Contacts of the strand formed by residues 599 - 603 (chain A) in PDB entry 2PTM
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 ILE 599 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591A ASP* 3.9 30.5 - - + +
592A ILE 3.3 7.2 - - - +
593A ILE* 4.3 17.9 - - + -
597A GLY 3.6 5.8 + - - +
598A VAL* 1.3 82.6 - - - +
600A ALA* 1.3 61.7 + - - +
601A THR* 3.5 26.5 - - - +
602A SER* 4.4 2.7 - - - +
627A GLU* 5.7 0.2 - - - +
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Residues in contact with ALA 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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401A CMP 4.0 20.6 - - - +
592A ILE* 2.8 17.7 + - + +
594A MET* 4.0 26.7 - - + -
598A VAL* 3.4 5.4 + - - -
599A ILE* 1.3 73.4 - - - +
601A THR* 1.3 65.5 + - - +
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Residues in contact with THR 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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401A CMP 3.5 37.7 - - + +
592A ILE* 2.8 41.1 + - + -
599A ILE* 3.3 10.8 - - - +
600A ALA* 1.3 82.8 - - - +
602A SER* 1.3 74.1 + - - +
603A LEU* 4.3 5.5 - - + +
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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
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589A ILE* 4.3 13.0 - - - -
590A VAL 3.1 13.2 - - - -
591A ASP* 2.7 20.7 + - - -
592A ILE 4.7 0.4 - - - +
599A ILE* 4.4 3.5 - - - +
601A THR* 1.3 85.0 + - - +
603A LEU* 1.3 67.8 + - - +
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Residues in contact with LEU 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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401A CMP 4.1 17.3 - - + +
585A ILE* 3.9 8.2 - - + +
589A ILE* 3.3 6.3 - - - +
590A VAL* 2.8 39.5 + - + +
592A ILE* 3.9 28.3 - - + -
601A THR* 4.3 4.7 - - + +
602A SER* 1.3 82.8 - - - +
604A SER* 1.3 62.4 + - - +
607A SER* 3.6 15.9 - - - +
608A TYR 3.6 24.2 - - - +
609A PHE* 3.9 13.9 - - + -
661A ARG* 3.9 11.4 - - - +
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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