Contacts of the strand formed by residues 594 - 599 (chain A) in PDB entry 6IWQ
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 LYS 594 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A PHE* 3.7 54.7 - - + -
557A VAL 6.2 0.2 - - - +
588A LYS* 3.8 6.2 - - - +
589A GLY 3.6 20.5 + - - -
592A GLY* 3.4 12.4 - - - -
593A SER* 1.3 88.0 - - - +
595A VAL* 1.3 64.1 + - - +
634A GLN* 5.9 7.5 - - + +
635A VAL 4.0 11.7 - - - +
636A PHE* 4.3 2.2 - - + +
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Residues in contact with VAL 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A PHE* 3.5 7.1 - - - +
557A VAL* 3.0 36.3 + - + +
579A LEU* 6.1 0.4 - - + -
586A LEU* 3.6 33.0 - - + -
587A THR 3.5 14.4 - - - +
588A LYS* 5.7 0.4 - - - -
594A LYS* 1.3 78.5 - - - +
596A MET* 1.3 62.6 + - - +
608A TRP* 4.1 10.5 - - + -
626A LEU* 4.0 15.7 - - + -
635A VAL* 3.9 26.0 + - + +
636A PHE* 4.4 1.1 - - - -
637A ILE* 4.1 16.2 - - + -
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Residues in contact with MET 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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554A GLY* 3.4 29.2 - - - +
555A GLY 3.1 18.8 - - - +
556A PHE* 3.8 19.7 - - + +
557A VAL 4.5 0.2 - - - +
585A CYS 3.7 0.2 - - - +
586A LEU* 3.3 6.9 - - - +
587A THR* 3.1 57.9 + - + +
588A LYS 4.7 0.2 - - - -
589A GLY* 4.3 20.0 - - - +
595A VAL* 1.3 75.6 - - - +
597A ILE* 1.3 64.4 + - - +
598A THR* 3.6 13.7 - - + +
605A PHE* 5.9 0.2 - - + -
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Residues in contact with ILE 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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548A SER* 3.0 29.4 - - - +
551A LYS* 3.5 16.4 - - + +
552A THR* 4.6 0.4 - - - -
553A ASN 3.1 3.4 + - - +
554A GLY* 2.2 34.6 + - - -
555A GLY 2.9 11.0 + - - +
557A VAL* 4.2 22.2 - - + -
571A PHE* 5.2 1.6 - - + -
581A GLN* 4.6 8.5 - - + +
584A GLN* 3.2 39.0 - - + +
585A CYS 3.2 10.8 - - - +
586A LEU* 4.5 11.9 - - + -
596A MET* 1.3 77.3 - - - +
598A THR* 1.3 61.2 + - - +
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Residues in contact with THR 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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553A ASN* 3.7 12.1 - - - +
554A GLY* 3.8 17.0 - - - +
584A GLN* 2.8 25.5 - - - +
585A CYS* 3.1 13.9 + - - -
587A THR* 4.0 9.4 - - - +
596A MET* 3.6 21.6 - - + +
597A ILE* 1.3 73.4 - - - +
599A HIS* 1.3 71.5 + - + +
605A PHE* 4.2 11.9 - - + -
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Residues in contact with HIS 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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553A ASN* 3.2 19.9 + - - +
583A ASP* 2.6 38.6 + - - +
584A GLN* 3.8 4.0 - - + -
598A THR* 1.3 81.5 - - - +
600A CYS* 1.3 81.1 + - - +
601A ASN* 3.8 11.1 + - - -
604A GLU* 4.5 3.3 - - - +
605A PHE* 3.4 18.4 - - - -
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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