Contacts of the strand formed by residues 626 - 632 (chain A) in PDB entry 3K5N
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 LYS 626 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622A GLN* 2.9 14.8 - - - +
623A GLU* 2.5 47.5 + - + +
624A GLY 3.0 0.2 - - - -
625A ASP* 1.3 110.5 - - + +
627A GLN* 1.3 63.1 + - - +
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Residues in contact with GLN 627 (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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599A CYS* 5.4 1.4 - - - -
620A LEU* 4.0 37.3 - - + +
621A ILE 3.1 4.9 - - - -
622A GLN* 3.7 33.4 + - + +
626A LYS* 1.3 77.5 - - - +
628A ARG* 1.3 61.2 + - - +
658A ARG* 3.4 31.8 + - - +
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Residues in contact with ARG 628 (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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620A LEU* 3.4 2.5 - - - -
621A ILE* 2.5 69.7 + - + +
623A GLU* 2.3 46.1 + - - +
626A LYS* 6.0 0.2 - - + -
627A GLN* 1.3 76.0 - - - +
629A MET* 1.3 74.2 + - - +
630A VAL* 4.8 4.3 - - - +
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Residues in contact with MET 629 (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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619A GLY 3.2 8.5 - - - +
620A LEU* 3.6 20.4 - - + -
628A ARG* 1.3 83.6 - - - +
630A VAL* 1.3 68.7 + - - +
631A PHE* 3.9 33.0 - - + -
650A GLN* 3.8 29.4 - - + +
654A LEU* 3.6 33.7 - - + -
657A PHE* 3.9 20.4 - - + -
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Residues in contact with VAL 630 (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* 4.0 16.8 - - + -
617A TYR* 4.6 18.8 - - + +
618A ALA* 3.3 6.8 - - - +
619A GLY 3.1 23.8 + - - +
621A ILE* 3.6 31.0 - - + -
628A ARG* 4.8 7.9 - - - +
629A MET* 1.3 81.0 - - - +
631A PHE* 1.3 75.7 + - - +
632A LYS* 5.3 3.4 - - + +
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Residues in contact with PHE 631 (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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617A TYR 3.9 1.3 - - - -
618A ALA* 3.8 15.7 - - + -
629A MET* 3.9 36.1 - - + -
630A VAL* 1.3 82.3 - - - +
632A LYS* 1.3 66.6 + - - +
634A LEU* 4.3 13.7 - - + -
636A THR* 4.1 29.2 - - + -
637A VAL* 3.9 22.5 - - + +
649A GLN* 4.4 2.5 - - + -
650A GLN* 3.8 35.9 - - + -
653A TYR* 3.5 29.8 - + + -
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Residues in contact with LYS 632 (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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615A LYS 4.2 13.2 - - - +
616A ARG* 2.9 26.3 - - - +
617A TYR* 3.0 56.1 + - + +
630A VAL* 5.3 3.3 - - + +
631A PHE* 1.3 78.8 + - - +
633A GLY* 1.3 68.1 + - - +
634A LEU* 3.1 4.0 + - - +
637A VAL* 4.7 0.7 - - - -
911P T 4.3 31.6 + - - +
912P A 5.0 5.8 - - - -
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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