Contacts of the strand formed by residues 537 - 544 (chain G) in PDB entry 3HR4
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 VAL 537 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535G SER 4.0 0.8 + - - -
536G ARG* 1.3 71.7 - - + +
538G ARG* 1.3 67.0 + - - +
539G VAL* 4.9 0.4 - - + -
564G ALA 4.1 8.3 - - - +
565G PHE* 3.1 64.4 - - + +
566G ASN 3.3 3.2 + - - -
584G ARG* 3.2 51.6 - - + +
585G LEU* 6.2 0.7 - - + -
684G PHE* 4.2 8.1 - - + +
686G VAL* 6.4 0.9 - - + -
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Residues in contact with ARG 538 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536G ARG 3.5 7.2 + - - +
537G VAL* 1.3 81.1 - - - +
539G VAL* 1.3 67.0 + - - +
540G THR* 6.0 0.4 - - - +
566G ASN* 3.5 40.9 - - - +
568G LYS* 6.5 0.2 - - - -
583G GLU* 5.0 9.0 - - + -
584G ARG* 4.3 17.3 + - + +
585G LEU 4.3 3.1 + - - +
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Residues in contact with VAL 539 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537G VAL* 4.9 0.2 - - + -
538G ARG* 1.3 83.0 - - - +
540G THR* 1.3 68.1 + - - +
541G ILE* 4.0 11.4 - - + -
561G PHE* 3.9 25.1 - - + -
565G PHE* 3.5 35.2 - - + -
566G ASN 3.5 6.9 + - - +
567G PRO* 3.3 12.7 - - + +
568G LYS* 3.2 23.0 + - - +
583G GLU* 3.8 4.0 - - - -
585G LEU* 3.9 17.3 - - + +
587G LEU* 3.9 19.3 - - + -
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Residues in contact with THR 540 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538G ARG* 6.0 0.5 - - - +
539G VAL* 1.3 76.4 + - - +
541G ILE* 1.3 62.5 + - - +
542G LEU* 3.4 25.1 + - + -
568G LYS* 3.8 5.3 - - + +
570G VAL* 4.2 16.8 - - + -
575G TYR* 3.9 17.7 + - + -
583G GLU* 2.5 40.0 + - - -
585G LEU 3.6 0.2 + - - -
586G LEU* 3.4 5.7 - - - +
587G LEU 2.9 26.2 + - - +
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Residues in contact with ILE 541 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539G VAL* 4.0 5.4 - - + -
540G THR* 1.3 74.5 - - - +
542G LEU* 1.3 65.5 + - - +
554G ALA* 4.0 26.5 - - + +
557G LEU* 3.9 20.6 - - + +
558G GLY* 3.5 34.5 - - - +
561G PHE* 4.6 1.3 - - + -
567G PRO* 3.9 16.8 - - + -
568G LYS 2.8 13.8 + - - +
569G VAL* 3.3 11.1 - - + +
570G VAL 2.8 28.9 + - - +
587G LEU* 3.3 33.9 - - + +
589G VAL* 4.9 1.6 - - + -
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Residues in contact with LEU 542 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540G THR* 3.4 30.5 - - + +
541G ILE* 1.3 74.8 - - - +
543G PHE* 1.3 60.9 + - - +
570G VAL* 3.0 14.8 - - + +
571G CYS 4.9 2.0 - - - +
572G MET* 4.4 13.7 - - + -
575G TYR* 4.2 37.2 - - + -
580G LEU* 5.4 0.4 - - + -
586G LEU* 3.7 24.5 - - + -
587G LEU 2.8 16.6 + - - +
588G VAL* 3.4 14.2 - - + +
589G VAL* 3.0 25.8 + - - +
605G LEU* 4.8 15.0 - - + -
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Residues in contact with PHE 543 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542G LEU* 1.3 75.0 - - - +
544G ALA* 1.3 68.4 + - - +
545G THR* 4.1 10.5 - - + -
550G SER 3.9 2.5 - - - +
551G GLU* 2.8 51.6 - - - -
554G ALA* 3.6 21.5 - - + -
555G TRP* 4.3 5.8 - + - -
569G VAL* 3.9 20.9 - - + -
570G VAL 3.1 25.4 + - - -
571G CYS* 3.3 44.6 - - + -
572G MET* 3.1 28.1 + - - +
589G VAL 3.1 13.5 - - - +
601G ASN* 4.8 2.7 - - - -
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Residues in contact with ALA 544 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543G PHE* 1.3 75.8 - - - +
545G THR* 1.3 61.8 + - - +
550G SER* 3.3 15.6 - - - -
572G MET* 3.2 32.8 - - + -
589G VAL 3.4 4.2 + - - -
590G THR* 3.3 8.5 - - - +
591G SER* 3.4 14.4 + - - -
599G PRO* 4.3 10.1 - - + -
601G ASN* 4.0 5.6 - - + -
602G GLY* 4.1 18.2 - - - +
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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