Contacts of the helix formed by residues 627 - 634 (chain A) in PDB entry 1RTK
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 627 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602A ASP* 2.9 44.1 + - - +
623A LYS* 4.0 10.3 - - + +
625A GLY 2.7 4.7 + - - -
626A ASP* 1.3 87.3 + - - +
628A LYS* 1.3 64.7 + - - +
629A GLY 3.5 1.6 - - - -
630A SER* 3.4 13.9 + - - +
631A CYS* 3.3 20.1 + - - +
662A SER* 3.2 35.5 + - - +
663A PRO* 3.9 9.2 - - - +
714A ARG* 5.4 1.5 + - - +
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Residues in contact with LYS 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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623A LYS* 3.2 29.4 - - - +
624A ASN* 4.3 19.3 + - - +
625A GLY 2.9 15.5 + - - +
626A ASP 3.5 0.2 - - - -
627A LYS* 1.3 75.0 - - - +
629A GLY* 1.3 69.3 + - - +
631A CYS* 3.0 14.3 + - - +
632A GLU* 3.0 48.3 + - + +
653A PRO* 6.3 0.8 - - - +
655A PHE 5.5 4.7 - - - -
657A CYS* 5.8 1.6 - - + -
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Residues in contact with GLY 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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626A ASP 5.1 2.0 - - - -
627A LYS 3.5 0.8 - - - +
628A LYS* 1.3 78.6 - - - +
630A SER* 1.3 56.6 + - - +
632A GLU* 3.8 11.6 - - - +
633A ARG* 3.0 52.8 + - - +
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Residues in contact with SER 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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626A ASP 4.7 3.3 + - - -
627A LYS* 3.4 18.4 + - - +
628A LYS 3.1 0.6 - - - -
629A GLY* 1.3 74.5 - - - +
631A CYS* 1.3 65.9 + - - +
633A ARG* 3.5 24.1 + - - +
634A ASP* 3.1 28.1 + - - +
714A ARG* 4.2 8.7 - - - -
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Residues in contact with CYS 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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623A LYS* 3.6 30.5 - - + -
627A LYS 3.3 4.0 + - - +
628A LYS 3.0 9.0 + - - +
630A SER* 1.3 77.9 - - - +
632A GLU* 1.3 62.6 + - - +
634A ASP* 3.4 17.3 + - - +
657A CYS* 2.0 58.8 - - + -
658A THR 3.9 3.6 - - - -
714A ARG* 3.5 36.8 - - - +
716A PHE* 3.8 2.8 - - - -
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Residues in contact with GLU 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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628A LYS* 3.0 52.3 + - + +
629A GLY* 3.8 10.2 - - - +
631A CYS* 1.3 71.8 - - - +
633A ARG* 1.3 60.1 + - + +
634A ASP 3.1 2.0 - - - -
635A ALA* 2.9 31.5 + - - +
647A ILE* 4.4 4.0 - - + +
648A SER* 6.1 0.5 - - - -
651A VAL* 3.9 34.4 - - + +
652A THR 5.2 2.4 - - - +
655A PHE 4.7 8.1 - - - +
657A CYS* 4.7 10.7 - - + +
716A PHE* 4.0 9.6 - - - -
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Residues in contact with ARG 633 (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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629A GLY* 3.0 42.6 + - - +
630A SER* 3.5 31.1 + - - +
631A CYS 3.4 0.4 - - - -
632A GLU* 1.3 76.2 - - + +
634A ASP* 1.3 58.2 + - - +
635A ALA 2.9 4.9 + - - -
636A GLN* 3.0 38.4 + - - +
647A ILE* 4.5 20.9 - - + +
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Residues in contact with ASP 634 (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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630A SER* 3.1 13.1 + - - +
631A CYS 3.5 9.9 - - - +
632A GLU 3.0 1.4 + - - -
633A ARG* 1.3 77.7 - - - +
635A ALA* 1.3 59.2 + - - +
636A GLN 3.0 1.8 - - - -
637A TYR* 3.1 32.3 + - - -
696A VAL* 3.5 14.4 - - - +
711A ALA 4.5 0.2 - - - +
712A HIS* 3.4 28.5 - - + +
714A ARG* 2.9 41.3 + - + -
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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