Contacts of the helix formed by residues 653 - 667 (chain A) in PDB entry 5LUQ
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 LEU 653 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A GLY 4.2 4.9 - - - +
513A GLU* 3.0 47.8 - - + +
568A PHE* 3.4 24.5 - - + -
572A VAL* 6.3 2.7 - - + -
649A PHE* 3.1 17.4 - - - -
652A GLU* 1.3 79.0 + - - +
654A ILE* 1.3 88.1 + - + +
655A LEU 3.6 2.5 - - - +
656A GLN* 3.1 45.7 - - + +
657A SER 3.0 12.8 + - - -
722A LYS* 5.3 3.3 - - - +
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Residues in contact with ILE 654 (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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509A ARG* 2.8 47.1 - - + +
512A GLY* 3.8 8.1 - - - -
513A GLU* 3.6 11.9 - - + +
602A MSE 6.0 0.2 - - - -
653A LEU* 1.3 81.4 - - + +
655A LEU* 1.3 58.0 + - - +
657A SER* 2.4 32.1 + - - -
658A THR* 2.9 11.3 + - - -
722A LYS* 3.1 31.4 - - - +
726A LEU* 3.4 12.6 - - + +
729A CYS* 3.4 26.7 - - + -
730A LEU* 3.9 12.6 - - + +
733A LEU* 3.5 1.3 - - - +
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Residues in contact with LEU 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A ARG* 3.3 33.4 - - + +
510A ALA* 4.4 18.8 - - + -
513A GLU* 3.0 42.4 - - + +
614A PRO* 4.7 9.9 - - + +
617A PRO* 4.3 14.1 - - + +
618A LYS* 4.8 18.6 - - + +
653A LEU* 3.6 0.8 - - - +
654A ILE* 1.3 80.6 - - + +
656A GLN* 1.3 54.7 + - - +
658A THR* 2.7 40.1 + - + +
659A ARG* 3.1 22.3 + - - +
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Residues in contact with GLN 656 (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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513A GLU* 4.0 1.0 + - - -
564A LEU* 3.8 32.4 - - + +
568A PHE* 4.1 12.4 - - + -
569A VAL* 6.3 0.4 - - - +
613A HIS* 5.0 2.0 - - + -
617A PRO* 5.1 4.2 - - + +
645A TRP* 3.7 17.8 - - + +
648A SER* 3.1 40.9 + - - +
649A PHE* 3.9 13.0 + - + +
651A TYR* 5.3 4.9 - - - +
652A GLU 5.1 1.8 - - - +
653A LEU* 3.1 46.8 - - + +
654A ILE 3.1 0.2 - - - -
655A LEU* 1.3 77.4 - - - +
657A SER* 1.3 62.3 + - - +
659A ARG 3.6 1.7 + - - -
660A LEU* 3.1 22.8 - - - +
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Residues in contact with SER 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A PHE* 4.2 15.2 - - - -
653A LEU 3.0 7.0 + - - -
654A ILE 2.4 22.6 + - - -
656A GLN* 1.3 74.3 - - - +
658A THR* 1.3 50.5 + - - -
660A LEU* 2.6 39.6 + - - +
661A PRO* 2.9 11.3 - - - +
730A LEU* 3.6 25.0 - - - +
733A LEU* 3.2 22.0 + - - +
734A LEU* 4.5 5.4 - - - +
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Residues in contact with THR 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A ARG* 3.3 33.8 + - - +
654A ILE* 2.9 4.5 + - - +
655A LEU* 2.7 41.1 + - + +
657A SER* 1.3 71.1 - - - +
659A ARG* 1.3 80.1 + - - +
661A PRO* 3.2 9.7 - - - +
662A LEU* 3.3 19.0 - - + +
729A CYS* 5.0 0.2 - - - +
733A LEU* 3.0 32.8 - - + +
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Residues in contact with ARG 659 (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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509A ARG* 4.7 2.2 - - - +
617A PRO* 3.1 55.2 + - + +
618A LYS* 4.4 14.3 - - - +
620A PHE* 4.3 4.9 - - + -
621A SER* 2.9 38.3 + - - +
641A PHE* 4.7 1.7 - - + -
645A TRP* 3.9 28.7 - - + -
655A LEU* 3.1 6.4 + - - +
656A GLN 3.6 0.2 + - - -
657A SER 3.0 0.6 + - - -
658A THR* 1.3 112.6 + - - +
660A LEU* 1.3 63.3 + - - +
662A LEU* 3.0 39.4 - - - +
663A ILE* 3.1 31.3 + - + +
