Contacts of the helix formed by residues 770 - 784 (chain C) in PDB entry 3V53
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 ARG 770 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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766C LEU* 3.1 15.4 + - + +
769C ARG* 1.3 92.5 - - + +
771C ILE* 1.3 63.5 + - + +
772C ARG 3.7 1.1 - - - -
773C PRO* 3.8 4.0 - - - +
774C TRP* 3.4 29.6 + - - +
777C LYS* 5.9 0.2 - - - +
829C LEU* 3.9 23.7 - - + +
832C TYR* 5.4 0.2 - - - -
833C GLU* 3.2 47.8 + - + +
812D ALA 5.5 0.4 + - - -
813D MET 3.5 17.2 + - - -
814D VAL 5.4 0.4 - - - -
816D ASP* 2.6 45.3 + - - +
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Residues in contact with ILE 771 (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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762C VAL* 4.5 5.2 - - + -
766C LEU* 3.5 43.1 - - + +
767C MET* 3.3 33.5 + - + +
770C ARG* 1.3 82.8 - - + +
772C ARG* 1.3 60.9 + - - +
773C PRO 3.5 0.2 - - - -
774C TRP* 3.9 3.3 - - - +
775C ILE* 3.0 49.6 + - + +
798C VAL* 5.0 2.2 - - + -
826C MET* 5.1 4.3 - - - -
829C LEU* 4.5 14.8 - - + -
830C LEU* 3.8 35.0 - - + -
833C GLU* 5.8 4.0 - - + -
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Residues in contact with ARG 772 (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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767C MET* 2.7 35.1 + - - +
768C GLU* 4.4 14.9 - - - +
771C ILE* 1.3 71.0 - - - +
773C PRO* 1.4 64.1 - - + +
775C ILE* 3.6 2.5 + - - +
776C ASN* 3.0 27.1 + - + +
791C VAL* 4.0 9.4 - - + +
792C ASP* 3.0 38.0 + - - +
795C CYS* 3.9 35.8 - - - +
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Residues in contact with PRO 773 (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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768C GLU 3.3 20.4 - - - +
769C ARG 3.3 22.4 - - - +
770C ARG* 3.8 1.8 - - - +
771C ILE 3.7 4.5 - - - +
772C ARG* 1.4 89.1 - - + +
774C TRP* 1.3 54.7 + - - +
776C ASN* 3.2 7.2 + - + +
777C LYS* 2.7 38.4 + - - +
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Residues in contact with TRP 774 (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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770C ARG* 3.4 28.1 + - - +
771C ILE 3.7 3.1 + - - +
772C ARG 3.4 0.4 - - - -
773C PRO* 1.3 79.1 - - - +
775C ILE* 1.3 74.8 + - + +
777C LYS* 3.2 35.1 - - - +
778C LYS* 3.0 53.9 + - + +
822C PHE* 3.5 24.0 - + - -
825C LYS* 3.8 20.9 - - + -
826C MET* 3.2 45.1 - - + -
829C LEU* 3.7 35.8 - - + +
812D ALA 5.9 1.4 + - - -
816D ASP* 6.3 0.2 - - + -
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Residues in contact with ILE 775 (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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771C ILE* 3.0 36.3 + - + +
772C ARG 3.8 3.8 - - - +
774C TRP* 1.3 92.1 - - + +
776C ASN* 1.3 63.5 + - - +
778C LYS* 3.2 4.9 + - - +
779C ILE* 3.0 35.2 + - + +
791C VAL* 4.0 28.9 - - + +
794C VAL* 3.7 23.1 - - + -
795C CYS* 3.7 24.5 - - - +
798C VAL* 5.0 1.8 - - + -
822C PHE* 4.1 11.2 - - + -
826C MET* 4.2 12.1 - - - -
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Residues in contact with ASN 776 (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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772C ARG* 3.0 19.4 + - + +
773C PRO* 3.4 7.7 - - + +
775C ILE* 1.3 76.9 - - - +
777C LYS* 1.3 64.6 + - - +
779C ILE* 3.3 2.5 + - - +
780C ILE* 3.2 33.8 + - - +
786C GLU* 3.6 33.3 + - - +
