Contacts of the helix formed by residues 706 - 714 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498C LEU* 3.2 24.1 - - - +
499C GLY 2.9 15.8 + - - -
501C SER* 3.5 10.8 - - - -
705C GLU* 1.3 74.6 - - - +
707C THR* 1.3 68.8 + - - +
709C ASN* 3.6 0.7 - - - +
710C GLU* 2.9 33.6 + - - +
722C LYS* 4.4 10.8 - - - +
726C ASN* 4.2 15.5 - - - -
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Residues in contact with THR 707 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405C TYR* 3.0 22.6 + - - +
496C MET* 3.7 22.0 - - + -
498C LEU* 3.6 26.2 - - + -
705C GLU* 4.2 2.3 + - - +
706C SER* 1.3 80.9 + - - +
708C MET* 1.3 91.1 + - - +
710C GLU* 3.2 15.1 - - - +
711C TYR* 2.9 24.8 + - - +
732C TYR* 4.1 3.8 + - - -
767C TRP* 3.9 10.9 + - + +
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Residues in contact with MET 708 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C GLU* 4.3 19.5 - - - +
403C SER 4.8 7.6 - - - +
405C TYR* 3.6 25.6 - - + -
450C TYR* 3.9 18.4 - - - +
478C PRO* 4.0 8.3 - - + -
686C THR* 5.3 10.8 - - + +
704C LEU* 3.6 20.2 - - + -
705C GLU* 3.9 10.9 + - - +
706C SER 3.6 0.2 - - - -
707C THR* 1.3 106.7 + - - +
709C ASN* 1.3 62.7 + - - +
711C TYR* 3.5 6.2 - - - +
712C ILE* 2.9 35.3 + - + +
732C TYR* 3.4 22.7 - - - +
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Residues in contact with ASN 709 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501C SER* 3.1 29.7 + - - +
502C ILE 3.4 22.4 + - - -
503C MET* 3.2 17.6 - - - +
704C LEU* 3.5 18.4 - - + +
705C GLU 3.4 6.4 + - - +
706C SER 3.3 2.4 + - - +
707C THR 3.1 0.6 - - - -
708C MET* 1.3 79.1 - - - +
710C GLU* 1.3 58.3 + - - +
712C ILE* 3.5 1.7 + - - +
713C GLU* 2.9 27.1 + - - +
720C THR* 5.6 0.7 + - - -
721C MET 4.8 0.2 - - - -
722C LYS* 3.2 39.6 + - + +
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Residues in contact with GLU 710 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706C SER* 2.9 22.6 + - - +
707C THR* 3.2 18.7 - - - +
709C ASN* 1.3 74.2 - - - +
711C TYR* 1.3 67.9 + - - +
713C GLU* 3.3 17.3 + - - +
714C GLN* 3.2 26.5 + - + +
722C LYS* 4.3 9.5 - - + +
763C LYS* 4.4 16.8 + - - -
767C TRP* 4.0 20.6 + - + -
768C TYR* 4.2 15.8 + - - -
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Residues in contact with TYR 711 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403C SER* 3.5 39.2 - - - -
404C PRO* 3.5 26.7 - - + +
407C MET* 4.0 13.0 - - - +
707C THR 2.9 18.3 + - - +
708C MET* 3.5 4.7 - - - +
709C ASN 3.2 0.2 - - - -
710C GLU* 1.3 76.9 - - - +
712C ILE* 1.3 79.9 + - + +
714C GLN* 2.8 23.6 + - + +
715C ARG* 3.0 52.0 + - + +
766C TRP 3.6 20.0 - - - -
767C TRP* 3.8 23.8 - + - +
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Residues in contact with ILE 712 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403C SER* 5.4 4.5 - - - +
503C MET* 4.6 12.1 - - + -
686C THR* 6.0 3.8 - - + -
690C VAL* 4.7 24.5 - - + -
694C ARG* 4.4 19.0 + - - +
704C LEU* 5.8 1.1 - - + -
708C MET* 2.9 23.4 + - + +
709C ASN 4.1 2.5 - - - +
711C TYR* 1.3 95.2 - - + +
713C GLU* 1.3 61.3 + - - +
715C ARG* 3.0 28.4 + - + +
718C CYS* 5.5 0.7 - - - -
720C THR* 4.6 13.5 + - + +
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Residues in contact with GLU 713 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709C ASN* 2.9 17.7 + - - +
710C GLU* 3.4 13.0 - - - +
711C TYR 3.1 0.2 - - - -
712C ILE* 1.3 77.4 - - - +
714C GLN* 1.3 67.3 + - + +
715C ARG 3.3 0.4 - - - +
718C CYS* 4.9 2.7 - - - +
720C THR* 4.5 21.1 + - - +
721C MET* 4.8 4.9 - - - +
722C LYS* 3.1 48.9 + - - +
773C CYS* 3.1 19.6 - - - +
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Residues in contact with GLN 714 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710C GLU* 3.4 14.9 + - + +
711C TYR* 2.8 11.3 + - + +
713C GLU* 1.3 87.3 + - - +
715C ARG* 1.3 66.2 + - + +
767C TRP* 4.7 16.6 - - + +
768C TYR* 5.9 10.8 - - + -
770C LYS 4.2 1.1 - - - +
771C GLY* 4.1 16.8 - - - -
772C GLU* 3.0 24.4 + - - +
773C CYS* 3.5 19.2 + - - +
774C GLY 4.7 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