Contacts of the helix formed by residues 650 - 665 (chain H) in PDB entry 5A31
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 650 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1392A THR* 5.0 5.4 - - + -
1395A LEU* 4.3 27.7 - - + +
621H LEU* 6.1 0.4 - - - +
645H TYR* 2.9 38.5 + - + +
648H GLN* 3.5 36.3 - - + +
649H GLU* 1.3 73.5 - - - +
651H PHE* 1.3 63.2 + - - +
652H SER* 3.4 5.2 - - - +
653H LEU* 3.2 26.6 + - + +
654H ALA* 3.2 16.1 + - - +
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Residues in contact with PHE 651 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646H TYR* 3.6 56.3 - + - -
649H GLU* 2.8 50.5 + - + -
650H LYS* 1.3 70.2 - - - +
652H SER* 1.3 65.7 + - - +
654H ALA* 3.1 3.9 + - - -
655H GLU* 3.0 20.1 + - - +
678H VAL* 3.3 13.1 - - + +
681H ALA* 4.1 26.7 - - + -
682H LEU* 3.2 25.6 - - + -
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Residues in contact with SER 652 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650H LYS* 4.2 2.9 - - - +
651H PHE* 1.3 76.9 + - - +
653H LEU* 1.3 75.8 + - - +
655H GLU* 3.3 17.7 + - - +
656H MET 3.4 4.0 + - - -
682H LEU* 3.7 19.8 - - - +
527K ILE* 4.2 24.8 - - - +
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Residues in contact with LEU 653 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645H TYR* 3.8 37.9 - - + -
650H LYS* 3.3 27.4 - - + +
651H PHE 3.2 0.4 - - - -
652H SER* 1.3 90.7 + - - +
654H ALA* 1.3 61.0 + - - +
656H MET* 3.0 13.3 + - - +
657H HIS* 2.9 40.1 + - + +
523K ILE* 3.4 33.2 - - + -
524K GLU* 6.4 0.7 - - + -
527K ILE* 5.0 1.6 - - + -
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Residues in contact with ALA 654 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642H GLY* 3.7 29.4 - - - +
645H TYR* 4.3 1.9 - - - +
646H TYR* 3.9 23.1 - - + +
650H LYS 3.2 5.1 + - - +
651H PHE* 3.1 9.7 + - - +
653H LEU* 1.3 77.8 - - - +
655H GLU* 1.3 64.9 + - - +
658H PHE* 2.9 39.2 + - + -
678H VAL* 4.1 7.9 - - + -
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Residues in contact with GLU 655 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651H PHE 3.0 11.8 + - - +
652H SER 3.4 11.4 - - - +
653H LEU 3.2 0.4 - - - -
654H ALA* 1.3 76.7 - - - +
656H MET* 1.3 57.1 + - - +
658H PHE* 4.0 3.0 - - - +
659H GLN* 2.9 34.0 + - - +
675H ILE* 4.9 7.1 - - + +
678H VAL* 3.6 15.6 - - + +
679H GLN* 3.5 35.0 + - + +
682H LEU* 3.1 13.8 - - + +
684H LYS* 2.2 36.8 + - - -
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Residues in contact with MET 656 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652H SER 3.4 4.8 + - - +
653H LEU* 3.0 15.3 + - - +
655H GLU* 1.3 80.3 - - - +
657H HIS* 1.3 66.5 + - + +
659H GLN* 3.4 6.8 + - - +
660H LYS* 2.9 54.8 + - - +
496K GLU* 6.3 0.2 - - - -
499K VAL* 4.4 5.8 - - + -
523K ILE* 3.2 50.7 - - + +
526K TYR* 3.2 51.1 - - + -
527K ILE* 4.6 11.2 - - + -
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Residues in contact with HIS 657 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638H TRP* 3.7 22.7 - - + +
641H LEU* 4.3 4.4 - - + +
642H GLY* 3.8 20.6 - - - +
645H TYR* 3.1 40.2 - + - -
653H LEU* 2.9 33.3 + - - +
654H ALA* 4.4 0.7 - - - -
656H MET* 1.3 76.8 - - + +
658H PHE* 1.3 63.0 + - - +
660H LYS* 3.1 32.0 + - - +
661H ALA* 3.0 20.3 + - - +
503K HIS* 3.2 29.1 - + - -
523K ILE* 4.1 18.1 - - + +
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Residues in contact with PHE 658 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639H TYR* 3.3 52.3 - + - -
