 7.2 - - - +
601A LEU* 1.3 75.6 - - - +
603A HIS* 1.3 64.4 + - - +
605A ARG* 3.3 42.7 + - - +
606A VAL* 3.7 10.9 + - - +
703A IPH 3.9 16.0 + - - -
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Residues in contact with HIS 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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592A LEU* 4.2 11.9 - - + +
594A PHE* 3.5 25.8 - + + -
599A ASP 3.0 17.0 + - - +
600A MET 3.5 4.3 - - - +
601A LEU 3.2 0.2 - - - -
602A GLU* 1.3 76.7 - - - +
604A PHE* 1.3 86.1 + + - +
606A VAL 3.1 3.6 + - - -
607A HIS* 2.8 72.1 + + + +
608A PRO 5.3 0.8 + - - -
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Residues in contact with PHE 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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566A LEU* 4.7 6.3 - - + -
589A VAL* 4.3 19.5 - - + -
590A GLN* 5.0 1.1 - - + -
592A LEU* 3.9 18.8 - - + -
594A PHE* 4.1 8.1 - + - -
600A MET* 3.1 50.5 + - + +
601A LEU 3.2 0.4 + - - -
603A HIS* 1.3 91.9 - + - +
605A ARG* 1.3 62.6 + - - +
606A VAL 3.2 0.4 - - - -
607A HIS 3.3 15.0 - - - +
608A PRO 4.2 1.3 - - - -
609A ILE* 3.7 23.6 - - + -
610A PRO* 3.5 28.9 - - + -
620A VAL* 3.3 9.2 - - - +
621A LEU* 2.8 43.5 + - + -
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Residues in contact with ARG 605 (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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601A LEU 2.9 13.2 + - - +
602A GLU* 3.5 29.6 + - - +
603A HIS 3.2 0.6 - - - -
604A PHE* 1.3 76.5 - - - +
606A VAL* 1.3 79.6 + - - +
620A VAL* 3.6 16.7 - - - +
621A LEU* 3.6 14.2 - - - +
622A VAL 5.6 0.4 - - - +
703A IPH 3.5 38.6 - - + -
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Residues in contact with VAL 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A GLU 3.7 7.6 + - - +
603A HIS 3.1 2.5 + - - +
605A ARG* 1.3 113.0 - - - +
607A HIS* 1.3 86.5 + - + +
608A PRO* 4.2 2.9 - - - +
620A VAL* 3.9 8.4 - - - +
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Residues in contact with HIS 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A HIS* 2.8 57.0 + + + +
604A PHE* 3.3 23.6 - - - +
606A VAL* 1.3 101.8 - - + +
608A PRO* 1.3 74.3 - - + +
620A VAL* 3.7 2.2 - - - -
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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