Contacts of the helix formed by residues 580 - 589 (chain A) in PDB entry 4PED
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 THR 580 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A ASP* 3.4 34.7 + - + +
578A PHE 3.4 1.6 - - - -
579A GLY* 1.3 76.4 - - - +
581A GLN* 1.3 64.2 + - - +
582A SER* 3.8 6.7 + - - -
583A THR* 3.1 28.6 + - - +
584A THR* 2.8 26.2 + - - -
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Residues in contact with GLN 581 (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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287A ALA* 3.0 41.7 - - + +
288A PHE* 4.7 3.2 - - - -
579A GLY 3.4 2.0 + - - -
580A THR* 1.3 73.2 - - - +
582A SER* 1.3 63.2 + - - +
584A THR* 3.8 0.7 - - - -
585A GLU* 2.9 57.7 + - - +
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Residues in contact with SER 582 (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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580A THR* 3.2 6.5 + - - -
581A GLN* 1.3 87.6 + - - +
583A THR* 1.3 62.8 + - - +
585A GLU* 3.4 6.1 + - - +
586A LYS* 3.0 38.8 + - - +
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Residues in contact with THR 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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565A ILE* 3.8 28.6 - - + +
576A PHE* 3.9 30.4 - - + -
577A ASP 4.4 3.2 + - - -
578A PHE* 3.9 15.3 - - - +
580A THR* 3.1 20.7 + - - -
582A SER* 1.3 76.1 - - - +
584A THR* 1.3 64.3 + - - +
586A LYS* 3.3 7.8 + - - +
587A ILE* 3.1 30.4 + - + +
617A PHE* 5.1 3.4 - - + -
621A SER* 4.9 2.7 - - - +
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Residues in contact with THR 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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286A ASP* 3.8 34.3 - - + +
287A ALA* 4.1 14.1 - - - +
288A PHE* 3.9 9.0 - - + -
578A PHE 3.6 2.1 + - - -
579A GLY 3.8 5.7 + - - -
580A THR 2.8 21.4 + - - -
581A GLN 3.8 3.1 - - - -
583A THR* 1.3 76.9 - - - +
585A GLU* 1.3 62.0 + - - +
587A ILE* 3.5 0.4 + - - -
588A HIS* 3.0 36.2 + - + -
618A LEU* 3.9 13.4 - - + +
621A SER* 3.5 21.3 + - - -
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Residues in contact with GLU 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A PHE* 3.8 27.3 - - + +
581A GLN* 2.9 40.6 + - - +
582A SER* 3.7 6.2 - - - +
584A THR* 1.3 74.2 - - - +
586A LYS* 1.3 60.6 + - + +
588A HIS* 3.3 2.3 + - - +
589A ASN* 2.8 52.6 + - - +
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Residues in contact with LYS 586 (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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558A ALA 4.6 1.7 - - - +
561A ASP* 4.4 28.0 + - + +
562A ALA* 3.5 21.6 - - - +
565A ILE* 3.5 35.6 - - + +
568A GLU* 5.7 0.6 + - - -
582A SER* 3.0 28.8 + - - +
583A THR 3.3 3.8 + - - +
585A GLU* 1.3 76.1 - - + +
587A ILE* 1.3 63.1 + - + +
589A ASN* 3.2 8.1 + - - +
590A LEU 3.2 17.3 + - - -
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Residues in contact with ILE 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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562A ALA* 4.0 14.4 - - + +
565A ILE* 3.7 21.5 - - + -
566A LEU* 3.7 28.7 - - + -
583A THR* 3.1 22.6 + - + +
586A LYS* 1.3 78.2 - - - +
588A HIS* 1.3 63.3 + - - +
590A LEU* 3.3 19.4 + - + +
591A ILE* 4.0 7.1 - - - +
614A GLY* 3.4 39.5 - - - +
617A PHE* 4.5 11.2 - - + -
618A LEU* 3.7 19.3 - - + -
621A SER* 5.8 0.4 - - - +
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Residues in contact with HIS 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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281A LEU 3.8 13.4 + - - -
282A SER* 3.2 32.5 - - - -
286A ASP* 2.8 26.6 + - - -
288A PHE* 3.2 40.7 - + + -
289A ILE* 3.6 16.5 - - + +
386A PRO* 5.6 0.6 - - - +
584A THR* 3.0 27.6 + - + +
585A GLU 3.7 2.9 - - - +
587A ILE* 1.3 78.4 - - - +
589A ASN* 1.3 56.9 + - - +
590A LEU 3.1 0.4 - - - -
591A ILE* 3.1 33.8 + - - +
592A PRO* 3.5 4.0 - - - +
618A LEU* 3.6 18.6 - - + +
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Residues in contact with ASN 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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288A PHE* 3.6 18.3 - - - -
387A GLU* 4.4 15.6 - - - +
555A MSE 4.8 1.4 - - - +
558A ALA* 3.5 27.2 - - + +
585A GLU* 2.8 50.0 + - - +
586A LYS* 3.2 7.5 + - - +
588A HIS* 1.3 68.9 - - - +
590A LEU* 1.3 61.8 + - - +
591A ILE 3.3 0.4 - - - -
592A PRO* 3.4 15.0 - - + +
593A VAL* 3.9 2.9 - - - +
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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