Contacts of the helix formed by residues 796 - 805 (chain D) in PDB entry 6VVT
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 796 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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733D ALA 5.0 0.9 - - - +
734D ASP* 4.0 20.7 + - - +
792D TYR* 4.6 5.1 - - + +
793D PRO* 3.1 40.4 + - + +
794D ALA 3.4 1.0 - - - -
795D ASP* 1.3 78.0 + - - +
797D PRO* 1.3 75.8 - - - +
798D ILE* 3.0 44.5 - - - +
799D ILE* 2.9 16.7 + - + +
800D THR* 2.7 27.5 + - - -
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Residues in contact with PRO 797 (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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998C LYS* 5.3 4.5 - - - +
727D GLY 4.6 8.1 - - - +
728D VAL* 4.3 13.2 - - + +
729D THR 3.4 29.6 - - - +
730D VAL* 5.6 2.5 - - + -
734D ASP* 3.1 22.0 - - - +
795D ASP 3.4 5.4 - - - +
796D ASN* 1.3 96.5 - - - +
798D ILE* 1.3 62.3 + - + +
800D THR* 3.8 5.7 - - - -
801D ILE* 3.2 31.4 + - - +
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Residues in contact with ILE 798 (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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914C PRO* 3.9 30.5 - - + +
730D VAL* 5.5 9.6 - - + -
734D ASP* 3.0 41.3 - - + +
735D VAL* 4.1 18.4 - - + -
796D ASN* 3.0 13.2 - - - +
797D PRO* 1.3 78.0 - - + +
799D ILE* 1.3 66.2 + - + +
801D ILE* 3.6 7.0 + - - +
802D VAL* 3.1 29.2 + - + +
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Residues in contact with ILE 799 (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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788D LEU* 5.6 7.2 - - + -
789D GLU* 6.0 2.9 - - - -
792D TYR* 4.1 16.8 - - + +
793D PRO 3.9 12.1 - - - +
794D ALA* 3.8 7.6 - - - +
796D ASN* 2.9 26.1 + - + +
798D ILE* 1.3 81.0 - - + +
800D THR* 1.3 62.2 + - - +
802D VAL* 3.0 10.4 + - + +
803D LYS* 2.8 70.4 + - + +
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Residues in contact with THR 800 (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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583D THR* 5.0 11.0 - - - +
586D TYR* 4.4 23.2 - - + -
587D TYR* 5.9 4.3 - - + -
726D SER* 5.1 3.6 - - - +
728D VAL* 4.7 16.4 - - + -
794D ALA 4.6 1.7 + - - -
795D ASP* 3.5 21.0 + - - +
796D ASN 2.7 21.8 + - - -
797D PRO* 3.8 8.5 - - - +
799D ILE* 1.3 72.9 - - - +
801D ILE* 1.3 63.7 + - - +
802D VAL 3.2 0.2 + - - -
803D LYS* 3.9 7.0 - - - +
804D SER* 3.0 24.8 + - - -
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Residues in contact with ILE 801 (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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910C THR* 3.9 17.7 - - - +
912C GLY 5.9 2.9 - - - +
913C VAL* 5.2 6.5 - - + -
914C PRO* 4.6 10.3 - - + -
583D THR* 4.0 13.5 - - + -
728D VAL* 3.8 29.8 - - + -
730D VAL* 6.1 2.2 - - + -
797D PRO 3.2 16.8 + - - +
798D ILE* 3.9 6.5 - - - +
800D THR* 1.3 76.2 - - - +
802D VAL* 1.3 61.4 + - - +
804D SER* 3.0 18.8 + - - -
805D GLY 3.5 4.5 + - - -
806D ALA* 3.6 16.8 + - + -
807D THR* 3.7 24.5 - - + +
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Residues in contact with VAL 802 (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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914C PRO* 3.4 32.8 - - + -
798D ILE* 3.1 18.4 + - + +
799D ILE* 3.0 15.3 + - + +
801D ILE* 1.3 75.0 - - - +
803D LYS* 1.3 69.6 + - + +
805D GLY* 3.2 12.8 + - - -
807D THR* 4.2 9.4 - - + +
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Residues in contact with LYS 803 (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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586D TYR* 3.5 26.7 - - + +
688D HIS* 3.5 19.6 + - + +
794D ALA* 3.7 19.3 - - - +
799D ILE* 2.8 49.4 + - + +
800D THR* 3.9 4.3 - - - +
802D VAL* 1.3 77.4 - - + +
804D SER* 1.3 63.1 + - - +
805D GLY* 3.1 1.7 + - - -
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Residues in contact with SER 804 (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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582D VAL* 3.3 13.9 - - - +
583D THR* 3.2 21.9 - - - +
586D TYR* 3.4 41.6 - - - -
688D HIS* 3.7 4.7 - - - +
689D LYS* 3.1 25.5 + - - +
800D THR 3.0 9.8 + - - -
801D ILE 3.0 15.4 + - - -
803D LYS* 1.3 77.1 - - - +
805D GLY* 1.3 57.6 + - - +
806D ALA 3.5 3.0 + - - -
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Residues in contact with GLY 805 (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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582D VAL* 4.4 2.2 - - - -
689D LYS* 3.2 29.5 + - - +
801D ILE 3.5 0.8 + - - -
802D VAL 3.2 11.7 + - - -
803D LYS 3.1 5.5 - - - -
804D SER* 1.3 79.6 + - - +
806D ALA* 1.3 66.3 + - - +
807D THR 3.3 10.9 + - - +
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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