Contacts of the helix formed by residues 706 - 714 (chain D) in PDB entry 5VOT
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 706 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498D LEU* 3.0 27.1 - - - +
499D GLY 3.2 24.1 + - - -
501D SER* 3.3 17.8 + - - -
705D GLU* 1.3 72.8 - - - +
707D THR* 1.3 74.9 + - - +
709D ASN* 2.8 12.3 + - - +
710D GLU* 2.9 19.3 + - - +
722D LYS* 4.8 7.5 - - - +
726D ASN* 4.2 9.6 - - - -
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Residues in contact with THR 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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404D PRO* 5.7 0.4 - - - -
405D TYR* 2.6 31.3 + - - +
496D MET* 4.2 17.5 - - + -
497D SER 5.3 0.9 - - - +
498D LEU* 3.8 22.4 - - + -
706D SER* 1.3 84.6 + - - +
708D MET* 1.3 82.3 + - - +
710D GLU* 3.4 12.9 - - - +
711D TYR* 2.9 25.6 + - - +
732D TYR* 4.1 3.5 + - - -
763D LYS* 6.4 0.9 - - - -
767D TRP* 3.7 20.0 + - + +
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Residues in contact with MET 708 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402D GLU* 5.0 14.1 - - + +
403D SER 4.1 15.9 - - - +
404D PRO* 5.5 0.4 - - - -
405D TYR* 3.4 26.2 - - + -
450D TYR* 3.8 13.2 - - - +
478D PRO* 4.2 8.1 - - + -
686D THR* 5.2 12.6 - - + -
704D LEU* 3.7 18.2 - - + -
705D GLU* 3.2 35.2 - - + +
706D SER 3.3 0.2 - - - -
707D THR* 1.3 106.4 + - - +
709D ASN* 1.3 57.4 + - - +
711D TYR* 3.3 6.3 + - - +
712D ILE* 2.9 38.7 + - + +
732D TYR* 4.1 2.5 - - - +
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Residues in contact with ASN 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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501D SER* 3.3 30.2 + - - +
502D ILE 3.5 17.0 + - - -
503D MET* 3.1 22.0 - - - +
704D LEU* 3.4 10.6 - - + +
705D GLU 3.1 5.5 + - - +
706D SER 2.8 10.9 + - - +
708D MET* 1.3 77.3 - - - +
710D GLU* 1.3 62.7 + - - +
711D TYR 3.0 0.7 + - - -
712D ILE* 3.1 2.9 + - - +
713D GLU* 2.9 19.6 + - - +
720D THR* 5.2 0.9 + - - -
721D MET 4.3 0.7 - - - -
722D LYS* 3.2 46.0 + - + +
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Residues in contact with GLU 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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706D SER* 2.9 16.8 + - - +
707D THR* 3.4 17.2 - - - +
709D ASN* 1.3 74.8 - - - +
711D TYR* 1.3 65.6 + - - +
713D GLU* 3.3 31.2 - - - +
714D GLN* 3.4 15.2 + - - +
722D LYS* 4.9 9.7 - - + +
763D LYS* 4.4 14.4 + - - -
767D TRP* 3.5 25.0 + - + -
768D TYR* 4.7 12.9 + - - -
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Residues in contact with TYR 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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403D SER* 3.5 26.9 - - - -
404D PRO* 3.5 30.7 - - + +
407D MET* 4.2 13.0 - - - +
707D THR 2.9 20.0 + - - +
708D MET* 3.4 7.0 - - - +
709D ASN 3.0 0.4 - - - -
710D GLU* 1.3 75.4 - - - +
712D ILE* 1.3 71.9 + - + +
714D GLN* 2.8 25.6 + - + +
715D ARG* 3.1 59.2 + - + +
766D TRP* 3.1 29.4 - - - -
767D TRP* 4.4 19.1 - + + -
770D LYS* 6.2 0.4 - - + -
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Residues in contact with ILE 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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403D SER* 5.9 2.2 - - - -
503D MET* 4.1 13.9 - - + -
686D THR* 6.4 1.6 - - + -
690D VAL* 4.5 23.3 - - + -
694D ARG* 4.5 13.9 - - - +
704D LEU* 5.4 1.1 - - + -
708D MET* 2.9 25.4 + - + +
709D ASN 3.7 3.8 - - - +
711D TYR* 1.3 88.7 - - + +
713D GLU* 1.3 61.0 + - - +
715D ARG* 3.0 30.2 + - + +
718D CYS* 5.2 1.2 - - - -
719D ASP* 5.6 0.7 - - - +
720D THR* 3.6 31.4 + - + +
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Residues in contact with GLU 713 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709D ASN* 2.9 13.2 + - - +
710D GLU* 3.3 26.9 - - - +
711D TYR 3.1 0.4 - - - -
712D ILE* 1.3 77.1 - - - +
714D GLN* 1.3 69.8 + - - +
715D ARG 3.4 0.2 - - - -
718D CYS* 4.8 3.2 - - - +
720D THR* 3.7 20.9 + - - +
721D MET* 5.5 1.5 - - - +
722D LYS* 4.3 23.6 - - - +
773D CYS* 3.1 20.8 - - - +
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Residues in contact with GLN 714 (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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710D GLU 3.5 12.3 - - - +
711D TYR* 2.8 14.4 + - + +
713D GLU* 1.3 98.6 + - - +
715D ARG* 1.3 60.5 + - + +
767D TRP 4.4 16.2 - - - +
768D TYR* 6.0 5.2 - - + -
771D GLY* 3.8 16.1 - - - -
772D GLU* 2.6 31.4 + - - +
773D CYS* 3.6 29.1 + - - +
774D GLY 4.4 4.9 - - - +
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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