Contacts of the helix formed by residues 598 - 604 (chain A) in PDB entry 4PP7
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 ALA 598 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A HIS 5.5 0.4 - - - +
575A ARG* 4.0 33.4 - - + +
595A PHE 4.8 5.8 - - - +
596A GLY 3.5 5.0 + - - +
597A LEU* 1.3 79.8 - - - +
599A THR* 1.3 58.3 + - - +
600A VAL 3.4 1.2 - - - +
601A LYS* 3.4 29.6 - - + +
602A SER* 3.3 23.6 + - - -
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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
----------------------------------------------------------
497A ALA* 5.8 4.3 - - + +
501A GLU* 2.6 31.1 + - - +
597A LEU 2.8 7.2 + - - -
598A ALA* 1.3 70.3 - - - +
600A VAL* 1.3 57.0 + - - +
601A LYS 3.2 0.2 - - - -
602A SER* 3.7 4.4 - - - +
603A ARG* 2.8 66.8 + - + +
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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
----------------------------------------------------------
468A PHE* 5.6 4.7 - - - +
485A LEU* 5.6 2.5 - - + -
487A VAL* 5.8 1.3 - - + -
497A ALA* 4.8 9.2 - - + +
498A PHE* 4.8 8.3 - - + -
501A GLU* 4.4 10.7 - - + +
597A LEU* 3.7 41.2 - - + -
598A ALA 4.0 0.4 - - - +
599A THR* 1.3 78.1 - - - +
601A LYS* 1.3 61.8 + - + +
603A ARG* 5.0 0.4 - - - -
604A TRP* 3.3 73.8 + - + +
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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
----------------------------------------------------------
467A SER* 6.3 0.2 - - - -
468A PHE* 3.6 34.8 - - + +
576A ASP* 5.1 11.9 + - - -
597A LEU* 5.7 1.3 - - + -
598A ALA* 3.4 31.4 - - + +
599A THR 3.2 0.2 - - - -
600A VAL* 1.3 81.8 - - + +
602A SER* 1.3 58.6 + - - +
604A TRP 4.1 1.9 - - - +
605A SER* 3.0 25.7 - - - -
613A LEU 5.6 8.7 - - - +
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Residues in contact with SER 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ALA 3.3 13.3 + - - -
599A THR* 3.2 7.4 + - - -
601A LYS* 1.3 78.1 - - - +
603A ARG* 1.3 66.6 + - - +
604A TRP 3.3 1.8 - - - -
605A SER* 3.3 15.8 + - - -
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Residues in contact with ARG 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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493A GLN* 4.3 26.8 - - - +
497A ALA* 4.4 17.7 - - + +
599A THR* 2.8 45.3 + - + +
602A SER* 1.3 75.2 - - - +
604A TRP* 1.3 78.6 + - + +
605A SER 3.9 0.4 - - - -
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Residues in contact with TRP 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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485A LEU* 5.3 4.3 - - + -
487A VAL* 4.1 35.4 - - + -
490A PRO* 5.5 0.2 - - + -
493A GLN* 6.0 1.0 - - - +
494A GLN* 3.5 59.4 - - + +
497A ALA* 4.2 8.8 - - + +
498A PHE* 4.9 3.1 - + + -
525A LEU* 4.7 12.8 - - + -
600A VAL* 3.3 65.8 + - + +
601A LYS* 4.1 1.7 - - - +
603A ARG* 1.3 94.5 - - + +
605A SER* 1.3 58.9 + - - +
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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