Contacts of the strand formed by residues 572 - 579 (chain A) in PDB entry 2LTO
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 572 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563A PHE* 3.7 28.9 - - + -
564A ALA 3.4 4.0 - - - -
565A LEU* 3.8 40.8 - - + -
571A LYS* 1.3 93.6 - - + +
573A TYR* 1.3 68.1 + - - +
604A ASN* 4.0 11.9 - - - -
606A LYS* 3.7 36.1 - - + -
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Residues in contact with TYR 573 (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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563A PHE* 3.2 11.2 - - - -
564A ALA* 2.9 31.0 + - - +
566A TYR* 3.5 20.6 - + + -
568A GLU* 4.8 5.7 + - - -
569A ASP* 2.7 33.7 + - - -
571A LYS* 3.1 37.8 - - + +
572A PHE* 1.3 75.0 - - - +
574A ARG* 1.3 61.6 + - - +
575A ALA 3.4 0.3 + - - -
591A PHE* 3.9 20.6 - - + -
594A TYR* 3.5 29.6 - + + -
617B DA2 3.5 16.6 - - - -
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Residues in contact with ARG 574 (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 CYS 3.6 8.5 - - - +
563A PHE* 3.4 21.7 - - + -
573A TYR* 1.3 71.2 - - - +
575A ALA* 1.3 58.2 + - - +
591A PHE* 3.3 10.0 - - - +
592A ILE* 2.9 59.9 + - + +
593A ASP* 2.7 55.5 + - - +
594A TYR* 5.1 1.9 - - + -
608A ILE* 4.5 10.5 - - + +
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Residues in contact with ALA 575 (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 CYS* 2.9 35.2 + - - +
564A ALA* 4.5 5.6 - - + -
573A TYR 3.4 1.2 + - - -
574A ARG* 1.3 73.9 - - - +
576A GLU* 1.3 60.2 + - - +
577A VAL* 3.6 2.6 + - - +
589A VAL* 3.7 26.0 - - + +
590A LYS 3.1 22.7 - - - +
591A PHE* 3.6 15.9 - - + -
592A ILE* 3.7 6.3 - - - -
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Residues in contact with GLU 576 (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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560A ASP 3.9 5.6 - - - +
561A GLU* 4.0 23.0 + - + +
575A ALA* 1.3 68.4 - - - +
577A VAL* 1.3 66.3 + - - +
578A GLU* 3.4 1.4 + - - +
590A LYS* 2.8 51.6 + - + +
592A ILE* 3.5 32.4 - - + +
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Residues in contact with VAL 577 (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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556A TRP* 5.0 0.9 - - + -
557A LYS 3.2 27.6 - - - +
558A PRO* 3.6 2.9 - - + -
559A GLY* 3.1 27.6 + - - +
560A ASP* 3.0 26.2 + - + +
562A CYS* 3.6 22.9 - - + -
575A ALA 3.6 0.6 + - - +
576A GLU* 1.3 72.7 - - - +
578A GLU* 1.3 60.7 + - - +
580A LEU* 3.4 36.3 - - + -
589A VAL* 3.6 18.2 - - + -
605A ILE* 5.3 0.4 - - + -
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Residues in contact with GLU 578 (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 PRO* 3.4 17.2 - - - +
559A GLY 4.5 0.5 + - - -
576A GLU 3.4 5.6 + - - +
577A VAL* 1.3 73.9 - - - +
579A ALA* 1.3 72.5 + - + +
581A HIS* 4.5 0.7 - - - -
588A VAL* 3.0 20.9 + - + +
589A VAL* 4.5 1.6 - - - -
590A LYS* 4.8 2.5 - - + +
597A TYR* 3.2 50.0 + - + -
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Residues in contact with ALA 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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558A PRO* 4.3 1.3 - - - -
578A GLU* 1.3 95.6 - - + +
580A LEU* 1.3 60.7 + - - +
581A HIS* 3.3 29.9 + - + +
582A SER* 4.0 13.3 + - - +
583A SER* 5.3 0.7 - - - -
587A ALA* 3.8 1.0 - - - -
588A VAL* 2.9 35.5 + - + +
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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