Contacts of the helix formed by residues 547 - 558 (chain E) in PDB entry 3LVQ
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 547 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544E CYS 4.6 4.7 + - - +
545E THR* 2.6 59.6 + - + +
548E PRO* 1.3 75.1 - - + +
549E GLN* 3.0 45.6 + - - +
550E ARG* 3.6 37.0 + - + +
551E LEU* 3.7 12.8 + - - +
566E ALA* 6.0 0.5 - - - +
571E GLN* 2.9 24.9 + - - +
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Residues in contact with PRO 548 (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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545E THR* 5.0 4.0 - - + -
547E GLU* 1.3 93.5 - - + +
549E GLN* 1.3 61.9 + - - +
551E LEU* 3.9 1.0 + - + -
552E TRP* 3.8 15.1 + - - +
571E GLN* 4.3 4.0 - - - +
577E LEU* 3.9 36.3 - - + +
578E PRO* 4.5 21.5 - - + +
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Residues in contact with GLN 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 GLU* 3.0 23.2 + - - +
548E PRO* 1.3 80.6 - - - +
550E ARG* 1.3 72.3 + - + +
551E LEU 3.2 0.2 + - - -
552E TRP* 3.2 10.6 + - - +
553E THR* 3.0 35.7 + - - +
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Residues in contact with ARG 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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544E CYS* 3.3 40.8 + - - +
547E GLU* 3.6 32.7 + - + +
549E GLN* 1.3 84.5 - - + +
551E LEU* 1.3 53.8 + - - +
553E THR* 3.0 9.8 + - - -
554E ALA* 2.6 38.4 + - + +
562E SER* 5.9 6.1 - - - -
565E GLU* 5.2 10.3 + - - -
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Residues in contact with LEU 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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547E GLU 3.7 13.1 + - - +
548E PRO 4.2 0.7 - - - +
549E GLN 3.2 0.8 + - - -
550E ARG* 1.3 78.9 - - - +
552E TRP* 1.3 61.5 + - - +
554E ALA* 4.4 3.4 - - + -
555E ILE* 3.1 46.1 + - + +
562E SER 5.2 0.2 - - - +
563E VAL* 4.3 18.8 - - + -
566E ALA* 3.8 25.4 - - + -
571E GLN* 3.4 24.9 - - + +
573E PHE* 4.2 20.4 - - + -
577E LEU* 3.9 13.2 - - + -
589E VAL* 3.8 28.0 - - + -
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Residues in contact with TRP 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 PRO 3.8 8.1 + - - +
549E GLN* 3.2 9.9 + - - +
551E LEU* 1.3 78.3 - - - +
553E THR* 1.3 61.0 + - - +
555E ILE* 3.9 1.4 + - - +
556E CYS* 3.3 29.1 + - - -
577E LEU* 3.5 47.5 - - + +
578E PRO 4.2 7.2 - - - +
579E GLY* 3.7 16.6 - - - -
580E PRO* 3.7 25.5 - - + +
587E GLU* 4.0 33.0 - - + -
588E LEU 6.2 0.9 - - - -
592E LEU* 3.7 42.1 - - + +
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Residues in contact with THR 553 (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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549E GLN* 3.0 31.6 + - - +
550E ARG* 3.0 10.2 + - - -
552E TRP* 1.3 77.0 - - - +
554E ALA* 1.3 60.3 + - - +
556E CYS* 3.5 3.7 + - - +
557E ASN* 2.9 50.3 + - - +
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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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550E ARG* 2.6 21.1 + - + +
551E LEU* 3.9 5.8 - - - +
553E THR* 1.3 70.6 - - - +
555E ILE* 1.3 64.0 + - - +
557E ASN* 3.2 4.5 + - - +
558E ARG 2.9 4.0 + - - -
559E ASP* 2.8 43.4 + - + +
562E SER* 3.8 29.4 - - - -
563E VAL* 4.3 10.5 - - + +
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Residues in contact with ILE 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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551E LEU* 3.1 30.9 + - + +
552E TRP 4.0 3.8 - - - +
554E ALA* 1.3 77.1 - - - +
556E CYS* 1.3 57.6 + - - +
558E ARG* 2.9 24.1 + - - +
563E VAL* 4.3 14.8 - - + -
577E LEU* 5.4 1.6 - - + -
589E VAL* 3.8 33.2 - - + +
592E LEU* 4.1 24.9 - - + -
593E ALA* 3.8 33.0 - - + -
596E VAL* 4.1 8.9 - - + +
601E SER* 5.0 3.1 + - - +
604E LEU* 3.7 16.6 - - + +
608E ILE* 4.9 4.9 - - + -
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Residues in contact with CYS 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 TRP* 3.3 26.2 + - - +
553E THR* 3.5 3.9 + - - +
554E ALA 3.4 0.2 - - - -
555E ILE* 1.3 72.8 - - - +
557E ASN* 1.3 59.7 + - - +
558E ARG* 3.0 29.3 + - - +
592E LEU* 4.1 16.4 - - - -
596E VAL* 3.9 30.7 - - + -
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Residues in contact with ASN 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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553E THR* 2.9 41.0 + - - +
554E ALA* 3.2 9.7 + - - +
556E CYS* 1.3 75.0 - - - +
558E ARG* 1.3 73.2 + - - +
559E ASP* 4.2 10.3 - - + +
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Residues in contact with ARG 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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555E ILE 2.9 18.0 + - - +
556E CYS* 3.4 20.3 + - - +
557E ASN* 1.3 87.7 - - - +
559E ASP* 1.3 58.2 + - - +
560E LEU* 3.3 7.9 + - - +
596E VAL* 4.0 16.5 + - - +
598E ASN* 3.1 33.3 + - - +
600E ALA* 5.1 7.6 - - + +
601E SER* 4.0 29.4 - - - +
604E LEU* 4.0 13.0 - - + +
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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
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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