Contacts of the helix formed by residues 605 - 611 (chain A) in PDB entry 2MYS
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 605 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A ARG 5.8 0.2 - - - -
603A LEU 2.8 23.2 + - - +
604A ASN* 1.3 72.4 - - - +
606A THR* 1.3 62.2 + - - +
607A VAL 3.3 0.2 - - - -
608A ILE* 3.7 9.0 - - + +
609A GLY* 3.1 17.5 + - - -
626A TYR* 3.8 34.9 + - + -
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Residues in contact with THR 606 (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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400A ALA* 3.0 33.7 - - + -
403A TYR 5.4 0.2 - - - +
404A PRO* 4.0 1.6 - - - +
405A ARG* 3.1 52.3 + - + +
604A ASN* 2.9 10.2 + - - -
605A GLU* 1.3 74.9 - - - +
607A VAL* 1.3 60.9 + - - +
609A GLY* 2.9 20.8 + - - -
610A LEU* 3.3 13.6 + - + +
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Residues in contact with VAL 607 (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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361A TYR* 5.3 0.2 - - - +
397A LEU* 3.9 20.0 - - + -
400A ALA* 3.8 13.0 - - + -
401A LEU* 3.4 23.3 - - + -
429A LEU* 4.2 11.7 - - + -
604A ASN* 2.8 33.9 + - - +
606A THR* 1.3 72.0 - - - +
608A ILE* 1.3 55.3 + - - +
609A GLY 2.8 4.9 - - - -
610A LEU* 2.7 33.0 + - + +
611A TYR* 3.0 40.0 + - + +
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Residues in contact with ILE 608 (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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429A LEU* 4.2 9.9 - - + -
603A LEU* 3.8 30.5 - - + -
604A ASN 3.2 18.6 + - - +
605A GLU* 3.7 11.2 - - + +
607A VAL* 1.3 74.1 - - - +
609A GLY* 1.3 63.8 + - - +
611A TYR* 3.0 9.9 + - + +
612A GLN* 2.8 29.6 + - - +
623A PHE* 3.7 46.0 - - + -
626A TYR* 4.4 26.9 - - + -
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Residues in contact with GLY 609 (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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605A GLU 3.1 10.2 + - - -
606A THR 2.9 10.9 + - - -
607A VAL 2.8 1.4 - - - -
608A ILE* 1.3 76.2 - - - +
610A LEU* 1.3 55.8 + - - +
612A GLN* 2.8 42.2 + - - +
613A MLY 3.2 19.5 + - - +
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Residues in contact with LEU 610 (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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392A LEU* 3.9 21.6 - - + +
393A ASN 5.3 0.7 - - - +
396A GLU* 3.8 29.6 - - + +
397A LEU* 3.6 38.1 - - + +
400A ALA* 4.2 9.9 - - + -
606A THR* 3.5 16.8 - - + +
607A VAL* 2.7 18.3 + - - +
609A GLY* 1.3 73.1 - - - -
611A TYR* 1.3 64.9 + - + +
613A MLY 3.0 30.8 + - + +
614A SER* 3.2 10.0 + - - -
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Residues in contact with TYR 611 (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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361A TYR* 3.0 37.1 + - - -
390A MET* 4.2 7.0 - - + -
392A LEU* 4.0 16.8 - - + -
429A LEU* 3.6 21.9 - - + +
433A VAL* 3.7 14.2 - - + +
607A VAL* 3.0 32.0 + - + +
608A ILE* 3.0 14.6 + - - +
610A LEU* 1.3 75.9 - - - +
612A GLN* 1.3 60.6 + - - +
613A MLY 2.8 7.1 + - - -
614A SER* 2.8 19.8 + - - -
619A LEU* 3.9 24.0 - - + -
620A ALA* 3.5 10.6 - - - -
623A PHE* 3.2 48.2 - + + -
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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