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Residues in contact with LEU 660 (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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641A PHE* 5.4 1.3 - - + -
642A PHE* 5.8 4.3 - - + -
645A TRP* 3.1 39.0 - - + +
646A VAL* 3.4 45.3 - - + +
649A PHE* 4.8 6.1 - - + -
656A GLN 3.1 23.6 - - - +
657A SER* 2.6 29.0 + - - +
659A ARG* 1.3 76.8 - - - +
661A PRO* 1.3 54.4 - - + +
663A ILE* 2.8 16.5 - - + +
664A SER* 2.1 32.0 + - - +
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Residues in contact with PRO 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A SER* 2.9 23.8 - - - +
658A THR 3.2 13.9 - - - +
660A LEU* 1.3 80.8 - - + +
662A LEU* 1.3 64.9 + - - +
664A SER* 3.7 7.9 - - - +
665A GLY* 2.8 23.4 + - - -
666A PHE* 5.5 0.3 - - - -
733A LEU* 3.1 41.1 - - + +
736A LEU* 3.3 35.4 - - + +
737A PRO* 4.2 7.9 - - + -
740A ILE* 4.3 2.1 - - + +
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Residues in contact with LEU 662 (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 SER* 5.0 7.4 - - - -
624A ILE* 6.1 0.9 - - + -
658A THR* 3.3 24.7 - - + +
659A ARG* 3.0 39.9 - - - +
661A PRO* 1.3 80.4 - - + +
663A ILE* 1.3 59.9 + - + +
666A PHE* 2.9 69.0 + - + +
732A PHE* 6.2 0.4 - - + -
733A LEU* 4.9 2.9 - - + -
736A LEU* 4.5 16.8 - - + -
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Residues in contact with ILE 663 (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 PHE* 6.3 0.4 - - + -
624A ILE* 3.8 29.4 - - + -
629A PHE* 5.4 0.7 - - - -
638A GLN* 6.0 0.2 - - - -
641A PHE* 3.4 41.7 - - + -
642A PHE* 5.1 9.0 - - + +
659A ARG* 3.1 21.7 + - + +
660A LEU* 2.8 24.2 - - + +
662A LEU* 1.3 77.0 - - + +
664A SER* 1.3 80.3 + - - +
666A PHE* 3.1 3.7 + - - +
667A TYR* 2.9 61.7 + - + +
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Residues in contact with SER 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A GLN* 4.5 5.6 + - - +
642A PHE* 4.0 23.8 - - - -
660A LEU 2.1 30.7 + - - -
661A PRO* 3.1 3.9 + - - +
663A ILE* 1.3 86.6 - - - +
665A GLY* 1.3 60.7 + - - +
667A TYR* 3.6 27.1 - - - +
737A PRO* 5.5 2.8 - - - +
740A ILE* 3.4 26.8 - - - +
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Residues in contact with GLY 665 (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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661A PRO 2.8 12.9 + - - -
664A SER* 1.3 73.4 - - - +
666A PHE* 1.3 71.0 + - - +
667A TYR 3.4 5.7 - - - +
668A LYS* 5.3 0.3 - - - -
736A LEU* 6.1 2.2 - - - -
740A ILE* 3.1 28.8 - - - +
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Residues in contact with PHE 666 (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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624A ILE* 6.2 2.2 - - + -
625A ASN* 4.6 22.2 - - + -
629A PHE* 3.9 27.4 - + + -
662A LEU* 2.9 58.1 + - + +
663A ILE* 3.8 2.0 - - - +
665A GLY* 1.3 81.3 - - - +
667A TYR* 1.3 66.2 + - - +
668A LYS* 2.9 19.4 + - - +
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Residues in contact with TYR 667 (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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624A ILE* 4.9 2.3 - - - +
629A PHE* 3.8 20.4 - + - -
634A LEU* 3.5 26.5 - - + -
637A LYS* 3.5 37.4 - - + +
638A GLN* 3.3 47.5 + - + +
641A PHE* 3.8 13.3 - - - -
642A PHE* 6.4 0.2 - + - -
663A ILE* 2.9 57.5 + - + +
664A SER* 3.6 16.6 - - - +
665A GLY 3.9 4.5 - - - +
666A PHE* 1.3 73.5 - - - +
668A LYS* 1.3 50.9 + - - +
669A LEU* 2.5 23.0 + - - +
740A ILE* 5.4 1.2 - - - +
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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