Contacts of the helix formed by residues 595 - 601 (chain A) in PDB entry 4BSN
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 CYS 595 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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552A PRO* 3.9 20.4 - - - -
555A LEU* 4.1 15.5 - - - -
556A ARG* 3.6 29.4 - - + +
562A LEU* 4.3 9.4 - - + -
591A ILE* 2.9 31.9 + - + +
592A ALA 4.1 0.4 - - - -
594A LYS* 1.3 75.0 - - - +
596A ARG* 1.3 63.5 + - - +
597A ARG 3.1 3.6 - - - -
598A HIS* 3.1 12.0 + - + +
599A PHE* 3.0 28.8 + - + -
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Residues in contact with ARG 596 (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 ALA 3.2 16.8 + - - +
593A GLN* 2.7 50.6 + - - +
594A LYS 3.2 4.0 - - - +
595A CYS* 1.3 77.1 - - - +
597A ARG* 1.3 66.1 + - + +
598A HIS 3.5 0.3 + - - -
599A PHE* 3.8 15.4 + - - +
600A VAL* 4.4 4.5 - - - +
639A TYR* 2.7 58.6 + - - +
640A MET* 4.0 11.2 - - - +
642A GLY 5.5 0.6 - - - -
643A ALA* 3.7 31.0 - - + +
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Residues in contact with ARG 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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556A ARG* 5.9 4.0 - - - -
594A LYS 4.8 2.0 + - - +
595A CYS 3.1 1.6 + - - -
596A ARG* 1.3 85.3 - - + +
598A HIS* 1.3 65.5 + - + +
599A PHE 3.4 0.2 - - - -
600A VAL* 4.5 2.0 + - - +
601A GLN* 3.2 38.1 + - - +
643A ALA* 4.8 6.3 - - + -
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Residues in contact with HIS 598 (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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555A LEU 5.1 0.6 + - - -
556A ARG* 2.5 55.2 + - + +
557A ALA 5.3 2.0 - - - -
559A TRP* 3.4 36.9 - - + +
562A LEU* 4.2 15.5 - - + -
595A CYS* 3.1 13.4 + - + +
597A ARG* 1.3 83.3 - - + +
599A PHE* 1.3 62.5 + - - +
600A VAL 3.7 0.2 - - - -
601A GLN* 4.3 3.7 - - - +
603A GLN* 3.2 43.1 + - - +
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Residues in contact with PHE 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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559A TRP* 4.7 5.5 - + - -
562A LEU* 4.4 9.6 - - + -
566A VAL* 3.9 33.7 - - + -
588A PHE* 4.8 5.6 - + - -
591A ILE* 4.1 11.0 - - + -
592A ALA* 4.2 11.2 - - - -
595A CYS* 3.0 42.2 - - + -
596A ARG* 3.8 7.8 + - - +
597A ARG 3.4 0.8 - - - -
598A HIS* 1.3 79.5 - - - +
600A VAL* 1.3 67.5 + - + +
601A GLN 4.0 2.4 - - - +
610A PHE* 3.6 53.0 + + + +
611A ILE* 3.9 8.0 + - + +
614A ILE* 5.2 0.4 - - + -
640A MET* 3.6 43.3 - - + -
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Residues in contact with VAL 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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596A ARG 4.4 7.5 + - - +
597A ARG* 4.5 2.1 + - - +
599A PHE* 1.3 76.7 - - + +
601A GLN* 1.3 68.0 + - + +
602A VAL 3.6 0.7 + - - -
609A PRO* 3.4 22.2 - - - +
611A ILE* 4.0 14.6 - - + -
640A MET 3.3 28.9 - - - +
641A ILE* 4.5 5.6 - - + -
643A ALA* 5.1 0.4 - - + -
644A GLN* 3.4 51.1 - - + +
653A LEU* 4.6 16.6 - - + -
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Residues in contact with GLN 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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559A TRP* 5.6 1.6 - - - -
597A ARG* 3.2 31.3 + - - +
598A HIS* 4.3 2.1 - - - +
599A PHE 3.6 6.1 - - - +
600A VAL* 1.3 83.3 - - + +
602A VAL* 1.3 60.8 + - - +
603A GLN* 3.1 32.7 + - - +
609A PRO* 4.6 4.0 - - - +
610A PHE 5.2 0.2 + - - -
644A GLN* 5.2 8.7 - - - +
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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