Contacts of the helix formed by residues 561 - 573 (chain D) in PDB entry 3K0J
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 GLU 561 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510D HIS* 4.0 1.8 - - - -
559D PHE* 3.3 12.0 - - - +
560D LYS* 1.3 92.8 - - + +
562D VAL* 1.3 64.7 + - - +
563D SER* 3.1 25.1 - - - +
564D SER* 3.3 13.3 + - - +
565D ALA 3.3 14.0 + - - -
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Residues in contact with VAL 562 (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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508D PRO* 3.0 38.8 - - + +
509D ASN* 3.0 17.7 - - - +
510D HIS* 3.7 23.8 - - + +
560D LYS 5.5 0.4 - - - +
561D GLU* 1.3 72.2 - - - +
563D SER* 1.3 57.3 + - - +
565D ALA* 2.8 3.3 + - - +
566D THR* 2.6 38.0 + - - +
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Residues in contact with SER 563 (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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561D GLU* 3.1 23.5 - - - +
562D VAL* 1.3 78.7 - - - +
564D SER* 1.3 62.2 + - - -
566D THR* 3.7 7.1 - - - +
567D ASN* 2.7 38.7 + - - +
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Residues in contact with SER 564 (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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537D PHE* 2.7 29.7 + - - +
538D GLY* 3.9 9.2 - - - -
539D GLN 4.9 0.7 + - - -
559D PHE* 3.7 15.0 - - - -
560D LYS* 5.3 1.0 - - - +
561D GLU* 3.3 22.4 + - - +
562D VAL 3.2 0.2 - - - -
563D SER* 1.3 83.8 + - - +
565D ALA* 1.3 63.2 + - - +
567D ASN* 3.5 6.1 - - - +
568D ALA* 3.0 23.9 + - - +
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Residues in contact with ALA 565 (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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509D ASN 3.7 14.6 - - - +
510D HIS* 3.6 18.8 - - - +
512D ILE* 3.9 13.8 - - + +
559D PHE* 3.3 30.0 - - + -
561D GLU 3.3 2.2 + - - +
562D VAL 2.8 9.6 + - - +
564D SER* 1.3 78.4 - - - +
566D THR* 1.3 64.8 + - - +
568D ALA* 2.9 5.4 + - - +
569D LEU* 2.9 23.7 + - - +
586D TYR* 4.8 0.2 - - + -
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Residues in contact with THR 566 (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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508D PRO* 3.6 14.0 - - + +
562D VAL* 2.6 20.3 + - - +
563D SER* 3.7 7.9 - - - +
565D ALA* 1.3 73.1 - - - +
567D ASN* 1.3 64.4 + - - +
569D LEU* 3.7 2.4 + - - +
570D ARG* 3.2 25.4 + - + +
586D TYR* 2.4 42.4 + - - +
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Residues in contact with ASN 567 (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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537D PHE* 3.7 24.6 + - + +
563D SER 2.7 23.1 + - - +
564D SER* 3.5 7.6 - - - +
566D THR* 1.3 77.6 - - - +
568D ALA* 1.3 57.7 + - - +
570D ARG* 3.5 3.5 + - - +
571D SER* 2.6 36.5 + - - -
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Residues in contact with ALA 568 (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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512D ILE* 4.6 0.9 - - + -
534D PHE* 3.9 8.7 - - + -
537D PHE* 3.3 43.7 - - + -
559D PHE* 3.8 15.5 - - + -
564D SER 3.0 9.7 + - - +
565D ALA 2.9 7.7 + - - +
567D ASN* 1.3 74.5 - - - +
569D LEU* 1.3 56.9 + - - +
571D SER 3.1 0.9 + - - -
572D MET* 2.6 38.4 + - - +
584D ILE* 4.9 0.4 - - - -
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Residues in contact with LEU 569 (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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512D ILE* 4.1 10.4 - - + +
565D ALA 2.9 15.0 + - - +
566D THR* 3.9 5.8 - - - +
568D ALA* 1.3 78.2 - - - +
570D ARG* 1.3 73.1 + - + +
573D GLN* 3.2 27.7 + - + +
584D ILE* 3.7 23.9 - - + +
585D GLN* 3.1 45.3 - - - +
586D TYR* 3.8 30.3 - - + +
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Residues in contact with ARG 570 (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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336B ARG* 3.9 12.5 + - - +
566D THR* 3.2 17.3 + - + +
567D ASN* 3.9 3.8 - - - +
569D LEU* 1.3 89.7 - - + +
571D SER* 1.3 66.1 + - - +
573D GLN* 3.5 12.4 - - - +
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Residues in contact with SER 571 (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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336B ARG* 3.2 23.8 + - - +
537D PHE* 4.0 12.2 - - - -
567D ASN* 2.6 27.9 + - - -
568D ALA 3.1 3.2 + - - -
570D ARG* 1.3 74.7 - - - +
572D MET* 1.3 75.9 + - - +
573D GLN 2.9 10.3 + - - -
575D PHE* 5.3 1.0 - - - +
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Residues in contact with MET 572 (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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275A PHE* 6.5 0.4 - - + -
533D ILE* 3.6 22.2 - - + -
534D PHE* 3.3 21.8 - - + -
536D ARG* 4.5 13.2 - - - +
537D PHE* 3.3 34.8 - - + -
568D ALA 2.6 16.5 + - - +
571D SER* 1.3 79.6 - - - +
573D GLN* 1.3 60.7 + - - -
574D GLY 3.1 3.8 + - - -
575D PHE* 3.4 37.6 + - + +
582D MET* 3.5 15.2 - - + +
584D ILE* 3.1 22.0 - - + +
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Residues in contact with GLN 573 (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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331B HIS* 6.0 0.3 - - - -
332B ALA* 2.7 48.8 - - - +
333B ILE* 4.4 0.5 - - - -
335B SER* 5.6 6.3 - - - -
336B ARG* 2.5 28.8 + - - +
569D LEU* 3.2 19.0 + - + +
570D ARG* 3.5 12.3 - - - +
571D SER 2.9 3.8 + - - -
572D MET* 1.3 75.3 - - - +
574D GLY* 1.3 56.1 + - - +
583D ARG* 4.0 1.9 - - - +
584D ILE* 3.0 54.4 + - - +
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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