Contacts of the helix formed by residues 582 - 597 (chain H) in PDB entry 5G04
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 582 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577H PHE* 3.3 18.3 + - + +
580H GLN* 2.9 16.9 + - + +
581H ARG* 1.3 73.9 - - - +
583H HIS* 1.3 63.1 + - - +
584H ASP* 3.3 14.3 - - - +
585H ILE* 3.3 36.8 + - + +
586H ALA 3.2 15.8 + - - -
18L ARG* 4.6 25.8 + - + +
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Residues in contact with HIS 583 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578H SER 4.2 4.9 + - - -
581H ARG* 3.0 42.9 + - + +
582H GLU* 1.3 71.8 - - - +
584H ASP* 1.3 71.3 + - - +
586H ALA* 3.1 4.4 + - - +
587H ILE* 2.9 30.6 + - + +
610H GLU* 3.0 29.4 - - - +
613H LEU* 3.6 43.4 + - + +
614H THR* 3.8 29.7 - - + +
23L ARG* 5.7 6.1 - - - -
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Residues in contact with ASP 584 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581H ARG 5.4 0.2 - - - +
582H GLU* 4.4 9.5 - - - +
583H HIS* 1.3 83.2 + - - +
585H ILE* 1.3 65.6 + - + +
587H ILE* 3.4 15.4 + - - +
588H LYS* 3.5 19.5 + - - +
614H THR* 5.5 8.1 - - - +
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Residues in contact with ILE 585 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E VAL* 3.5 38.8 - - + -
577H PHE* 3.5 31.6 - - + -
582H GLU* 3.3 42.0 + - + +
583H HIS 3.3 0.4 - - - -
584H ASP* 1.3 75.8 - - + +
586H ALA* 1.3 64.7 + - - +
587H ILE 3.5 0.2 + - - -
588H LYS* 3.6 8.7 + - - +
589H PHE* 3.3 25.9 + - + -
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Residues in contact with ALA 586 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574H GLY 3.6 9.0 - - - +
577H PHE* 3.7 8.7 - - - +
578H SER* 3.5 35.0 - - - +
582H GLU 3.2 9.7 + - - +
583H HIS 3.1 9.8 + - - +
585H ILE* 1.3 75.6 - - - +
587H ILE* 1.3 57.7 + - - +
589H PHE* 3.4 6.9 + - - +
590H PHE* 2.9 38.5 + - + -
610H GLU* 4.1 8.5 - - - +
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Residues in contact with ILE 587 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583H HIS* 2.9 24.3 + - + +
584H ASP* 3.6 9.9 - - - +
585H ILE 3.3 0.2 - - - -
586H ALA* 1.3 73.2 - - - +
588H LYS* 1.3 60.6 + - - +
590H PHE* 3.3 1.4 + - - +
591H GLN* 2.8 59.6 + - - +
607H LEU* 3.9 16.4 - - + -
610H GLU* 3.8 23.3 - - + -
611H PHE* 4.0 23.6 - - + -
614H THR* 3.7 24.9 - - + +
616H GLU* 4.6 4.3 - - - +
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Residues in contact with LYS 588 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E VAL* 3.9 22.2 - - + +
89E LEU* 3.4 23.4 - - + +
90E GLU* 3.6 28.9 - - - +
93E GLU* 5.4 1.8 - - - -
584H ASP 3.5 17.2 + - - +
585H ILE* 3.6 13.5 - - - +
587H ILE* 1.3 77.2 - - - +
589H PHE* 1.3 62.3 + - + +
591H GLN* 3.6 18.8 + - - +
592H ARG* 3.0 28.1 + - - +
595H GLN* 4.4 0.2 - - - +
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Residues in contact with PHE 589 (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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82E LEU* 4.0 20.0 - - + -
85E LEU* 3.6 26.5 - - + -
86E VAL* 3.8 25.6 - - + -
89E LEU* 3.8 21.1 - - + -
570H TRP* 3.5 37.6 - + - +
573H ALA* 3.5 30.3 - - + -
574H GLY* 3.8 13.2 - - - +
577H PHE* 4.2 11.2 - + - -
585H ILE* 3.3 19.7 - - + +
586H ALA 3.4 8.9 + - - +
587H ILE 3.3 0.2 - - - -
588H LYS* 1.3 80.5 - - + +
590H PHE* 1.3 58.2 + - - +
592H ARG* 3.2 4.6 - - - +
593H ALA* 3.0 22.5 + - - +
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Residues in contact with PHE 590 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571H CYS* 3.5 36.3 - - - -