787C GLU 4.7 1.6 + - - -
788C ALA* 5.6 0.5 + - - -
791C VAL* 3.6 27.1 - - + +
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Residues in contact with LYS 777 (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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773C PRO 2.7 18.5 + - - +
774C TRP* 3.2 46.3 - - - +
776C ASN* 1.3 73.9 - - - +
778C LYS* 1.3 78.5 + - - +
780C ILE* 3.5 12.6 + - - +
781C GLU* 3.1 25.6 + - - +
816D ASP* 4.2 11.9 - - - +
817D GLU* 4.0 32.0 - - + +
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Residues in contact with LYS 778 (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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774C TRP* 3.0 59.0 + - + +
775C ILE 3.4 4.9 - - - +
777C LYS* 1.3 94.8 - - + +
779C ILE* 1.3 65.2 + - - +
781C GLU* 3.1 35.9 + - - +
782C TYR* 3.0 52.9 + - + +
822C PHE* 3.7 15.0 - - + -
825C LYS* 3.9 21.4 - - - +
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Residues in contact with ILE 779 (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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775C ILE* 3.0 22.6 + - + +
776C ASN* 3.3 5.8 + - - +
778C LYS* 1.3 76.0 - - - +
780C ILE* 1.3 54.5 + - + +
782C TYR* 3.1 6.5 + - + +
783C ILE* 2.8 41.5 + - + +
785C GLU 4.5 4.9 - - - +
787C GLU* 4.4 28.5 - - + +
790C LEU* 4.6 19.7 - - + +
791C VAL* 4.1 15.3 - - + -
794C VAL* 5.2 2.0 - - + -
811C VAL* 5.8 0.9 - - + -
815C LEU* 4.7 15.9 - - + -
822C PHE* 4.0 28.9 - - + -
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Residues in contact with ILE 780 (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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776C ASN* 3.2 35.1 + - - +
777C LYS* 3.6 11.9 - - - +
779C ILE* 1.3 75.9 - - + +
781C GLU* 1.3 57.8 + - - +
784C GLY* 2.9 31.7 + - - -
785C GLU* 3.3 26.7 - - - +
786C GLU* 3.7 23.6 - - + +
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Residues in contact with GLU 781 (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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777C LYS* 3.1 16.7 + - - +
778C LYS* 3.1 48.2 + - - +
780C ILE* 1.3 80.1 - - - +
782C TYR* 1.3 71.0 + - + +
784C GLY* 4.6 1.7 + - - -
825C LYS* 5.5 4.2 + - - -
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Residues in contact with TYR 782 (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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778C LYS* 3.0 44.3 + - + +
779C ILE* 3.1 6.9 + - + +
781C GLU* 1.3 93.2 + - + +
783C ILE* 1.3 62.8 + - - +
784C GLY* 3.3 0.9 + - - -
815C LEU* 4.0 30.1 - - + -
818C GLU* 3.7 47.1 - - + +
821C VAL* 3.9 12.9 - - + +
822C PHE* 3.4 53.7 + + + -
825C LYS* 4.7 1.7 - - - -
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Residues in contact with ILE 783 (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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779C ILE* 2.8 25.2 + - + +
782C TYR* 1.3 73.9 - - + +
784C GLY* 1.3 60.9 + - - +
785C GLU* 3.6 25.5 + - + +
787C GLU* 5.8 3.4 - - + -
815C LEU* 5.3 8.7 - - + -
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Residues in contact with GLY 784 (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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780C ILE* 2.9 18.5 + - - -
781C GLU 5.2 1.8 - - - -
782C TYR 3.3 3.4 + - - -
783C ILE* 1.3 75.9 - - - +
785C GLU* 1.3 61.9 + - - +
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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