Contacts of the strand formed by residues 642 - 647 (chain A) in PDB entry 3E20
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 ARG 642 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583A ILE* 3.1 26.2 - - - +
634A PHE* 3.1 32.6 - - + -
638A GLN* 3.0 33.0 + - - +
639A TYR* 3.8 16.9 + - + +
641A GLY* 1.3 80.0 - - - +
643A PHE* 1.3 65.7 + - - +
644A THR* 6.4 0.4 - - + -
655A GLY 3.6 6.3 - - - +
656A LYS* 4.7 4.2 - - + +
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Residues in contact with PHE 643 (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 PHE* 4.0 9.6 - + - -
562A ALA* 3.8 21.1 - - + -
564A ILE* 4.5 4.7 - - + -
581A MET* 3.5 22.0 - - + -
582A HIS 3.3 15.7 - - - +
583A ILE* 3.5 21.8 - - + -
623A LEU* 4.1 9.0 - - + -
641A GLY 3.6 9.6 - - - -
642A ARG* 1.3 77.6 - - - +
644A THR* 1.3 65.1 - - - +
645A LEU* 3.2 34.8 - - + -
654A VAL* 3.5 2.2 - - - +
655A GLY* 2.9 64.8 + - - +
656A LYS 3.6 14.4 - - - -
657A VAL* 3.7 3.4 - - + -
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Residues in contact with THR 644 (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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580A VAL 3.9 0.3 - - - +
581A MET* 3.5 0.5 - - - -
582A HIS* 3.1 39.3 + - + +
642A ARG* 6.4 0.4 - - + -
643A PHE* 1.3 79.0 - - - +
645A LEU* 1.3 67.0 + - - +
646A ARG* 4.2 13.7 + - - -
651A THR* 4.1 16.9 + - + +
653A ALA 3.5 10.5 - - - -
654A VAL* 4.1 13.2 - - + +
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Residues in contact with LEU 645 (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 ILE* 4.5 7.2 - - + -
579A CYS* 3.7 17.7 - - - -
580A VAL 3.4 1.8 - - - +
581A MET* 3.8 15.7 - - + -
590A VAL* 4.5 3.8 - - + -
592A PHE* 3.8 33.0 - - + -
623A LEU* 4.8 4.7 - - + -
643A PHE* 3.2 43.5 - - + -
644A THR* 1.3 75.0 - - - +
646A ARG* 1.3 67.4 + - - +
651A THR* 3.4 2.6 - - - +
652A VAL* 2.9 36.4 + - + -
653A ALA* 2.7 29.4 + - + +
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Residues in contact with ARG 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A CYS* 4.0 4.8 - - - -
580A VAL* 2.7 37.0 + - - +
582A HIS* 3.3 36.5 + - - -
644A THR* 4.2 10.0 + - - +
645A LEU* 1.3 82.0 - - - +
647A ASP* 1.3 54.1 + - - +
648A GLN* 2.7 44.0 + - + +
650A THR* 3.3 10.0 - - - +
651A THR* 3.5 27.4 + - - +
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Residues in contact with ASP 647 (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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569A LEU* 4.8 1.0 - - - +
570A PRO* 5.0 7.6 - - + +
577A TYR* 2.7 28.2 + - - +
578A SER 5.0 0.5 - - - +
579A CYS* 4.3 6.6 - - - +
646A ARG* 1.3 66.1 - - - +
648A GLN* 1.3 49.6 - - - +
649A GLY* 2.0 26.8 + - - -
650A THR* 3.2 9.4 + - + +
652A VAL* 3.7 20.1 - - + +
396B GLN* 3.2 28.8 + - - +
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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