Contacts of the strand formed by residues 617 - 623 (chain A) in PDB entry 3K57
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 617 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A TYR* 3.8 24.0 - + - -
550A PHE* 3.5 29.9 - + - -
598A PHE* 4.7 12.3 - + - -
601A PHE* 3.6 27.1 - + + -
602A LEU 3.4 16.2 - - - +
603A MET* 4.1 5.2 - - + -
604A PRO* 4.2 1.6 - - - -
615A LYS 5.0 0.9 - - - -
616A ARG* 1.3 83.7 - - - +
618A ALA* 1.3 61.8 + - - +
630A VAL* 5.1 1.8 - - + -
632A LYS* 2.7 65.3 + - + +
634A LEU* 3.5 12.2 - - - +
912P A 4.7 1.3 - - - -
913P DOC 2.4 30.8 + - - -
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Residues in contact with ALA 618 (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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601A PHE* 3.4 10.5 - - - -
602A LEU* 2.8 30.5 + - + -
617A TYR* 1.3 79.3 - - - +
619A GLY* 1.3 59.4 + - - +
630A VAL 3.1 6.5 - - - +
631A PHE* 3.5 29.2 - - + -
634A LEU* 3.7 1.1 - - + +
653A TYR* 3.6 28.0 - - + -
657A PHE* 3.9 5.4 - - + -
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Residues in contact with GLY 619 (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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598A PHE* 3.5 19.5 - - - -
600A ARG 3.3 11.7 - - - -
601A PHE* 4.1 0.4 - - - -
618A ALA* 1.3 77.6 - - - +
620A LEU* 1.3 61.1 + - - -
628A ARG 4.1 0.2 - - - +
629A MET* 3.3 5.9 - - - +
630A VAL 2.8 33.5 + - - -
657A PHE* 3.9 10.2 - - - -
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Residues in contact with LEU 620 (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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598A PHE* 3.4 4.4 - - - -
599A CYS* 2.8 46.4 + - - -
600A ARG* 2.8 30.5 + - + -
619A GLY* 1.3 73.7 - - - -
621A ILE* 1.3 61.7 + - - +
627A GLN* 3.9 39.9 - - + +
628A ARG 3.7 7.6 - - - +
629A MET* 3.6 23.6 - - + -
654A LEU* 4.1 14.1 - - + -
657A PHE* 4.1 27.7 - - + +
658A ARG* 4.8 4.0 - - + -
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Residues in contact with ILE 621 (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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596A THR* 3.6 26.5 - - + +
597A HIS 4.2 11.4 - - - +
598A PHE* 3.7 16.8 - - + -
599A CYS* 4.5 1.8 - - - -
619A GLY 5.0 0.2 - - - +
620A LEU* 1.3 78.5 - - - +
622A GLN* 1.3 69.6 + - - +
623A GLU* 3.7 23.6 + - + +
627A GLN* 3.1 6.3 - - - -
628A ARG* 2.7 66.4 + - + +
630A VAL* 3.9 20.9 - - + -
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Residues in contact with GLN 622 (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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559A GLU* 3.5 43.9 + - + +
597A HIS 4.9 1.4 + - - -
599A CYS* 4.1 14.4 - - - +
621A ILE* 1.3 79.0 - - - +
623A GLU* 1.3 59.4 + - - +
624A GLY 3.3 23.3 + - - +
625A ASP* 3.9 11.7 + - - +
626A LYS 3.8 6.0 + - - -
627A GLN* 3.1 38.5 + - - +
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Residues in contact with GLU 623 (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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621A ILE* 3.8 17.1 - - + +
622A GLN* 1.3 78.1 - - - +
624A GLY* 1.3 67.7 + - - +
625A ASP 3.1 0.2 + - - -
626A LYS* 2.6 73.8 + - - +
628A ARG* 2.8 41.7 + - - +
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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