Contacts of the strand formed by residues 582 - 590 (chain A) in PDB entry 3DPK
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 LEU 582 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577A PHE* 3.7 15.0 - - + -
579A ARG* 3.1 16.9 + - - +
580A ASN* 4.1 5.8 - - - +
581A ASN* 1.3 80.0 - - - +
583A GLN* 1.3 59.7 + - - +
584A PHE* 4.1 16.8 + - + -
599A ALA* 4.7 2.2 - - + -
600A THR 3.3 7.0 - - - +
601A ALA* 3.5 30.1 - - + -
602A PHE* 4.8 1.8 - - - -
613A VAL* 4.2 13.5 - - + -
615A VAL* 4.4 15.0 - - + -
653A CYS* 4.1 7.6 - - - -
660A LEU* 4.0 26.7 - - + -
662A ILE* 4.0 24.2 - - + -
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Residues in contact with GLN 583 (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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582A LEU* 1.3 73.4 - - - +
584A PHE* 1.3 70.6 - - - +
585A GLY 3.8 0.2 + - - -
599A ALA* 3.3 3.8 - - - -
600A THR* 2.9 40.4 + - - +
602A PHE* 4.2 26.7 - - + -
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Residues in contact with PHE 584 (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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579A ARG* 5.9 2.2 - - + -
582A LEU* 4.6 14.4 - - + -
583A GLN* 1.3 81.6 - - - +
585A GLY* 1.3 64.4 - - - +
597A VAL* 3.3 29.8 - - + -
598A GLU 4.0 1.1 - - - -
599A ALA* 4.2 7.2 - - + -
615A VAL* 4.0 15.9 - - + -
617A MET* 3.9 19.1 - - + -
660A LEU* 3.8 24.9 - - + -
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Residues in contact with GLY 585 (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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583A GLN 3.8 1.6 + - - -
584A PHE* 1.3 80.5 - - - +
586A LYS* 1.3 65.0 + - - +
587A THR* 4.0 0.7 + - - -
597A VAL* 4.3 6.1 - - - +
598A GLU* 2.8 18.3 + - - +
599A ALA* 4.2 0.8 - - - +
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Residues in contact with LYS 586 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585A GLY* 1.3 73.5 - - - -
587A THR* 1.3 65.0 + - - +
588A LEU* 4.1 15.4 - - + +
597A VAL* 3.3 3.1 - - - -
598A GLU* 2.9 59.2 + - - +
612A LYS* 5.9 0.4 - - - +
665A TYR* 3.6 12.5 + - - -
923A 8C5 4.7 19.1 - - - -
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Residues in contact with THR 587 (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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585A GLY 5.1 0.7 + - - -
586A LYS* 1.3 77.2 - - - +
588A LEU* 1.3 62.9 + - - +
589A GLY* 3.7 22.2 - - - +
590A ALA* 5.1 3.4 - - + -
595A LYS* 4.9 14.3 + - + +
596A VAL 3.7 9.9 - - - +
597A VAL* 3.8 15.0 - - + +
923A 8C5 3.6 15.9 - - - -
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Residues in contact with LEU 588 (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 LYS* 4.1 23.8 - - - +
587A THR* 1.3 75.3 - - - +
589A GLY* 1.3 58.2 + - - +
596A VAL* 2.9 28.4 + - + +
597A VAL 4.2 0.7 - - - +
598A GLU* 3.9 33.4 - - + +
614A ALA* 4.4 1.8 - - + -
665A TYR* 3.8 25.8 - - + -
923A 8C5 3.8 85.0 - - + +
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Residues in contact with GLY 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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587A THR* 3.6 8.7 - - - +
588A LEU* 1.3 81.7 - - - +
590A ALA* 1.3 63.4 + - - +
595A LYS* 3.4 1.6 - - - +
596A VAL* 3.0 26.9 + - - +
800A ALA 3.7 5.7 - - - +
923A 8C5 3.8 14.0 - - - +
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Residues in contact with ALA 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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587A THR* 5.1 4.5 - - + -
589A GLY* 1.3 77.2 - - - +
591A GLY* 1.3 66.0 + - - +
594A GLY 3.2 14.1 - - - +
595A LYS* 3.5 13.9 - - + -
619A LYS* 4.4 8.1 - - + +
800A ALA 3.3 10.0 + - - -
802A ASP* 3.2 28.9 + - - +
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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