Contacts of the strand formed by residues 570 - 576 (chain A) in PDB entry 3VN4
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 570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566A ARG* 4.5 4.9 + - - -
569A GLU* 1.3 76.3 - - - +
571A VAL* 1.3 63.3 + - - +
572A THR 4.2 0.2 - - - -
594A HIS* 2.5 36.2 + + - -
596A ALA* 3.7 25.6 - - + -
603A TYR* 3.6 17.5 - + - +
607A GLY* 3.0 36.1 + - - -
609A MET* 2.8 38.7 + - + -
610A SER 3.5 0.3 + - - -
656A GLN* 3.5 23.4 - - + +
657A VAL 3.3 4.0 - - - -
658A TYR* 3.4 19.3 - + + -
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Residues in contact with VAL 571 (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 PHE* 4.3 18.4 - - + -
565A GLY* 4.2 8.5 - - - -
566A ARG* 3.6 62.6 - - + +
569A GLU* 4.5 4.0 - - + +
570A TYR* 1.3 78.5 - - - +
572A THR* 1.3 75.9 + - - +
573A PHE* 3.2 3.3 + - - -
656A GLN* 3.9 3.4 - - - -
657A VAL* 2.9 36.1 + - + +
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Residues in contact with THR 572 (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 PHE* 5.3 0.5 - - - -
571A VAL* 1.3 80.8 - - - +
573A PHE* 1.3 60.4 + - - +
574A LEU 3.8 20.9 - - - +
575A THR* 3.8 20.4 - - + -
598A ARG* 3.8 11.1 + - - -
654A ASP* 4.1 15.1 + - + -
655A ILE 3.8 5.4 - - - +
656A GLN* 3.1 23.8 + - - +
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Residues in contact with PHE 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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562A PHE* 3.5 44.1 - + + -
571A VAL 3.2 1.7 + - - -
572A THR* 1.3 74.5 - - - +
574A LEU* 1.3 76.2 + - + +
585A ILE* 3.9 8.3 - - + -
595A LEU* 4.0 3.6 - - + -
655A ILE* 3.1 40.1 + - + -
656A GLN 3.6 26.2 - - - -
657A VAL* 3.9 10.3 - - + -
673A ILE* 3.6 36.8 - - + -
675A PHE* 4.0 24.6 - + - -
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Residues in contact with LEU 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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572A THR* 3.7 2.8 - - - +
573A PHE* 1.3 95.1 - - + +
575A THR* 1.3 81.0 + - - +
576A VAL* 4.3 16.4 - - + +
580A LEU* 4.8 3.6 - - + -
583A VAL* 5.3 1.1 - - + -
585A ILE* 4.4 16.4 - - + -
654A ASP* 3.7 1.0 - - - -
655A ILE* 2.7 37.3 + - + +
675A PHE* 3.7 37.5 - - + -
677A TYR* 4.3 28.5 - - + +
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Residues in contact with THR 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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572A THR* 3.8 14.1 - - + -
574A LEU* 1.3 88.0 - - - +
576A VAL* 1.3 64.0 + - - +
577A THR* 3.4 16.6 + - - +
580A LEU* 4.0 5.4 - - - +
652A ASP* 4.7 6.6 + - - -
653A ALA 3.4 5.4 - - - -
654A ASP* 3.4 24.2 - - - +
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Residues in contact with VAL 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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574A LEU* 4.3 11.4 - - + -
575A THR* 1.3 69.9 - - - +
577A THR* 1.3 73.0 + - - +
580A LEU* 3.9 10.8 - - + +
583A VAL* 4.0 31.0 - - + -
645A ILE* 3.9 32.1 - - + -
649A LEU* 5.8 2.2 - - + -
651A GLU 4.4 1.0 - - - +
652A ASP* 3.5 4.2 - - - -
653A ALA* 2.7 37.6 + - + +
655A ILE* 3.8 24.7 - - + -
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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