Contacts of the strand formed by residues 577 - 583 (chain A) in PDB entry 3LLT
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 TYR 577 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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555A ILE* 3.7 28.3 - - + -
568A LEU* 4.3 15.7 - - + -
569A CYS 3.4 10.5 - - - -
570A GLN* 3.3 32.3 + - + -
575A LYS 3.9 5.6 - - - -
576A LYS* 1.3 75.8 - - - +
578A TYR* 1.3 69.6 + - - +
632A PRO* 3.3 30.5 - - + +
689A TYR* 5.8 4.5 - - - -
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Residues in contact with TYR 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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552A PHE* 3.5 27.4 - + + -
567A LEU 3.6 0.2 - - - +
568A LEU* 3.6 8.2 - - - +
569A CYS* 2.8 35.9 + - - +
571A HIS* 3.7 20.6 - + + -
574A ASN* 3.1 20.4 + - - -
576A LYS* 3.5 43.0 + - + -
577A TYR* 1.3 78.7 - - - +
579A ALA* 1.3 60.8 + - - +
580A VAL* 3.8 3.3 + - + -
617A HIS* 3.7 31.3 - + + -
629A ILE* 3.6 27.6 - - + -
630A PHE 3.5 12.6 - - - +
631A GLU* 5.3 0.4 - - - -
632A PRO* 4.2 2.9 - - - -
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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 MET* 3.9 10.3 - - - -
566A VAL* 3.8 13.9 - - + -
567A LEU 3.6 4.5 - - - -
578A TYR* 1.3 70.1 - - - +
580A VAL* 1.3 62.4 + - - +
581A LYS 4.0 0.2 - - - -
628A LEU 3.6 1.9 - - - +
629A ILE* 3.8 0.2 - - - -
630A PHE* 2.8 41.1 + - + +
631A GLU 3.6 19.7 - - - +
632A PRO* 4.1 3.3 - - + -
877A ANP 3.7 24.9 - - + +
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Residues in contact with VAL 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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548A LEU* 4.4 10.8 - - + -
552A PHE* 4.1 22.7 - - + -
565A ARG 3.3 4.3 - - - +
566A VAL* 4.1 1.6 - - - -
567A LEU* 2.8 40.3 + - + +
569A CYS* 3.8 30.5 - - + -
578A TYR* 4.5 4.5 - - + -
579A ALA* 1.3 73.9 - - - +
581A LYS* 1.3 61.5 + - - +
582A VAL* 3.5 16.1 + - + +
620A PHE* 4.4 6.1 - - + -
627A CYS* 4.1 25.1 - - + -
628A LEU 3.5 6.1 - - - +
629A ILE* 4.8 6.7 - - + -
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Residues in contact with LYS 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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564A GLY* 4.0 16.2 - - - -
565A ARG 3.5 3.4 - - - -
566A VAL* 3.8 22.4 - - + +
579A ALA 3.8 1.6 + - - -
580A VAL* 1.3 69.0 - - - +
582A VAL* 1.3 59.6 + - - +
583A VAL* 3.6 10.3 + - + +
596A GLU* 2.6 37.2 + - - -
626A MET 3.5 2.8 - - - +
627A CYS* 3.2 5.9 - - - -
628A LEU* 2.9 45.8 + - + +
630A PHE* 3.8 21.7 - - + -
720A ASP* 4.5 1.4 + - - -
877A ANP 2.7 56.9 + - + +
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Residues in contact with VAL 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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539A HIS* 4.9 1.4 + - - -
540A PHE* 3.7 39.0 + - + +
548A LEU* 4.7 4.7 - - + -
564A GLY* 3.4 1.1 - - - -
565A ARG* 2.7 42.9 + - - +
567A LEU* 4.1 20.6 - - + -
580A VAL* 4.1 14.1 - - + +
581A LYS* 1.3 72.7 - - - +
583A VAL* 1.3 63.1 + - - +
584A ARG* 3.9 0.3 + - - +
622A TYR* 5.7 0.7 - - + -
625A HIS* 3.8 29.2 - - + +
626A MET 3.7 2.5 - - - -
627A CYS* 3.9 17.3 - - - -
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Residues in contact with VAL 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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540A PHE* 6.1 0.2 - - - -
563A PHE* 3.4 19.3 - - + +
564A GLY* 4.1 1.8 - - - -
581A LYS* 4.3 23.3 - - + +
582A VAL* 1.3 73.7 - - - +
584A ARG* 1.3 62.4 + - - +
589A TYR* 3.5 37.7 - - + +
590A THR* 4.6 1.1 - - - +
593A ALA* 3.8 19.7 - - + -
596A GLU* 5.5 0.7 - - - +
625A HIS* 2.7 35.8 + - - +
626A MET* 2.9 28.4 + - + +
628A LEU* 4.9 3.8 - - + -
877A ANP 5.9 0.2 - - - +
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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