Contacts of the helix formed by residues 615 - 620 (chain N) in PDB entry 3AOI
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 ARG 615 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607N LEU 4.9 1.2 + - - +
608N SER 6.0 0.2 - - - -
609N GLY 3.9 13.4 + - - +
610N LYS* 3.2 46.1 + - - +
611N GLN* 5.8 0.4 - - - -
612N GLY 4.3 6.3 - - - +
613N ARG 3.2 1.0 - - - +
614N PHE* 1.3 76.8 - - - +
616N GLN* 1.3 62.6 + - - +
617N ASN 3.6 0.2 - - - -
618N LEU* 4.1 16.9 - - - +
619N LEU* 3.3 50.1 + - + +
1096N ARG* 5.5 9.5 - - - +
1439N SER* 3.9 23.2 + - - +
1440N PHE* 4.5 24.0 - - - -
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Residues in contact with GLN 616 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017M THR* 5.0 15.6 + - - +
1019M GLN* 5.1 4.8 - - - +
1058M ASP* 6.1 0.7 - - - +
1084M SER* 5.5 6.3 - - - +
611N GLN* 5.8 0.9 - - - +
612N GLY 3.3 20.8 + - - +
613N ARG* 3.1 37.7 + - - +
614N PHE 3.1 0.4 - - - -
615N ARG* 1.3 75.6 - - - +
617N ASN* 1.3 60.5 + - - +
618N LEU 3.0 10.0 + - - -
619N LEU* 4.0 4.6 + - - +
620N GLY 4.1 10.4 + - - +
621N LYS* 3.5 39.9 + - - +
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Residues in contact with ASN 617 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053M LEU* 5.2 10.9 - - - +
1082M PRO* 5.9 0.3 - - - +
1084M SER* 3.3 31.1 + - - -
1088M LEU* 6.3 0.2 - - + -
613N ARG 3.8 4.8 + - - +
614N PHE 4.1 3.6 + - - +
615N ARG 3.6 0.4 - - - -
616N GLN* 1.3 79.6 - - - +
618N LEU* 1.3 59.0 + - - +
620N GLY* 5.0 0.7 - - - -
1466N VAL* 2.7 54.4 + - - +
1467N ILE* 2.9 37.7 + - + +
1469N GLY* 4.9 2.1 - - - -
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Residues in contact with LEU 618 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034M GLU* 3.6 41.4 - - + +
1037M VAL* 5.1 9.0 - - + +
1038M TRP* 5.2 4.3 - - + +
1041M GLU* 5.9 2.0 - - - +
614N PHE 4.6 7.4 + - - +
615N ARG* 3.7 18.2 + - - +
616N GLN 3.0 1.4 + - - -
617N ASN* 1.3 79.5 - - - +
619N LEU* 1.3 60.2 + - + +
620N GLY* 2.7 19.0 + - - -
1096N ARG* 4.5 6.1 - - - +
1439N SER* 5.3 9.9 - - - +
1463N LYS* 4.0 36.8 - - + +
1466N VAL* 5.2 9.4 - - + -
1467N ILE* 5.1 7.6 - - + -
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Residues in contact with LEU 619 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031M ARG* 4.4 17.1 + - - +
1033M GLY* 3.4 15.2 - - - -
1034M GLU* 3.7 22.2 + - + +
610N LYS 3.5 12.8 - - - +
611N GLN* 5.1 4.7 - - + -
615N ARG* 3.3 60.1 + - + +
616N GLN* 4.0 1.3 + - - +
618N LEU* 1.3 78.8 - - + +
620N GLY* 1.3 59.8 + - - +
621N LYS* 5.9 0.2 - - - +
1096N ARG* 5.4 1.8 - - - +
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Residues in contact with GLY 620 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031M ARG* 3.8 6.7 + - - -
1032M PHE* 5.3 1.1 - - - -
1033M GLY* 3.9 16.6 - - - -
1037M VAL* 5.8 2.9 - - - -
1053M LEU* 6.4 2.5 - - - -
616N GLN 4.1 9.9 + - - +
617N ASN 5.8 0.9 - - - -
618N LEU 2.7 12.9 + - - -
619N LEU* 1.3 77.1 - - - +
621N LYS* 1.3 84.5 + - - +
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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