Contacts of the helix formed by residues 619 - 625 (chain A) in PDB entry 5M64
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 ALA 619 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A THR* 4.1 7.2 - - + -
617A HIS* 3.0 16.4 + - + +
618A TYR* 1.3 77.1 - - - +
620A ASN* 1.3 63.9 + - - +
621A THR 3.4 0.7 - - - -
622A GLY* 3.5 10.3 + - - +
623A ALA* 3.8 8.3 + - - +
666A VAL 4.8 0.5 - - - +
667A ARG* 3.3 48.3 - - + +
668A GLY* 4.2 15.9 - - - +
669A LEU* 6.0 0.9 - - + -
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Residues in contact with ASN 620 (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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492A THR* 5.6 3.1 - - + +
495A ILE* 5.9 0.4 - - - +
589A MET* 4.8 1.8 - - - -
601A MET* 3.6 17.8 - - - +
603A HIS* 3.7 26.8 + - + -
616A LEU* 3.4 21.4 - - + +
617A HIS* 3.7 22.0 + - + +
618A TYR 3.5 0.6 - - - -
619A ALA* 1.3 76.5 - - - +
621A THR* 1.3 59.6 + - - +
623A ALA* 3.2 4.6 + - - +
624A TYR* 3.1 61.0 + - - +
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Residues in contact with THR 621 (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 ILE* 6.4 1.8 - - - -
616A LEU* 5.7 4.3 - - - +
617A HIS 3.9 10.3 + - - +
618A TYR* 3.3 22.4 - - - +
620A ASN* 1.3 78.6 - - - +
622A GLY* 1.3 59.0 + - - +
623A ALA 3.3 0.2 - - - -
624A TYR* 3.9 8.1 - - - +
625A ASN* 3.0 23.6 + - - -
626A ALA* 2.3 40.5 + - - +
627A ASP* 4.5 1.6 - - - -
628A PHE* 4.4 26.2 - - + -
633A MET* 6.2 2.0 - - - -
670A ILE* 5.9 4.9 - - + -
783B MET* 6.2 2.0 - - - -
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Residues in contact with GLY 622 (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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618A TYR 4.5 1.5 + - - -
619A ALA 3.5 8.0 + - - -
620A ASN 3.2 1.4 - - - -
621A THR* 1.3 84.9 - - - +
623A ALA* 1.3 59.8 + - - +
625A ASN* 3.7 8.7 + - - +
666A VAL* 4.7 14.6 - - - +
667A ARG* 6.3 0.7 - - - -
668A GLY 6.1 0.9 - - - -
670A ILE* 5.8 7.9 - - - -
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Residues in contact with ALA 623 (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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596A HIS* 3.0 28.5 + - - -
598A ALA* 4.0 24.0 - - + +
601A MET* 4.3 12.8 - - + -
619A ALA 3.8 6.5 + - - +
620A ASN* 3.2 9.6 + - - +
622A GLY* 1.3 77.7 - - - +
624A TYR* 1.3 63.9 + - - +
625A ASN* 3.2 2.1 + - - +
656A GLN 6.0 0.9 - - - +
666A VAL* 4.2 23.7 + - + +
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Residues in contact with TYR 624 (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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589A MET* 3.6 14.4 + - + +
591A ARG* 4.0 35.0 + - + +
596A HIS* 4.8 5.3 + - - -
598A ALA 3.3 23.3 - - - -
599A SER* 3.7 25.8 + - - +
600A MET 3.9 0.2 - - - -
601A MET* 3.3 37.0 + - + +
603A HIS* 4.1 0.7 + - - -
620A ASN* 3.1 50.2 + - - +
621A THR* 4.3 2.7 - - - +
623A ALA* 1.3 74.8 - - - +
625A ASN* 1.3 68.1 + - - +
626A ALA* 3.2 9.3 + - + +
633A MET* 3.6 35.9 - - + -
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Residues in contact with ASN 625 (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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591A ARG* 4.6 8.2 + - - +
596A HIS* 5.2 5.6 - - + +
621A THR 3.0 10.3 + - - -
622A GLY* 3.7 7.2 + - - +
623A ALA 3.2 6.5 - - - +
624A TYR* 1.3 77.7 - - - +
626A ALA* 1.3 60.0 + - - +
627A ASP* 4.7 5.6 - - - +
1195A GLU* 5.7 3.4 + - - -
1198A THR* 5.5 9.1 - - - +
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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