Contacts of the strand formed by residues 597 - 601 (chain A) in PDB entry 4N2I
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 ASP 597 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A LEU* 4.1 16.3 - - + +
330A LYS* 3.7 30.6 + - - +
331A THR* 4.3 15.9 - - + +
592A ILE 3.7 0.9 - - - +
594A LEU* 2.8 42.7 + - + +
595A ASP 3.2 0.2 - - - -
596A LYS* 1.3 106.7 + - - +
598A LEU* 1.3 58.8 + - - +
599A GLY 4.2 0.3 + - - -
628A GLU* 3.4 26.1 - - - +
630A THR* 5.2 0.7 + - - -
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Residues in contact with LEU 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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327A LEU* 4.2 2.6 - - - +
479A VAL* 3.9 23.1 - - + -
591A MET* 3.7 22.7 - - - -
592A ILE 3.3 3.4 - - - -
593A VAL* 4.0 18.6 - - + -
595A ASP 4.2 7.2 - - - +
596A LYS 4.2 5.2 - - - +
597A ASP* 1.3 79.7 - - - +
599A GLY* 1.3 59.8 + - - +
600A ILE* 3.6 15.5 + - + +
622A LEU* 3.9 24.2 - - + -
627A LEU* 4.2 25.1 - - + -
628A GLU 2.9 13.0 + - - +
629A CYS* 3.8 3.5 - - - -
630A THR* 2.9 30.5 + - - +
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Residues in contact with GLY 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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327A LEU* 3.8 27.0 - - - +
591A MET* 3.2 4.6 - - - +
592A ILE* 2.8 39.2 + - - -
598A LEU* 1.3 69.1 - - - +
600A ILE* 1.3 60.5 + - - -
630A THR 3.4 6.5 - - - -
632A ILE* 3.9 8.5 - - - -
710A MPD 3.2 10.6 + - - -
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Residues in contact with ILE 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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588A MET* 3.5 33.4 - - + +
591A MET* 4.0 18.6 - - + -
598A LEU* 4.0 18.6 - - + +
599A GLY* 1.3 75.5 - - - +
601A PRO* 1.3 73.8 - - + +
618A VAL* 4.0 18.6 - - + -
622A LEU* 4.2 2.7 - - + -
629A CYS* 3.8 34.3 - - + -
630A THR 2.7 11.1 + - - +
631A PHE* 3.1 29.2 - - + -
632A ILE* 2.7 24.2 + - - +
710A MPD 4.1 1.6 - - - -
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Residues in contact with PRO 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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586A PRO* 4.2 17.5 - - + -
587A ASN 3.4 17.7 - - - +
588A MET* 3.5 22.3 - - - +
590A ASN* 3.2 28.9 - - + +
599A GLY 4.0 1.1 - - - +
600A ILE* 1.3 92.4 - - + +
602A LYS* 1.3 63.3 + - - +
603A PRO* 3.3 8.7 - - - +
631A PHE* 3.9 0.3 - - - -
634A ASP* 4.6 4.5 - - - +
710A MPD 3.6 32.9 - - + +
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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