Contacts of the helix formed by residues 577 - 585 (chain A) in PDB entry 4CCZ
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 577 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540A ILE* 4.1 8.0 - - + +
575A GLY 3.2 4.3 + - - +
576A GLY* 1.3 72.8 - - - +
578A SER* 1.3 58.4 + - - +
580A LEU* 3.0 33.9 + - + +
595A HIS* 3.6 31.1 - - + -
598A PHE* 3.4 43.3 - - + -
599A LEU* 3.5 39.3 - - + -
607A MET* 5.5 1.8 - - + -
611A ILE 3.1 7.8 + - - +
612A VAL* 3.7 26.5 - - + -
617A LEU* 4.0 3.8 - - + -
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Residues in contact with SER 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A GLU* 2.7 31.4 + - - -
576A GLY 3.5 0.6 - - - -
577A LEU* 1.3 77.5 - - - +
579A ASN* 1.3 61.7 + - - +
580A LEU 3.2 0.4 + - - -
581A SER 3.4 5.2 + - - -
582A PHE* 4.0 2.6 + - - -
591A ARG* 2.8 28.2 + - - -
595A HIS* 3.7 22.4 - - - -
611A ILE 4.3 1.6 + - - -
613A ASN* 4.6 6.2 + - - +
1652A THG 3.4 29.6 - - - +
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Residues in contact with ASN 579 (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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540A ILE 3.1 20.9 - - - +
541A LEU* 4.8 1.3 - - - -
542A THR* 3.0 27.1 + - - +
576A GLY 2.9 13.4 - - - +
577A LEU 3.0 0.4 + - - -
578A SER* 1.3 74.8 - - - +
580A LEU* 1.3 64.2 + - - +
581A SER 3.2 0.5 + - - -
582A PHE* 3.4 34.5 + - + -
1652A THG 2.7 52.9 + - - +
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Residues in contact with LEU 580 (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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540A ILE* 3.9 12.4 - - + +
541A LEU 3.9 18.8 - - - +
542A THR* 3.7 0.9 - - - -
543A ILE* 3.3 53.5 + - + +
554A ALA* 4.0 18.8 - - + -
577A LEU* 3.0 17.9 + - + +
579A ASN* 1.3 80.0 - - - +
581A SER* 1.3 58.7 + - - +
582A PHE 3.8 0.2 + - - -
594A MET* 4.3 26.0 - - + +
595A HIS* 4.9 2.5 - - + -
598A PHE* 3.8 39.9 - - + -
635A ILE* 4.5 7.6 - - + -
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Residues in contact with SER 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A SER 3.5 0.3 + - - -
579A ASN 3.2 0.8 - - - -
580A LEU* 1.3 78.8 - - - +
582A PHE* 1.3 62.4 + - - +
583A SER* 3.1 3.9 + - - +
584A PHE 3.3 10.9 + - - +
591A ARG* 2.9 51.3 + - - +
594A MET* 3.9 24.2 - - - -
595A HIS* 2.6 33.4 + - - -
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Residues in contact with PHE 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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542A THR* 3.3 27.4 - - + +
578A SER 4.0 1.8 - - - -
579A ASN* 3.4 37.4 + - + -
580A LEU 3.6 2.8 + - - -
581A SER* 1.3 77.3 - - - +
583A SER* 1.3 58.6 + - - +
584A PHE 3.2 0.2 - - - -
585A ARG* 2.9 57.5 + - - +
591A ARG* 3.8 4.3 - - - -
1652A THG 3.3 52.3 - + - -
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Residues in contact with SER 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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542A THR* 3.1 11.8 - - - +
543A ILE 2.5 28.6 + - - -
544A GLY* 3.3 25.5 - - - +
545A THR* 3.4 8.6 - - - +
581A SER* 3.1 2.3 - - - -
582A PHE* 1.3 79.8 - - - +
584A PHE* 1.3 58.2 + - - +
585A ARG 3.6 1.3 + - - -
594A MET* 5.9 4.0 - - - -
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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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581A SER 3.3 8.6 + - - +
582A PHE 3.2 0.8 - - - -
583A SER* 1.3 79.6 - - - +
585A ARG* 1.3 66.0 + - - +
587A MET* 3.4 16.7 + - + +
590A ILE* 4.4 13.7 - - + -
591A ARG* 3.2 18.8 - - + +
594A MET* 4.0 25.1 - - + +
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Residues in contact with ARG 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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582A PHE* 2.9 70.4 + - - +
583A SER 3.6 1.6 + - - -
584A PHE* 1.3 79.7 - - - +
586A GLY* 1.3 57.6 + - - +
587A MET* 3.3 4.0 + - - +
591A ARG* 4.0 14.1 - - - +
1652A THG 2.9 28.8 + - - -
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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