Contacts of the strand formed by residues 585 - 591 (chain E) 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 LEU 585 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537E VAL* 5.3 0.2 - - + -
538E ARG 4.8 1.4 + - - -
539E VAL* 3.4 36.9 - - + +
540E THR 3.3 23.4 + - - -
561E PHE* 3.7 22.2 - - + -
565E PHE* 5.2 0.4 - - + -
583E GLU* 3.7 3.4 - - - +
584E ARG* 1.3 82.4 - - + +
586E LEU* 1.3 60.1 + - - +
587E LEU* 4.3 11.2 - - + -
619E PHE* 4.5 0.2 - - - +
620E ARG* 3.5 33.4 + - + -
621E TYR* 3.8 7.0 - - - +
653E LEU* 4.5 15.5 - - + -
680E ALA* 4.1 16.8 - - + -
684E PHE* 4.3 13.9 - - + -
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Residues in contact with LEU 586 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540E THR* 3.1 44.2 - - + +
542E LEU* 4.2 24.2 - - + -
575E TYR* 4.5 5.8 - - + +
580E LEU* 4.9 12.3 - - + -
583E GLU* 3.9 15.5 - - + +
585E LEU* 1.3 73.4 - - - +
587E LEU* 1.3 64.8 + - - +
588E VAL* 4.3 14.4 - - + +
619E PHE* 3.9 23.1 - - + -
620E ARG 3.1 7.3 + - - -
621E TYR* 3.0 28.3 - - + +
622E ALA 3.2 4.3 + - - +
645E LEU* 5.4 10.3 - - + -
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Residues in contact with LEU 587 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539E VAL* 3.9 14.1 - - + -
540E THR 3.1 6.1 + - - +
541E ILE* 3.3 13.2 - - + +
542E LEU* 2.9 25.1 + - - +
557E LEU* 4.0 28.9 - - + -
561E PHE* 3.5 39.9 - - + -
585E LEU* 4.3 11.9 - - + -
586E LEU* 1.3 82.4 - - - +
588E VAL* 1.3 63.4 + - - +
622E ALA* 3.2 35.9 - - + +
653E LEU* 5.8 0.4 - - + -
672E TRP* 4.7 4.7 - - + -
676E THR* 4.4 7.4 - - + +
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Residues in contact with VAL 588 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542E LEU* 3.2 42.4 - - + +
572E MET* 4.6 14.4 - - + -
586E LEU* 4.3 12.3 - - + +
587E LEU* 1.3 75.6 - - - +
589E VAL* 1.3 65.6 + - - +
590E THR* 5.7 1.1 - - + -
622E ALA 3.4 4.6 + - - +
623E VAL* 3.3 33.9 - - + -
624E PHE* 2.9 28.7 + - - +
641E ILE* 3.7 16.8 - - + -
645E LEU* 5.3 3.6 - - + -
672E TRP* 4.7 2.0 - - - -
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Residues in contact with VAL 589 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541E ILE* 4.9 0.9 - - + -
542E LEU 3.1 6.5 + - - +
543E PHE* 3.2 25.8 - - - +
544E ALA 3.4 1.4 + - - -
550E SER* 3.5 24.3 - - - +
553E LEU* 4.0 13.2 - - + -
554E ALA* 4.3 14.6 - - + +
557E LEU* 4.1 25.4 - - + -
572E MET* 5.2 0.2 - - - -
588E VAL* 1.3 81.2 - - - +
590E THR* 1.3 61.0 + - - +
624E PHE* 3.1 19.5 - - + +
626E LEU* 3.6 26.0 - - + -
669E PHE* 4.9 5.4 - - + -
672E TRP* 5.0 0.4 - - + -
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Residues in contact with THR 590 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544E ALA* 2.9 25.6 - - - +
550E SER* 3.1 10.9 + - - -
572E MET* 3.6 18.4 - - + -
588E VAL* 5.7 2.0 - - + -
589E VAL* 1.3 76.1 - - - +
591E SER* 1.3 65.2 + - - +
592E THR* 5.3 0.2 + - - -
599E PRO* 3.4 3.1 - - - +
623E VAL* 5.7 0.7 - - + -
624E PHE 3.3 4.9 + - - +
625E GLY* 3.2 2.6 - - - -
626E LEU 2.7 29.8 + - - -
637E PHE* 3.4 20.2 - - + +
638E ALA* 4.1 25.8 - - + +
641E ILE* 5.0 5.6 - - + -
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Residues in contact with SER 591 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544E ALA 3.9 0.6 + - - -
545E THR* 3.9 1.2 - - - -
550E SER* 3.1 2.5 + - - -
590E THR* 1.3 78.9 + - - +
592E THR* 1.3 62.9 + - - +
593E PHE* 3.2 9.4 - - - -
597E ASP 4.1 0.2 - - - +
599E PRO* 2.9 43.4 - - - +
626E LEU* 3.2 9.9 - - - -
637E PHE* 4.1 2.3 - - - -
999E FMN 2.8 50.9 + - - -
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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