Contacts of the helix formed by residues 706 - 712 (chain B) in PDB entry 3A8P
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 706 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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574A GLN* 5.8 0.8 - - - +
703A GLU* 2.9 30.7 + - + +
704A LEU* 3.2 31.0 + - - +
705A PRO 3.5 12.9 + - - -
706A ASN* 4.2 7.4 - - - +
707A PRO* 3.5 13.8 - - - +
690B PHE* 3.7 7.9 - - - -
704B LEU 3.6 1.0 + - - -
705B PRO* 1.3 70.2 - - - +
707B PRO* 1.3 71.2 - - - +
708B LYS* 2.8 37.9 + - - +
709B SER* 3.2 23.4 + - - +
710B LEU 3.8 1.0 + - - -
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Residues in contact with PRO 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706A ASN* 3.5 19.3 - - - +
707A PRO* 4.9 4.9 - - + -
708A LYS* 3.9 32.1 - - + +
574B GLN* 3.6 15.5 - - - +
690B PHE* 3.9 7.6 - - + -
705B PRO 3.3 8.7 - - - +
706B ASN* 1.3 89.1 - - - +
708B LYS* 1.3 66.3 + - + +
710B LEU 3.3 2.4 + - - -
711B LEU* 3.2 27.0 + - + +
730B VAL* 3.5 28.2 - - + +
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Residues in contact with LYS 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A GLN* 5.1 10.8 - - - +
575A SER* 3.0 42.3 + - - +
576A VAL* 4.7 0.8 - - - +
577A PRO* 3.8 24.4 - - + +
578A GLU* 3.8 24.5 + - - +
707A PRO* 4.0 24.0 - - + +
708A LYS* 5.8 6.7 - - - +
706B ASN* 2.8 22.2 + - - +
707B PRO* 1.3 77.6 - - + +
709B SER* 1.3 61.9 + - - +
711B LEU* 3.4 6.8 + - + -
712B ALA* 3.2 20.6 + - - +
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Residues in contact with SER 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A GLU* 3.4 31.0 + - - +
686B HIS* 5.2 5.6 + - - -
706B ASN* 3.2 17.1 + - - +
707B PRO 3.2 0.6 - - - -
708B LYS* 1.3 76.0 - - - +
710B LEU* 1.3 67.6 + - - +
712B ALA* 3.3 18.4 + - - +
713B ALA* 4.0 3.1 + - - +
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Residues in contact with LEU 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686B HIS* 3.6 40.4 - - + +
687B MET* 3.6 26.0 - - + +
690B PHE* 3.7 36.9 - - + -
706B ASN 3.8 2.0 + - - -
707B PRO 3.3 8.1 + - - +
709B SER* 1.3 78.4 - - - +
711B LEU* 1.3 59.5 + - - +
713B ALA* 2.9 25.0 + - - +
730B VAL* 3.7 24.7 - - + -
733B PHE* 3.7 24.9 - - + -
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Residues in contact with LEU 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A PRO* 3.6 34.5 - - + +
578A GLU* 4.8 6.7 - - + +
707B PRO* 3.2 17.8 + - + +
708B LYS* 3.8 6.1 - - + +
709B SER 3.3 0.4 - - - -
710B LEU* 1.3 78.3 - - - +
712B ALA* 1.3 60.8 + - - +
713B ALA 3.0 0.9 - - - -
714B THR* 3.0 27.9 + - - +
728B LEU* 3.3 43.1 - - + +
729B SER* 3.9 24.7 - - - +
730B VAL* 4.0 10.8 - - + +
733B PHE* 3.9 13.2 - - + -
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Residues in contact with ALA 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A PRO* 4.2 9.2 - - + -
603A GLN* 3.4 43.5 - - + +
708B LYS 3.2 12.8 + - - +
709B SER* 3.4 14.6 - - - +
710B LEU 3.1 0.8 - - - -
711B LEU* 1.3 77.5 - - - +
713B ALA* 1.3 59.1 + - - +
714B THR 3.3 3.9 + - - +
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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