Contacts of the helix formed by residues 548 - 561 (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 GLY 548 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545E THR* 2.9 21.4 + - - +
546E GLU 3.5 2.6 + - - -
547E THR* 1.3 73.8 - - - +
549E LYS* 1.3 57.0 + - - -
550E SER 3.4 2.0 - - - -
551E GLU* 3.2 8.6 + - - +
552E ALA* 2.8 31.0 + - - +
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Residues in contact with LYS 549 (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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547E THR* 2.9 31.6 + - - +
548E GLY* 1.3 71.4 - - - -
550E SER* 1.3 55.8 + - - +
552E ALA* 3.1 7.0 + - - +
553E LEU* 2.9 35.5 + - + +
626E LEU* 3.4 14.8 - - + -
661E GLU* 2.9 31.3 + - - +
665E GLN* 4.0 13.0 - - - +
999E FMN 2.8 46.7 + - - +
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Residues in contact with SER 550 (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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543E PHE* 4.0 2.1 - - - +
544E ALA 3.1 25.4 - - - -
545E THR* 4.0 0.2 - - - -
549E LYS* 1.3 73.2 - - - +
551E GLU* 1.3 56.9 + - - +
554E ALA* 3.1 26.2 + - - +
589E VAL* 3.5 19.4 - - - +
590E THR 3.1 24.8 - - - -
591E SER* 3.1 1.4 + - - -
626E LEU* 3.2 19.8 - - - +
999E FMN 2.7 22.8 + - - -
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Residues in contact with GLU 551 (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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543E PHE* 3.0 43.1 - - + -
545E THR* 3.9 15.0 + - + +
548E GLY* 3.2 14.0 + - - +
549E LYS 3.1 0.4 - - - -
550E SER* 1.3 78.9 - - - +
552E ALA* 1.3 64.4 + - - +
554E ALA* 3.4 2.8 + - - +
555E TRP* 3.0 54.0 + - + -
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Residues in contact with ALA 552 (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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548E GLY 2.8 17.4 + - - +
549E LYS* 3.1 7.4 + - - +
551E GLU* 1.3 75.5 - - - +
553E LEU* 1.3 62.9 + - + +
555E TRP* 3.6 4.3 + - - +
556E ASP* 2.5 35.7 + - - +
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Residues in contact with LEU 553 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549E LYS* 2.9 16.1 + - + +
550E SER 4.0 3.1 - - - +
552E ALA* 1.3 75.4 - - + +
554E ALA* 1.3 60.7 + - - +
556E ASP* 3.1 11.3 + - - +
557E LEU* 2.8 24.4 + - - +
589E VAL* 4.0 4.7 - - + -
624E PHE* 4.5 4.3 - - + -
626E LEU* 3.5 45.1 - - + -
665E GLN* 5.1 7.0 - - + +
666E GLU* 3.2 28.5 - - - +
669E PHE* 3.3 46.4 - - + -
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Residues in contact with ALA 554 (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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541E ILE* 4.1 16.9 - - + +
543E PHE* 3.9 20.0 - - + -
550E SER 3.1 19.2 + - - +
551E GLU 3.6 6.1 - - - +
552E ALA 3.3 0.4 - - - -
553E LEU* 1.3 75.9 - - - +
555E TRP* 1.3 57.5 + - - +
557E LEU* 2.8 11.3 + - - +
558E GLY 2.7 25.5 + - - -
569E VAL* 3.8 16.5 - - + +
589E VAL* 4.3 10.1 - - + +
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Residues in contact with TRP 555 (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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543E PHE* 4.0 7.9 - + - -
551E GLU* 3.0 51.7 + - + +
552E ALA* 3.6 4.5 + - - +
554E ALA* 1.3 79.3 - - - +
556E ASP* 1.3 59.7 + - - +
558E GLY* 3.9 1.2 - - - -
559E ALA* 3.0 25.3 + - - +
569E VAL* 3.6 51.0 - - + +
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Residues in contact with ASP 556 (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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552E ALA* 2.5 24.3 + - - +
553E LEU* 3.1 16.1 + - - +
554E ALA 3.0 0.6 - - - -
555E TRP* 1.3 77.1 - - - +
557E LEU* 1.3 61.7 + - - +
559E ALA* 3.4 7.3 + - - +
560E LEU* 3.0 22.9 + - - +
666E GLU* 5.4 4.0 - - - +
669E PHE* 4.3 6.5 - - + -
697E LEU* 5.9 2.1 - - - +
698E TYR* 3.2 26.5 + - - +
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Residues in contact with LEU 557 (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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541E ILE* 4.0 17.9 - - + -
553E LEU 2.8 12.2 + - - +
554E ALA* 3.1 9.6 - - - +
556E ASP* 1.3 74.4 - - - +
558E GLY* 1.3 59.7 + - - +
560E LEU* 3.1 7.8 + - + +
561E PHE* 2.8 45.8 + - + +
587E LEU* 4.0 33.2 - - + -
589E VAL* 4.1 16.6 - - + -
669E PHE* 4.1 5.8 - - + -
672E TRP* 3.9 17.9 - - + -
673E ALA* 3.7 30.7 - - + -
676E THR* 4.8 1.1 - - + -
698E TYR* 5.0 0.2 - - - -
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Residues in contact with GLY 558 (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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541E ILE* 3.7 19.0 - - - +
554E ALA 2.7 12.8 + - - -
555E TRP* 3.6 4.0 + - - -
557E LEU* 1.3 77.5 - - - +
559E ALA* 1.3 54.9 + - - +
561E PHE* 3.3 2.8 + - - -
562E SER* 2.8 31.7 + - - -
567E PRO* 3.5 14.6 - - - +
569E VAL* 4.3 8.3 - - - -
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Residues in contact with ALA 559 (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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555E TRP 3.0 16.2 + - - +
556E ASP* 3.5 11.4 - - - +
558E GLY* 1.3 75.3 - - - +
560E LEU* 1.3 57.1 + - - +
562E SER* 2.6 36.1 + - - -
563E CYS* 3.7 5.2 + - - -
695E PRO* 5.9 4.5 - - + -
698E TYR* 6.3 0.7 - - + -
42F ASN* 4.6 1.4 - - - +
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Residues in contact with LEU 560 (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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556E ASP 3.0 10.2 + - - +
557E LEU* 3.1 12.8 + - + +
559E ALA* 1.3 78.8 - - - +
561E PHE* 1.3 58.0 + - + +
563E CYS* 3.2 26.9 + - - +
673E ALA* 3.8 41.7 - - + +
674E VAL* 4.2 5.2 - - - +
677E PHE* 3.6 33.5 - - + -
694E ILE* 3.9 20.6 - - + -
695E PRO* 5.0 5.3 - - + +
698E TYR* 3.9 32.7 + - + -
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Residues in contact with PHE 561 (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* 4.0 17.7 - - + -
541E ILE* 4.9 1.8 - - + -
557E LEU* 2.8 36.3 + - + +
558E GLY* 3.4 9.0 - - - +
560E LEU* 1.3 69.6 - - + +
562E SER* 1.3 57.2 + - - +
563E CYS 2.9 6.0 + - - -
564E ALA 3.3 1.0 + - - -
565E PHE* 2.9 49.8 + + + +
567E PRO* 4.5 9.4 - - + -
585E LEU* 3.7 19.3 - - + -
587E LEU* 3.5 30.3 - - + -
676E THR* 4.2 7.6 - - + -
677E PHE* 3.3 51.4 - + + -
680E ALA* 4.0 13.5 - - + -
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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