Contacts of the strand formed by residues 528 - 532 (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 PHE 528 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A ALA* 3.9 3.5 - - - +
527A LYS* 1.3 97.1 - - + +
529A THR* 1.3 64.1 + - - +
530A LEU* 4.2 16.2 - - + -
547A LEU* 4.4 3.4 - - + -
552A PHE* 3.8 37.2 - + + -
553A ALA 3.4 1.8 + - - -
554A CYS* 3.3 14.1 - - - -
555A ASN 2.9 22.4 + - - -
578A LYS 3.7 2.9 - - - -
580A GLU* 3.2 33.9 - - + +
582A ILE* 3.9 7.6 - - + -
629A ILE* 3.7 36.1 - - + -
630A LEU* 3.9 16.8 - - + -
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Residues in contact with THR 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A PHE* 1.3 72.6 + - - +
530A LEU* 1.3 68.4 + - - +
531A LEU* 3.8 0.8 + - + +
555A ASN* 3.3 18.3 - - + +
557A VAL* 3.7 21.5 - - + -
576A LEU 3.4 20.1 + - - +
577A LEU* 4.4 11.4 - - + -
578A LYS* 2.7 36.7 + - - +
580A GLU 3.0 6.7 + - - +
581A VAL* 3.4 10.4 - - + +
582A ILE* 2.8 27.7 + - - +
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Residues in contact with LEU 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A PHE* 4.2 18.4 - - + -
529A THR* 1.3 77.2 - - - +
531A LEU* 1.3 54.2 - - - +
540A CYS* 3.5 46.9 - - + +
543A SER* 3.8 14.4 - - - -
544A ALA* 4.1 5.8 - - + +
547A LEU* 4.3 4.7 - - + -
554A CYS* 4.2 15.7 - - + -
555A ASN 2.9 17.0 + - - +
556A VAL* 3.4 6.4 - - + +
557A VAL* 2.9 31.5 + - - +
582A ILE* 3.5 9.6 - - + +
584A VAL* 5.1 1.6 - - + -
625A LEU* 4.4 2.7 - - + -
629A ILE* 3.8 25.8 - - + -
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Residues in contact with LEU 531 (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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529A THR* 3.8 1.5 + - + -
530A LEU* 1.3 71.0 - - - +
532A ALA* 1.3 65.3 + - - +
557A VAL* 3.5 24.9 - - + -
559A MSE 4.0 35.0 - - + -
565A PHE* 4.4 14.6 - - + -
577A LEU* 3.9 24.0 - - + -
581A VAL* 4.4 6.7 - - + -
582A ILE 2.9 10.9 + - - +
583A GLY* 4.4 1.6 - - - -
584A VAL* 2.9 25.8 + - - +
585A GLU* 5.9 0.4 - - + +
592A LEU* 4.3 9.2 - - + -
595A PHE* 4.6 4.9 - - + -
596A CYS* 4.2 26.7 - - - -
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Residues in contact with ALA 532 (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* 1.3 77.4 - - - +
533A SER* 1.3 56.0 - - - +
536A GLU 3.7 17.5 - - - +
537A VAL* 3.7 8.9 - - + +
540A CYS* 3.6 24.9 - - + -
556A VAL* 6.3 0.4 - - + -
557A VAL 3.0 10.8 + - - +
558A SER* 3.5 3.1 - - - -
559A MSE 2.7 32.8 + - - -
584A VAL 3.3 18.4 - - - +
585A GLU* 5.0 1.1 - - - -
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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