Contacts of the helix formed by residues 610 - 623 (chain D) in PDB entry 5IWM
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 ASP 610 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C THR* 4.7 3.3 + - - -
608D LEU* 3.8 2.5 - - - +
609D GLU* 1.3 80.0 - - + +
611D ALA* 1.3 57.8 + - - +
612D ILE* 2.8 39.4 + - - +
613D GLU* 3.7 31.1 + - + +
614D ALA* 3.1 28.2 + - - +
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Residues in contact with ALA 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525D TYR* 3.5 6.2 + - - -
529D ARG* 3.4 28.9 - - - +
608D LEU* 4.3 10.0 - - + +
609D GLU 4.0 2.6 + - - -
610D ASP* 1.3 72.1 + - - +
612D ILE* 1.3 66.8 + - + +
614D ALA 4.0 0.7 - - - -
615D ASP* 3.0 34.9 + - - +
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Residues in contact with ILE 612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610D ASP* 2.8 21.2 + - - +
611D ALA* 1.3 76.6 - - + +
613D GLU* 1.3 63.9 + - - +
615D ASP* 3.4 10.3 + - - +
616D GLN* 3.2 48.8 + - + +
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Residues in contact with GLU 613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ASN* 5.2 1.9 - - - +
15C THR* 3.9 27.9 + - + +
19C ARG* 6.0 0.3 - - - -
609D GLU* 5.9 1.2 - - - +
610D ASP* 3.4 29.6 + - + +
612D ILE* 1.3 79.2 - - - +
614D ALA* 1.3 52.1 + - - +
616D GLN* 3.5 15.1 + - - +
617D THR* 2.7 37.4 + - - +
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Residues in contact with ALA 614 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ILE* 4.9 1.3 - - + -
15C THR* 3.8 16.1 + - - +
525D TYR* 3.4 23.3 - - + +
608D LEU* 3.8 15.0 - - + -
610D ASP 3.1 19.6 + - - +
611D ALA 4.1 0.4 - - - +
612D ILE 3.2 0.2 - - - -
613D GLU* 1.3 76.1 - - - +
615D ASP* 1.3 65.0 + - - +
617D THR* 3.2 2.7 + - - -
618D PHE* 3.0 39.5 + - + -
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Residues in contact with ASP 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525D TYR* 2.7 31.3 + - - -
526D ARG* 3.5 23.9 + - - +
529D ARG* 4.9 8.7 + - - -
611D ALA* 3.0 23.0 + - - +
612D ILE* 3.4 12.0 + - - +
614D ALA* 1.3 76.2 - - - +
616D GLN* 1.3 62.4 + - + +
619D GLU* 3.3 27.1 + - - +
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Residues in contact with GLN 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D ILE* 3.2 36.0 + - - +
613D GLU* 3.7 14.4 - - - +
615D ASP* 1.3 76.4 - - + +
617D THR* 1.3 60.2 - - - +
619D GLU* 4.0 10.5 - - - +
620D MET* 3.1 29.9 + - - +
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Residues in contact with THR 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C THR* 3.3 23.0 - - + +
18C MET* 4.1 14.1 - - + -
19C ARG* 4.0 21.0 + - + -
613D GLU* 2.7 24.0 + - - +
614D ALA* 3.2 6.5 + - - -
616D GLN* 1.3 75.6 - - - +
618D PHE* 1.3 63.3 + - + +
620D MET* 3.2 10.2 + - + +
621D LEU* 2.9 52.9 + - + +
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Residues in contact with PHE 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ILE* 3.6 32.8 - - + -
15C THR* 5.8 0.9 - - - -
18C MET* 3.6 36.8 - - + -
465D GLU* 3.9 11.0 - - - +
521D LEU 3.9 1.1 - - - -
522D THR* 3.5 44.4 - - + -
525D TYR* 3.8 34.5 - + + -
526D ARG* 3.8 15.9 - - - +
614D ALA* 3.0 32.1 + - + +
617D THR* 1.3 81.9 - - - +
619D GLU* 1.3 57.9 + - - +
622D MET* 3.0 35.1 + - + +
623D GLY 3.6 1.2 + - - -
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Residues in contact with GLU 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465D GLU* 3.6 16.3 + - - +
526D ARG* 5.0 0.7 - - - +
615D ASP 3.3 20.0 + - - +
616D GLN* 4.1 10.7 - - - +
617D THR 3.3 0.4 - - - -
618D PHE* 1.3 78.5 - - - +
620D MET* 1.3 60.3 + - - +
623D GLY* 3.0 28.5 + - - +
625D VAL* 5.5 3.3 + - - +
628D ASN* 5.9 2.0 + - - +
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Residues in contact with MET 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ARG* 3.9 14.6 - - + +
616D GLN 3.1 20.9 + - - +
617D THR* 3.2 16.1 + - + +
619D GLU* 1.3 78.6 - - - +
621D LEU* 1.3 76.0 + - + +
625D VAL 4.5 2.8 - - - +
628D ASN* 4.0 30.0 - - + +
629D ARG* 3.4 25.2 + - - +
632D PHE* 3.7 39.5 - - + -
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Residues in contact with LEU 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C MET* 3.4 42.8 - - + +
19C ARG* 4.0 2.7 - - + +
22C PHE* 3.3 31.1 - - + -
617D THR* 2.9 34.5 + - + +
620D MET* 1.3 87.3 - - + +
622D MET* 1.3 69.5 + - + +
629D ARG* 3.0 29.4 + - + +
632D PHE* 3.6 39.9 - - + -
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Residues in contact with MET 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C MET* 3.8 21.1 - - + -
22C PHE* 3.7 25.8 - - + -
463D ASN* 3.2 28.7 + - - +
465D GLU* 3.5 20.0 - - + +
466D LYS* 3.3 11.0 - - - +
515D HIS* 4.9 3.1 - - - +
518D THR* 4.0 14.1 - - - +
519D LEU* 3.7 29.4 - - + -
522D THR* 3.3 26.2 - - + +
618D PHE* 3.0 15.8 + - - +
621D LEU* 1.3 82.5 - - + +
623D GLY* 1.3 65.6 + - - +
629D ARG* 3.8 0.9 - - - -
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Residues in contact with GLY 623 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465D GLU* 3.8 14.4 - - - -
466D LYS* 3.6 4.1 - - - -
618D PHE 3.6 2.2 + - - -
619D GLU* 3.0 25.9 + - - -
622D MET* 1.3 81.3 - - - +
624D ASP* 1.3 57.6 + - - -
625D VAL 3.2 5.8 - - - -
629D ARG* 2.7 34.4 + - - +
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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