Contacts of the helix formed by residues 660 - 670 (chain A) in PDB entry 3II5
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 ASN 660 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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658A ILE* 3.4 6.9 + - + +
659A ASN* 1.3 85.5 - - - +
661A ARG* 1.3 64.2 + - - +
662A ASP* 3.0 17.2 + - - +
663A GLN* 3.0 42.8 + - + +
664A ILE* 3.2 18.5 + - - +
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Residues in contact with ARG 661 (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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613A SER* 3.7 34.1 + - - +
614A GLY 3.2 20.1 + - - -
615A SER* 4.8 0.4 - - - +
616A ILE* 3.5 34.9 - - + +
659A ASN 4.2 1.6 + - - -
660A ASN* 1.3 72.1 + - - +
662A ASP* 1.3 67.2 + - - +
664A ILE* 3.4 11.8 + - - +
665A ILE* 3.1 44.8 + - + +
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Residues in contact with ASP 662 (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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660A ASN* 3.0 13.1 + - - +
661A ARG* 1.3 82.1 + - - +
663A GLN* 1.3 63.5 + - + +
665A ILE* 3.5 14.5 + - - +
666A PHE* 3.0 28.8 + - - +
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Residues in contact with GLN 663 (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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658A ILE* 5.0 6.5 - - + -
660A ASN* 3.0 32.8 + - + +
662A ASP* 1.3 80.6 + - + +
664A ILE* 1.3 58.6 + - - +
666A PHE* 3.9 24.8 - - - +
667A MET* 2.8 52.6 + - + +
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Residues in contact with ILE 664 (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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616A ILE* 3.6 23.1 - - + +
617A LEU* 5.0 7.4 - - + -
624A ILE* 6.2 0.7 - - + -
655A TYR* 3.8 39.0 - - + +
658A ILE* 3.5 45.3 - - + +
660A ASN 3.2 13.9 + - - +
661A ARG* 3.4 9.6 + - - +
663A GLN* 1.3 76.2 - - - +
665A ILE* 1.3 58.1 - - - +
667A MET* 5.5 0.2 - - - -
668A VAL* 2.8 40.3 + - + +
673A LEU* 4.5 7.6 - - + -
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Residues in contact with ILE 665 (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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616A ILE* 3.8 30.7 - - + -
624A ILE* 3.2 39.6 - - + +
661A ARG* 3.1 41.5 + - + +
662A ASP* 3.7 12.6 - - - +
664A ILE* 1.3 77.0 - - - +
666A PHE* 1.3 64.4 + - - +
669A GLY* 3.1 19.9 + - - -
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Residues in contact with PHE 666 (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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662A ASP 3.0 18.7 + - - +
663A GLN* 3.9 28.7 - - - +
665A ILE* 1.3 78.9 - - - +
667A MET* 1.3 63.8 + - + +
669A GLY* 3.9 0.5 - - - -
670A ARG* 3.0 71.0 + - + +
672A TYR* 4.2 22.9 - + - -
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Residues in contact with MET 667 (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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658A ILE* 4.1 15.0 - - + -
663A GLN* 2.8 41.0 + - + +
664A ILE 4.2 0.7 - - - +
666A PHE* 1.3 78.9 - - + +
668A VAL* 1.3 63.3 + - - +
670A ARG 3.5 0.3 + - - -
671A GLY 3.0 2.8 + - - -
672A TYR* 2.8 59.3 + - + +
673A LEU* 3.2 38.5 + - + +
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Residues in contact with VAL 668 (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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616A ILE 5.8 2.7 - - - +
619A MET 4.5 8.3 - - - +
621A PRO* 4.2 25.5 - - + +
624A ILE* 4.1 22.4 - - + -
639A TYR* 4.8 6.3 - - - +
655A TYR* 3.7 35.7 - - + +
664A ILE* 2.8 28.8 + - + +
665A ILE* 4.1 2.5 - - - +
667A MET* 1.3 72.9 - - - +
669A GLY* 1.3 64.3 + - - +
671A GLY* 3.2 13.7 + - - -
673A LEU* 4.1 19.6 - - + +
698A LYS* 5.9 0.5 - - - +
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Residues in contact with GLY 669 (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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621A PRO 4.2 5.6 - - - -
624A ILE* 3.7 19.5 - - - +
625A ARG* 2.8 48.3 + - - -
665A ILE 3.1 11.7 + - - -
666A PHE 3.9 0.7 - - - -
668A VAL* 1.3 78.8 - - - +
670A ARG* 1.3 57.7 + - - +
671A GLY 3.2 0.2 - - - -
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Residues in contact with ARG 670 (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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625A ARG* 5.3 0.7 - - - -
666A PHE* 3.0 52.3 + - + +
667A MET 4.2 0.2 - - - +
669A GLY* 1.3 76.5 - - - +
671A GLY* 1.3 58.9 + - - +
672A TYR* 3.3 52.8 + - + +
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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