642H GLY* 3.5 10.8 - - - -
643H MET* 3.5 27.8 - - + -
646H TYR* 4.6 5.8 - + + -
654H ALA* 2.9 32.7 + - + +
655H GLU* 4.0 1.3 - - - +
657H HIS* 1.3 74.7 - - - +
659H GLN* 1.3 57.5 + - - +
661H ALA* 2.9 7.4 + - - +
662H LEU* 2.8 27.7 + - - +
671H LEU* 4.2 9.2 - - + +
674H HIS* 4.2 20.4 - - + -
675H ILE* 3.7 22.3 - - + +
678H VAL* 3.8 26.9 - - + -
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Residues in contact with GLN 659 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655H GLU* 2.9 22.9 + - + +
656H MET* 3.6 8.5 - - - +
658H PHE* 1.3 75.3 - - - +
660H LYS* 1.3 61.4 + - - +
662H LEU* 3.2 19.9 + - - +
663H ASP* 3.0 31.5 + - - +
675H ILE* 3.9 25.9 - - + +
679H GLN* 5.3 3.2 - - - +
526K TYR* 6.4 2.2 - - + -
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Residues in contact with LYS 660 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638H TRP* 3.6 35.6 - - + -
656H MET* 2.9 41.0 + - - +
657H HIS* 3.1 34.6 + - - +
659H GLN* 1.3 75.3 - - - +
661H ALA* 1.3 62.2 + - - +
663H ASP* 3.4 16.5 + - - +
664H ILE* 3.4 20.2 + - + +
496K GLU* 5.8 8.7 - - + +
499K VAL* 3.1 36.4 - - - +
500K ASP 5.3 0.2 - - - +
526K TYR* 5.1 12.3 - - + +
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Residues in contact with ALA 661 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635H TYR* 4.2 7.7 - - + +
638H TRP* 3.8 21.7 - - + +
639H TYR 3.8 11.2 - - - +
657H HIS 3.0 11.1 + - - +
658H PHE* 2.9 11.1 + - - +
660H LYS* 1.3 78.4 - - - +
662H LEU* 1.3 62.9 + - - +
664H ILE* 3.2 9.3 + - - +
665H ASN* 3.1 19.4 + - - +
671H LEU* 3.9 25.5 - - + +
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Residues in contact with LEU 662 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658H PHE 2.8 9.4 + - - +
659H GLN* 3.2 23.3 + - - +
661H ALA* 1.3 72.9 - - - +
663H ASP* 1.3 62.3 + - - +
665H ASN 3.3 7.0 - - - +
666H PRO* 3.2 40.4 - - + +
668H SER 4.1 2.2 - - - +
671H LEU* 3.8 23.5 - - + +
672H LEU* 3.6 35.7 - - + -
675H ILE* 3.7 27.6 - - + -
694H LYS* 5.1 6.7 - - - +
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Residues in contact with ASP 663 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659H GLN* 3.0 20.4 + - - +
660H LYS* 3.4 13.9 - - - +
662H LEU* 1.3 79.4 - - - +
664H ILE* 1.3 61.8 + - + +
666H PRO* 4.5 7.3 - - - +
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Residues in contact with ILE 664 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478H SER 4.1 3.8 - - - +
479H TYR* 3.4 25.6 - - + -
632H PRO 4.5 6.1 - - - +
633H ARG* 3.6 45.6 + - + +
635H TYR* 3.8 19.7 - - + -
638H TRP* 3.2 38.4 - - + +
660H LYS* 3.4 15.5 - - + +
661H ALA* 3.2 5.9 + - - +
663H ASP* 1.3 80.0 - - + +
665H ASN* 1.3 57.0 + - - +
666H PRO* 3.5 7.0 - - - +
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Residues in contact with ASN 665 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479H TYR* 3.5 29.9 - - + +
511H GLU* 4.3 9.7 + - - +
635H TYR* 3.3 40.1 + - + -
661H ALA 3.1 8.5 + - - +
662H LEU* 3.3 13.2 - - - +
664H ILE* 1.3 77.1 - - - +
666H PRO* 1.3 68.0 - - - +
667H GLN* 3.2 22.7 + - - +
668H SER* 2.8 34.5 + - - +
671H LEU* 4.3 1.0 - - + +
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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
------------------------------------------------------------
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