Contacts of the strand formed by residues 588 - 593 (chain A) in PDB entry 4NAM
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 ASN 588 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A HIS* 5.8 4.7 - - + +
325A SER 5.9 1.0 - - - +
490A ARG* 2.9 47.3 + - - +
492A ILE* 6.4 0.7 - - + -
504A ARG* 4.4 4.3 + - - -
554A PHE* 3.5 4.5 - - - -
555A ASP* 2.8 50.1 + - + +
558A THR* 3.2 9.8 + - - +
586A LYS 3.4 13.1 + - - -
587A MET* 1.3 76.6 - - - +
589A ILE* 1.3 65.3 + - - +
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Residues in contact with ILE 589 (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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489A ALA* 5.3 0.9 - - + -
490A ARG* 2.9 10.1 + - - +
491A ILE* 3.3 19.8 - - + -
492A ILE* 2.8 35.1 + - - +
523A LEU* 4.5 7.4 - - + -
552A PHE* 4.4 6.1 - - + -
553A ASN 3.5 4.0 - - - +
554A PHE* 3.8 29.6 - - + -
558A THR* 4.2 5.2 - - + -
562A ILE* 5.6 1.6 - - + -
583A LEU* 3.9 30.5 - - + -
587A MET* 4.5 13.5 - - + -
588A ASN* 1.3 80.5 - - - +
590A LEU* 1.3 57.9 + - - +
591A ILE* 3.9 27.1 - - + -
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Residues in contact with LEU 590 (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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299A HIS* 4.4 17.9 - - + +
492A ILE* 3.4 31.9 - - + +
500A LEU* 4.3 10.5 - - + -
551A ASP* 3.6 2.8 - - - +
552A PHE* 3.7 0.2 - - - -
553A ASN* 2.8 52.0 + - + +
589A ILE* 1.3 73.3 - - - +
591A ILE* 1.3 65.0 + - - +
592A ARG* 4.0 27.3 + - + +
602A ASN* 3.5 34.1 - - - +
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Residues in contact with ILE 591 (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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491A ILE* 3.7 17.3 - - + -
492A ILE 2.7 11.1 + - - +
493A PHE* 3.3 23.4 - - + -
494A ASN* 3.2 24.3 + - - +
523A LEU* 5.1 0.7 - - + -
527A LEU* 3.6 31.2 - - + -
533A PHE* 5.5 0.4 - - + -
547A ILE* 5.0 6.3 - - + -
550A PHE* 3.5 21.3 - - + -
551A ASP 3.2 12.3 - - - +
552A PHE* 3.6 33.2 - - + -
589A ILE* 3.9 9.9 - - + -
590A LEU* 1.3 78.2 - - - +
592A ARG* 1.3 62.1 + - - +
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Residues in contact with ARG 592 (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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494A ASN* 3.3 12.8 - - + +
500A LEU* 5.3 1.3 - - + -
550A PHE* 3.2 6.3 - - - -
551A ASP* 2.9 58.6 + - - +
553A ASN* 3.1 19.6 + - - -
590A LEU* 4.0 25.5 - - + +
591A ILE* 1.3 79.4 - - - +
593A ASP* 1.3 64.3 + - - +
594A LYS 3.3 0.3 + - - -
598A TYR* 3.5 51.5 - - + +
599A ASP 5.4 0.2 + - - -
602A ASN* 2.8 37.4 + - - -
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Residues in contact with ASP 593 (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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494A ASN* 2.9 15.1 + - - +
495A GLY* 5.7 1.6 - - - -
498A LEU* 3.9 13.1 - - + +
545A LYS* 3.8 17.2 + - - +
549A GLU 3.8 5.0 - - - +
550A PHE* 3.6 16.6 - - + -
551A ASP* 5.5 0.2 - - - +
592A ARG* 1.3 69.0 - - - +
594A LYS* 1.3 63.1 + - - +
595A ARG* 2.8 56.8 + - - +
596A PHE* 3.5 8.0 + - + -
598A TYR* 2.6 36.2 + - - +
634A ASP* 4.6 0.2 - - - +
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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