Contacts of the helix formed by residues 651 - 660 (chain A) in PDB entry 5IYB
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 SER 651 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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533A PRO* 4.8 0.2 - - - +
602A CYS* 5.3 1.6 - - - -
605A THR* 5.0 0.9 - - - -
643A LYS 4.9 2.2 - - - -
644A SER* 3.1 19.3 + - - +
646A GLY 2.8 21.6 + - - -
648A SER* 2.0 36.1 + - - -
650A GLY* 1.3 76.7 - - - +
652A LEU* 1.3 63.4 + - - +
653A VAL* 3.6 15.7 - - - -
654A HIS* 3.9 6.8 - - - +
655A ILE* 3.1 30.2 + - - +
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Residues in contact with LEU 652 (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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592A PHE* 4.1 23.6 - - + -
596A ILE* 4.5 7.4 - - + -
600A ILE* 4.1 19.2 - - + +
602A CYS* 4.2 15.9 - - + -
605A THR* 5.7 0.2 + - - -
628A VAL* 5.8 0.9 - - + -
630A VAL* 3.7 30.1 - - + -
635A LEU* 5.7 0.4 - - + -
640A LEU* 4.3 14.6 - - + -
644A SER* 3.2 17.2 + - - +
645A LEU* 3.8 25.4 - - + -
651A SER* 1.3 72.8 - - - +
653A VAL* 1.3 58.4 + - - +
655A ILE* 4.0 2.5 - - - +
656A SER* 3.0 32.2 + - - -
668A PHE* 4.2 12.5 - - + -
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Residues in contact with VAL 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ILE* 5.5 2.1 - - + +
533A PRO* 4.1 13.0 - - + -
535A MET 4.8 1.6 - - - +
536A GLY* 5.2 0.7 - - - -
537A ILE* 5.4 7.4 - - + -
644A SER 5.0 0.2 + - - -
645A LEU* 4.1 16.2 - - + +
646A GLY 3.7 13.2 - - - +
651A SER* 3.6 17.3 - - - -
652A LEU* 1.3 75.0 - - + +
654A HIS* 1.3 59.3 + - - +
656A SER* 3.7 1.8 - - - -
657A TYR* 3.0 29.5 + - - +
665A THR* 4.2 3.9 - - - +
668A PHE* 4.0 21.1 - - + -
669A TYR* 3.4 43.5 - - + +
672A ILE* 6.5 0.7 - - + -
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Residues in contact with HIS 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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526A VAL* 3.6 25.9 - - + +
531A ASN 3.1 28.5 + - - -
532A ARG* 4.3 1.3 - - - -
533A PRO* 3.3 22.1 - - + +
649A ALA* 3.7 10.4 - - + -
650A GLY* 3.6 17.8 + - - +
651A SER 3.7 15.6 + - - +
652A LEU 3.4 0.4 - - - -
653A VAL* 1.3 79.1 - - - +
655A ILE* 1.3 67.6 + - + +
657A TYR* 3.2 5.1 + - - +
658A LEU* 3.0 47.6 + - + +
899A GLU 5.2 1.8 + - - -
900A SER* 6.1 0.2 - - - -
901A VAL 4.9 6.6 + - - -
902A GLU* 5.0 7.9 - - + -
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Residues in contact with ILE 655 (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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600A ILE* 4.7 5.8 - - + -
601A ASN 4.4 16.6 - - - +
602A CYS* 3.4 33.7 - - + +
650A GLY* 3.6 22.2 - - - +
651A SER 3.1 18.6 + - - +
652A LEU* 4.3 2.2 - - - +
654A HIS* 1.3 77.1 - - + +
656A SER* 1.3 57.4 + - - +
658A LEU* 3.5 7.3 + - + +
659A GLU* 2.9 29.2 + - + +
902A GLU* 6.1 0.7 - - - +
985A ARG* 3.7 41.0 + - - +
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Residues in contact with SER 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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597A PRO* 3.3 27.0 - - - +
600A ILE* 3.5 17.5 - - - +
652A LEU 3.0 21.3 + - - -
653A VAL 3.7 3.4 - - - -
655A ILE* 1.3 75.1 - - - +
657A TYR* 1.3 58.8 + - - +
660A MET* 2.5 37.6 + - - +
661A GLY 3.4 0.3 + - - -
665A THR* 3.6 10.9 + - - -
668A PHE* 4.0 15.5 - - - -
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Residues in contact with TYR 657 (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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522A PRO 3.6 3.1 + - - -
523A ARG* 3.6 24.9 + - - -
525A ILE* 3.5 38.8 + - + -
526A VAL* 3.4 35.9 + - + -
653A VAL 3.0 17.5 + - - +
654A HIS 3.4 5.4 - - - +
656A SER* 1.3 74.5 - - - +
658A LEU* 1.3 77.0 + - + +
661A GLY* 3.4 18.3 + - - +
662A HIS* 3.5 34.0 - + + +
665A THR* 3.2 13.5 + - + +
899A GLU* 5.2 8.8 + - + -
900A SER* 5.8 2.2 - - - -
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Residues in contact with LEU 658 (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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526A VAL* 5.7 0.4 - - + -
654A HIS* 3.0 40.5 + - + +
655A ILE* 4.0 4.9 - - - +
657A TYR* 1.3 90.4 - - + +
659A GLU* 1.3 65.6 + - - +
661A GLY* 4.7 0.7 + - - -
899A GLU 5.0 1.8 - - - +
900A SER* 4.2 30.7 - - - +
901A VAL 6.0 0.4 - - - +
902A GLU* 3.5 30.5 - - + +
985A ARG* 4.3 12.6 - - - +
1075A LYS* 4.9 12.3 - - - +
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Residues in contact with GLU 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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599A HIS* 3.5 38.4 + - + +
600A ILE* 4.9 5.4 - - + -
601A ASN* 5.3 1.9 + - - -
655A ILE* 2.9 22.1 + - + +
656A SER* 4.0 2.7 - - - +
658A LEU* 1.3 84.4 - - - +
660A MET* 1.3 66.1 + - + +
985A ARG* 2.9 18.6 + - - +
986A MET* 5.3 5.4 - - - +
989A ASN* 2.8 32.6 + - - +
1071A GLU* 4.1 14.6 - - - +
1075A LYS* 4.6 11.6 + - - +
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Residues in contact with MET 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A PRO* 3.6 33.4 - - + -
599A HIS* 3.4 47.3 - - + -
600A ILE* 4.2 6.1 - - + -
656A SER* 2.5 29.3 + - - +
659A GLU* 1.3 76.0 - - - +
661A GLY* 1.3 60.5 + - - +
664A ILE* 3.4 52.8 - - + +
665A THR* 4.9 0.2 - - - +
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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