Contacts of the helix formed by residues 706 - 712 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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574C GLN* 5.8 0.6 - - - +
703C GLU* 3.1 30.2 + - + +
704C LEU* 3.0 31.2 + - - +
705C PRO 3.1 16.0 + - - -
706C ASN* 4.2 7.4 - - - +
707C PRO* 3.6 10.8 - - - +
690D PHE* 3.6 8.2 - - - -
704D LEU 3.6 0.8 + - - -
705D PRO* 1.3 70.7 - - - +
707D PRO* 1.3 69.1 - - - +
708D LYS* 2.8 41.1 + - - +
709D SER* 3.2 24.2 + - - +
710D LEU 3.8 0.7 + - - -
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Residues in contact with PRO 707 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706C ASN* 3.3 26.2 - - - +
707C PRO* 4.7 7.4 - - + -
708C LYS* 4.1 22.9 - - + -
574D GLN* 3.8 13.2 - - - +
690D PHE* 3.8 11.0 - - + -
705D PRO 3.3 9.6 - - - +
706D ASN* 1.3 86.9 - - - +
708D LYS* 1.3 64.2 + - + +
710D LEU* 3.2 5.5 + - - +
711D LEU* 3.0 31.2 + - + +
730D VAL* 3.5 19.6 - - + +
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Residues in contact with LYS 708 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574C GLN* 5.0 8.9 - - - +
575C SER* 3.7 34.2 + - - +
576C VAL* 5.2 0.2 - - - +
577C PRO* 3.8 17.9 - - + +
578C GLU* 3.0 31.4 + - - +
707C PRO* 4.0 26.8 - - + +
729C SER* 6.3 1.0 - - - -
706D ASN* 2.8 20.6 + - - +
707D PRO* 1.3 75.5 - - + +
709D SER* 1.3 65.8 + - - +
711D LEU* 3.8 4.9 - - + +
712D ALA* 3.1 22.7 + - - +
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Residues in contact with SER 709 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703C GLU* 3.1 29.6 + - - +
686D HIS* 5.4 3.6 + - - -
690D PHE* 6.3 0.4 - - - -
693D ARG* 6.2 1.1 - - - -
706D ASN* 3.2 18.5 + - - +
707D PRO 3.2 0.8 - - - -
708D LYS* 1.3 78.4 - - - +
710D LEU* 1.3 63.1 + - - +
712D ALA* 3.3 18.5 - - - +
713D ALA* 4.0 3.3 + - - +
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Residues in contact with LEU 710 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686D HIS* 3.6 43.7 - - + +
687D MET* 3.9 20.0 - - + +
690D PHE* 3.7 37.4 - - + -
706D ASN 3.8 0.6 + - - -
707D PRO 3.2 9.0 + - - +
709D SER* 1.3 75.4 - - - +
711D LEU* 1.3 56.9 + - - +
712D ALA 2.9 4.7 - - - -
713D ALA* 2.8 29.8 + - - +
730D VAL* 3.7 29.6 - - + -
733D PHE* 3.9 19.6 - - + -
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Residues in contact with LEU 711 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577C PRO* 3.6 30.8 - - + +
578C GLU* 3.8 23.1 - - + +
707D PRO* 3.0 20.3 + - + +
708D LYS* 3.5 4.7 + - + -
710D LEU* 1.3 76.1 - - - +
712D ALA* 1.3 60.0 + - - +
713D ALA 3.0 1.8 - - - -
714D THR* 3.2 32.3 + - - +
719D LYS* 5.8 0.3 - - - +
728D LEU* 4.2 24.7 - - + +
729D SER* 3.8 34.8 - - - +
730D VAL* 3.8 12.8 - - + +
733D PHE* 4.1 8.7 - - + -
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Residues in contact with ALA 712 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577C PRO* 4.1 9.9 - - + -
603C GLN* 3.7 40.4 - - + +
708D LYS 3.1 11.9 + - - +
709D SER* 3.3 17.9 - - - +
710D LEU 2.9 1.0 + - - -
711D LEU* 1.3 76.8 - - - +
713D ALA* 1.3 59.0 + - - +
714D THR 3.3 4.5 + - - +
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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