Contacts of the helix formed by residues 660 - 665 (chain A) in PDB entry 3A8N
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 SER 660 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501A ILE 5.9 0.9 - - - -
503A GLN* 5.1 6.7 - - - +
516A CYS* 4.8 22.7 - - - -
517A LEU 5.6 2.0 - - - -
518A SER* 4.8 9.9 - - - -
524A ALA* 6.5 1.1 - - - -
658A SER* 3.0 6.9 - - - -
659A VAL* 1.3 79.1 - - - +
661A SER* 1.3 54.7 + - - +
663A HIS* 2.5 34.2 + - - +
664A ALA* 2.7 14.6 + - - +
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Residues in contact with SER 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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651A MET* 4.8 9.2 - - - -
655A GLY 4.4 4.3 - - - -
656A ILE 3.5 5.8 - - - -
657A PHE* 3.9 4.5 - - - -
658A SER* 2.5 45.9 + - - -
660A SER* 1.3 71.7 - - - +
662A PHE* 1.3 52.3 + - - -
664A ALA* 2.7 34.7 + - - +
665A LEU* 3.0 9.7 + - - +
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Residues in contact with PHE 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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616A MET* 4.4 9.7 - - - +
640A LEU* 5.8 4.9 - - - -
643A ALA* 4.8 18.6 - - + -
651A MET* 5.5 8.7 - - + +
657A PHE* 6.3 0.9 - - - -
658A SER 2.9 11.8 + - - +
659A VAL* 3.8 4.9 - - - +
661A SER* 1.3 71.6 - - - +
663A HIS* 1.3 56.2 + - - +
664A ALA 3.3 0.2 - - - -
665A LEU* 4.9 4.5 - - - +
666A VAL* 3.0 20.5 - - - +
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Residues in contact with HIS 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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501A ILE* 5.1 9.6 - - + -
518A SER* 4.1 21.2 - - - -
519A ASN 5.7 0.5 - - - +
522A GLY* 5.9 0.2 - - - -
616A MET* 5.4 5.2 - - + -
659A VAL 3.2 11.6 + - - +
660A SER* 2.5 19.8 + - - +
662A PHE* 1.3 72.0 - - - +
664A ALA* 1.3 63.5 + - - +
666A VAL* 3.6 13.1 - - - +
667A ALA* 4.0 9.7 + - - +
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Residues in contact with ALA 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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446A LEU* 5.4 7.0 - - + -
454A VAL* 5.2 4.9 - - + -
518A SER* 5.1 5.2 - - - -
522A GLY* 4.1 21.5 - - - +
523A ASP 5.3 4.7 - - - +
524A ALA* 5.4 10.1 - - + -
660A SER* 2.7 9.0 + - - +
661A SER* 2.7 15.0 + - - +
663A HIS* 1.3 78.7 - - - +
665A LEU* 1.3 64.5 + - - +
666A VAL 2.8 5.0 + - - -
667A ALA* 3.0 13.9 + - - +
668A ALA* 3.4 8.8 + - - +
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Residues in contact with LEU 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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454A VAL* 4.3 21.9 - - + +
647A THR 5.8 3.1 - - - +
650A ALA* 5.7 9.6 - - + -
651A MET* 6.2 2.2 - - - +
661A SER 3.0 8.7 + - - +
662A PHE* 5.2 3.4 - - - -
664A ALA* 1.3 78.9 - - - +
666A VAL* 1.3 62.1 + - - +
667A ALA 3.3 0.7 + - - -
668A ALA* 3.4 15.7 + - - +
669A ARG* 3.8 7.6 + - - +
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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