574H GLY* 3.3 29.2 - - - -
575H ASN* 3.5 18.8 - - - -
578H SER* 4.3 4.0 - - - -
586H ALA* 2.9 24.3 + - + +
587H ILE 3.7 3.6 - - - +
589H PHE* 1.3 73.3 - - - +
591H GLN* 1.3 66.1 + - - +
592H ARG 3.0 1.1 - - - -
593H ALA* 3.0 20.9 + - + +
594H ILE* 3.3 11.3 + - - +
603H ALA 4.6 3.3 - - - +
606H LEU* 3.5 33.9 - - + -
607H LEU* 3.8 21.5 - - + -
610H GLU* 3.7 32.1 - - + -
184L ARG* 5.9 0.7 - - - -
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Residues in contact with GLN 591 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E LEU* 6.0 0.2 - - - +
99E ILE* 3.3 45.3 - - + +
102E LEU* 4.9 0.5 - - - +
587H ILE* 2.8 41.1 + - - +
588H LYS* 3.7 18.5 + - - +
590H PHE* 1.3 71.0 - - - +
592H ARG* 1.3 52.0 + - - +
594H ILE* 3.3 14.4 - - - +
595H GLN* 2.7 49.3 + - - +
607H LEU* 3.9 16.1 - - + +
611H PHE* 4.3 10.5 - - - -
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Residues in contact with ARG 592 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E GLU* 4.3 4.6 + - - -
89E LEU* 3.5 46.4 + - + +
92E ASP* 3.2 38.8 + - - +
93E GLU* 5.4 0.2 - - - +
96E PHE* 3.3 29.7 - - - -
565H ASN* 5.1 3.8 + - - -
570H TRP* 3.9 35.3 - - + +
588H LYS 3.0 15.1 + - - +
589H PHE* 3.2 14.8 - - - +
591H GLN* 1.3 74.2 - - - +
593H ALA* 1.3 52.6 + - - +
595H GLN* 3.0 27.0 + - - +
596H VAL* 2.6 42.7 + - - +
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Residues in contact with ALA 593 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567H PRO* 3.5 30.6 - - - +
570H TRP* 3.8 16.7 - - + +
571H CYS* 4.0 11.9 - - + +
589H PHE 3.0 8.9 + - - +
590H PHE* 3.2 12.1 - - + +
592H ARG* 1.3 72.2 - - - +
594H ILE* 1.3 53.8 + - - +
596H VAL* 2.9 24.2 + - - +
597H ASP 2.9 13.8 + - - +
603H ALA* 4.1 16.2 - - + -
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Residues in contact with ILE 594 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E LEU* 3.6 22.4 - - + -
103E LEU* 4.7 4.7 - - + -
590H PHE 3.3 6.2 + - - +
591H GLN* 3.3 8.1 - - - +
593H ALA* 1.3 76.8 - - - +
595H GLN* 1.3 63.8 + - - +
597H ASP 2.9 28.1 - - - -
598H PRO* 3.0 7.9 - - + +
603H ALA* 3.8 23.3 - - + +
604H TYR* 3.4 61.7 - - + +
607H LEU* 3.8 31.2 - - + -
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Residues in contact with GLN 595 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E LEU* 4.9 5.3 + - - +
93E GLU* 4.6 17.4 + - - +
96E PHE* 3.7 37.3 - - + +
97E LYS* 4.1 15.1 + - - +
99E ILE* 4.2 12.7 - - + +
102E LEU* 4.1 22.0 - - + -
588H LYS 4.4 1.7 - - - +
591H GLN* 2.7 44.1 + - - +
592H ARG* 3.0 35.5 + - - +
594H ILE* 1.3 72.6 - - - +
596H VAL* 1.3 63.5 + - - +
598H PRO* 4.4 7.4 - - - +
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Residues in contact with VAL 596 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E PHE* 4.4 24.8 - - + -
565H ASN* 3.7 30.5 - - + -
566H SER* 3.7 21.1 - - - +
567H PRO* 4.0 1.8 - - + -
570H TRP* 4.0 23.8 - - + +
592H ARG* 2.6 24.4 + - - +
593H ALA 2.9 8.4 + - - +
595H GLN* 1.3 76.2 - - - +
597H ASP* 1.3 57.9 - - + +
598H PRO* 3.8 4.9 - - - +
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Residues in contact with ASP 597 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567H PRO* 3.9 28.7 - - + +
593H ALA 2.9 10.3 + - - +
594H ILE* 2.9 16.3 - - - +
596H VAL* 1.3 75.9 - - + +
598H PRO* 1.3 65.5 - - - +
599H ASN* 2.8 37.6 + - - +
600H TYR* 3.4 30.0 + - - +
603H ALA* 5.2 0.3 - - - +
604H TYR* 4.7 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
------------------------------------------------------------
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