Contacts of the strand formed by residues 649 - 654 (chain A) in PDB entry 3WSZ
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 THR 649 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421A GLN* 4.9 15.8 + - - +
634A SER* 2.2 33.6 + - - -
635A PRO* 3.7 7.0 - - - +
648A LYS* 1.3 75.3 + - - +
650A VAL* 1.3 59.6 + - - +
651A PHE* 3.5 34.8 - - + -
670A VAL* 4.3 15.3 - - + -
671A VAL 3.6 9.2 - - - +
672A VAL* 4.4 15.9 - - + +
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Residues in contact with VAL 650 (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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632A LEU* 3.8 42.1 - - + +
633A TRP 3.7 6.5 - - - +
634A SER* 3.7 16.6 - - - +
648A LYS* 3.9 23.6 - - + +
649A THR* 1.3 77.7 - - - +
651A PHE* 1.3 64.1 + - - +
669A PRO 3.7 1.7 - - - +
670A VAL* 3.5 4.5 - - - -
671A VAL* 2.9 47.8 + - + +
673A SER* 5.3 2.9 - - - +
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Residues in contact with PHE 651 (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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419A GLY 4.0 12.8 - - - -
420A LEU* 3.8 24.0 - - + -
501A PRO* 3.8 30.3 - - + -
632A LEU* 3.4 5.6 - - - -
633A TRP* 2.7 60.8 + + + +
635A PRO* 4.0 15.0 - - + -
649A THR* 3.5 32.5 - - + -
650A VAL* 1.3 76.7 - - - +
652A LYS* 1.3 62.0 + - - +
653A ARG* 3.6 16.7 + - + -
668A ARG* 5.3 2.0 - - + -
669A PRO 4.0 3.6 - - - -
670A VAL* 3.4 31.6 - - + -
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Residues in contact with LYS 652 (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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627A GLU* 3.3 29.4 + - - +
630A TYR* 3.7 41.8 - - + -
631A LYS 3.4 12.1 - - - +
632A LEU* 3.9 15.1 - - + +
651A PHE* 1.3 73.1 - - - +
653A ARG* 1.3 60.7 + - - +
666A PHE* 4.7 9.5 - - - -
668A ARG* 3.4 26.8 + - - +
669A PRO* 3.4 45.3 + - + +
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Residues in contact with ARG 653 (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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501A PRO* 3.5 24.8 + - + +
502A GLY 4.0 2.0 + - - -
503A LEU* 4.7 3.0 - - - +
524A SER* 2.8 49.1 + - - +
567A GLU* 4.1 8.3 + - - -
630A TYR* 3.5 6.4 - - - -
631A LYS* 3.0 35.4 + - + +
633A TRP* 3.2 58.7 - - + +
651A PHE* 3.6 13.2 + - + +
652A LYS* 1.3 78.4 - - - +
654A ARG* 1.3 70.2 + - - +
655A THR* 3.3 0.5 + - - -
668A ARG* 4.6 14.5 - - - +
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Residues in contact with ARG 654 (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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544A ASP* 5.7 0.4 + - - -
546A GLY 4.6 0.6 + - - -
547A GLY* 2.5 46.6 + - - -
565A THR* 3.1 14.5 + - - +
567A GLU* 4.6 7.0 - - - +
621A LEU* 5.6 0.6 - - - +
625A CYS* 3.8 26.0 - - - -
629A ASP 3.2 10.8 - - - +
630A TYR* 3.7 17.1 - - + -
653A ARG* 1.3 78.2 - - - +
655A THR* 1.3 80.2 + - - +
656A PRO* 3.2 21.4 + - - +
658A ALA* 2.5 37.3 + - + -
660A CYS* 3.8 12.1 + - - -
661A PHE* 5.7 0.2 - - - +
662A ASN* 5.0 11.9 - - - +
668A ARG* 4.6 7.8 - - - +
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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