Contacts of the strand formed by residues 580 - 584 (chain A) in PDB entry 3M6L
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 GLU 580 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527A LYS 3.0 13.5 + - - +
528A PHE* 3.2 26.0 - - + -
529A THR 3.0 18.2 + - - -
579A GLY* 1.3 72.6 - - - -
581A VAL* 1.3 60.1 + - - +
582A ILE* 3.5 20.0 - - + +
597A HIS* 3.6 21.8 - - + +
598A LYS* 4.0 30.4 + - + +
629A ILE 4.3 3.3 - - - +
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Residues in contact with VAL 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A THR* 3.4 11.4 - - - +
531A LEU* 4.4 7.6 - - + -
577A LEU* 3.8 47.6 - - + +
578A LYS 4.1 2.7 - - - +
579A GLY 3.9 7.9 - - - +
580A GLU* 1.3 73.4 - - - +
582A ILE* 1.3 63.0 + - - +
583A GLY 4.1 0.2 - - - -
595A PHE 3.4 24.5 - - - +
596A CYS* 3.5 15.3 - - - -
597A HIS* 2.7 50.3 + - + +
598A LYS 3.2 7.3 + - - -
1002A EDO 4.3 1.8 - - - +
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Residues in contact with ILE 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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528A PHE* 3.9 21.8 - - + -
529A THR 2.8 13.6 + - - +
530A LEU* 3.5 6.0 - - + -
531A LEU 2.9 25.2 + - - +
580A GLU* 3.5 24.2 - - + +
581A VAL* 1.3 76.2 - - - +
583A GLY* 1.3 71.4 + - - +
584A VAL* 3.9 14.3 - - + +
596A CYS* 4.1 2.7 - - - -
598A LYS* 3.3 26.0 - - + +
600A TYR* 4.5 1.6 - - + -
625A LEU* 4.6 0.7 - - + -
628A PHE* 4.1 22.7 - - + -
629A ILE* 4.0 31.2 - - + -
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Residues in contact with GLY 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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531A LEU* 3.3 8.7 - - - -
582A ILE* 1.3 69.1 - - - +
584A VAL* 1.3 64.4 + - - +
592A LEU* 4.3 13.5 - - - -
596A CYS* 3.5 22.7 - - - -
598A LYS 2.8 12.4 + - - -
599A VAL* 3.5 2.6 - - - -
600A TYR* 2.7 29.5 + - - +
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Residues in contact with VAL 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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530A LEU* 5.1 2.7 - - + -
531A LEU 2.9 5.8 + - - +
532A ALA* 3.3 18.5 - - - +
536A GLU* 3.6 18.2 - - + +
539A LEU* 4.2 16.2 - - + -
540A CYS* 3.7 31.4 - - - -
582A ILE* 3.9 22.2 - - + +
583A GLY* 1.3 80.7 - - - +
585A GLU* 1.3 71.1 + - - +
592A LEU* 4.5 1.0 - - - +
600A TYR* 3.4 19.3 - - + +
620A PHE* 4.3 2.0 - - + -
625A LEU* 4.0 16.2 - - + -
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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