Contacts of the helix formed by residues 538 - 544 (chain A) in PDB entry 3EA4
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 ASP 538 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537A GLY* 1.3 71.9 - - - -
539A GLY* 1.3 61.5 + - - +
541A PHE* 4.5 0.4 - - - -
542A ILE* 3.5 23.7 + - - +
562A LEU* 3.7 11.0 - - + +
563A LEU 3.9 2.0 + - - -
564A ASN* 3.4 30.1 - - - +
565A ASN* 3.2 9.5 + - - +
566A GLN* 3.3 24.4 + - - +
567A HIS 3.5 0.3 - - - +
588A LEU* 3.4 18.3 - - - +
598A PHE 5.0 2.1 - - - +
599A PRO* 5.7 1.4 - - - +
601A MET* 3.8 20.9 - - + +
698A TDM 3.2 0.9 + - - -
699A MG 2.4 30.8 - - - -
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Residues in contact with GLY 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A MET* 3.5 13.3 - - - +
538A ASP* 1.3 79.9 - - - +
540A SER* 1.3 61.6 + - - +
542A ILE* 3.4 20.1 - - - +
543A MET* 3.5 13.0 - - - +
568A LEU* 4.2 2.9 - - - -
588A LEU* 3.4 21.8 - - - -
698A TDM 3.1 13.3 + - - -
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Residues in contact with SER 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A GLY* 3.9 6.3 - - - -
485A VAL 3.4 19.2 + - - -
488A HIS* 3.8 0.5 - - - -
513A MET* 3.5 19.4 - - - +
514A GLY* 3.3 34.9 - - - +
536A ASP* 3.3 18.2 - - - -
537A GLY 3.3 1.3 + - - -
539A GLY* 1.3 71.1 - - - +
541A PHE* 1.3 67.4 + - - +
543A MET* 3.1 11.8 + - - +
698A TDM 2.6 25.3 + - - -
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Residues in contact with PHE 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A LEU* 3.9 25.6 - - + +
534A ASP* 4.3 1.8 - - - -
536A ASP* 3.4 22.6 + - + +
537A GLY 2.8 22.6 + - - +
538A ASP 4.3 2.0 - - - +
540A SER* 1.3 74.0 - - - +
542A ILE* 1.3 65.9 + - - +
543A MET 3.2 1.2 + - - -
544A ASN* 3.5 3.6 + - - +
545A VAL* 3.3 33.9 + - + -
548A LEU* 3.8 29.4 - - + -
560A VAL* 3.8 25.6 - - + -
562A LEU* 3.8 18.4 - - + -
601A MET* 4.0 33.9 - - + -
604A PHE* 5.0 2.7 - - + -
636A LEU* 4.4 12.8 - - + -
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Residues in contact with ILE 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A ASP 3.5 13.3 + - - +
539A GLY* 3.4 15.3 - - - +
541A PHE* 1.3 80.7 - - - +
543A MET* 1.3 68.4 + - + +
544A ASN 3.2 0.2 - - - -
545A VAL* 3.3 31.2 + - + +
546A GLN* 5.3 0.2 - - - +
588A LEU* 6.3 1.3 - - + -
599A PRO* 3.8 29.2 - - + -
601A MET* 4.4 7.2 - - + -
604A PHE* 3.9 20.6 - - + -
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Residues in contact with MET 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A GLN* 4.8 12.0 + - - +
513A MET* 3.5 45.5 - - + +
514A GLY* 4.0 6.5 - - - -
539A GLY 3.5 12.8 - - - +
540A SER 3.1 10.3 + - - +
542A ILE* 1.3 81.7 - - + +
544A ASN* 1.3 66.5 - - - +
546A GLN* 3.8 6.1 - - - +
698A TDM 3.8 23.6 - - + +
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Residues in contact with ASN 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A HIS* 4.7 4.3 + - - +
145A GLN* 2.9 39.1 + - - +
146A GLY 4.3 4.8 + - - -
149A PHE* 4.0 4.6 - - - -
514A GLY* 2.7 36.8 + - - +
517A LEU* 3.6 8.1 - - + +
518A PRO* 4.3 14.1 - - + -
540A SER 4.0 1.2 + - - -
541A PHE 3.5 6.4 + - - +
542A ILE 3.2 0.2 - - - -
543A MET* 1.3 82.9 - - - +
545A VAL* 1.3 63.6 + - - +
546A GLN* 3.1 26.3 + - - +
547A GLU* 3.1 19.8 + - + +
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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