Contacts of the helix formed by residues 718 - 727 (chain C) in PDB entry 3UEO
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 ILE 718 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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632C PRO* 5.4 4.7 - - + -
633C LEU* 5.9 1.8 - - + -
656C CYS* 4.1 6.3 - - - -
660C GLU* 4.1 6.5 - - - +
664C LEU* 3.7 43.3 - - + -
696C ILE* 3.8 21.3 - - + -
697C LEU 3.8 7.3 + - - +
698C LYS* 3.8 33.9 - - + -
717C THR* 1.3 74.9 - - - +
719C ALA* 1.3 55.1 + - - +
721C LEU* 2.8 25.7 + - - +
722C LEU* 3.1 25.5 + - + +
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Residues in contact with ALA 719 (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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717C THR* 3.1 10.9 + - - +
718C ILE* 1.3 77.8 - - - +
720C TRP* 1.3 64.2 + - - +
722C LEU* 3.7 11.4 - - + +
723C GLU* 3.0 27.0 + - - +
736C PHE* 3.8 14.7 - - + -
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Residues in contact with TRP 720 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646C LEU* 3.6 45.1 - - + -
651C ILE* 4.1 5.4 - - + -
694C HIS* 3.5 37.2 - + - -
696C ILE* 3.9 21.8 - - + -
716C VAL* 3.7 20.0 - - + -
717C THR 3.2 13.9 + - - +
718C ILE 3.1 0.8 - - - -
719C ALA* 1.3 78.6 - - - +
721C LEU* 1.3 78.6 + - - +
723C GLU 3.3 0.2 + - - -
724C THR* 3.1 30.9 + - - -
730C ARG* 4.4 5.4 - - + -
731C ALA* 2.8 40.7 + - + +
733C GLU* 3.4 25.6 - - + +
736C PHE* 3.7 35.5 - + + -
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Residues in contact with LEU 721 (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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646C LEU* 3.7 29.6 - - + -
653C PHE* 4.5 1.8 - - + -
664C LEU* 3.6 48.7 - - + +
667C LEU* 4.3 11.0 - - + -
668C ALA* 4.2 15.0 - - + +
671C LEU* 4.2 7.2 - - + -
696C ILE* 4.1 27.1 - - + -
717C THR 4.0 0.2 + - - -
718C ILE* 2.8 12.0 + - - +
720C TRP* 1.3 87.0 - - + +
722C LEU* 1.3 58.3 + - + +
724C THR* 3.6 2.8 + - - -
725C ALA* 3.0 26.2 + - - +
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Residues in contact with LEU 722 (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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632C PRO* 3.5 39.3 - - + +
633C LEU* 4.2 13.0 - - + -
637C VAL* 4.2 14.3 - - + +
638C PRO* 4.5 2.8 - - - +
664C LEU* 4.7 6.7 - - + -
667C LEU* 3.8 28.3 - - + -
718C ILE* 3.1 23.8 + - + +
719C ALA* 3.5 8.9 + - - +
720C TRP 3.3 0.2 - - - -
721C LEU* 1.3 80.6 - - + +
723C GLU* 1.3 57.4 + - - +
725C ALA* 3.4 7.2 - - + +
726C ARG* 3.1 25.6 + - - +
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Residues in contact with GLU 723 (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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719C ALA 3.0 18.4 + - - +
720C TRP 3.8 2.7 - - - +
722C LEU* 1.3 76.6 - - - +
724C THR* 1.3 66.2 + - - +
725C ALA 3.1 0.9 - - - -
726C ARG* 3.1 41.5 + - - +
727C THR* 3.1 30.3 + - + +
729C LYS 5.8 0.2 - - - +
731C ALA* 4.2 8.1 - - + -
736C PHE* 4.0 25.3 - - + -
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Residues in contact with THR 724 (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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645C PRO* 3.4 26.9 - - + +
646C LEU* 3.9 17.3 - - + -
671C LEU* 4.1 3.1 - - + -
720C TRP* 3.1 22.5 + - - -
721C LEU* 3.7 5.8 - - - -
723C GLU* 1.3 77.7 - - - +
725C ALA* 1.3 58.3 + - - +
728C GLY* 2.8 33.6 + - - -
729C LYS 3.1 19.4 + - - +
730C ARG* 3.7 8.2 - - - -
731C ALA* 2.7 22.2 + - - +
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Residues in contact with ALA 725 (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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637C VAL* 5.2 0.7 - - + -
638C PRO 3.8 9.6 - - - +
639C VAL* 3.1 18.0 - - + +
640C MET* 2.8 26.5 + - - +
667C LEU* 5.2 6.1 - - + -
671C LEU* 3.7 21.6 - - + +
721C LEU 3.0 18.0 + - - +
722C LEU* 3.4 16.8 - - + +
724C THR* 1.3 78.8 - - - +
726C ARG* 1.3 57.5 + - - +
728C GLY* 3.8 2.4 + - - -
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Residues in contact with ARG 726 (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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638C PRO* 3.7 36.2 + - + +
639C VAL 4.5 0.5 - - - -
640C MET* 3.5 24.1 + - - +
722C LEU 3.1 18.4 + - - +
723C GLU* 3.1 36.5 + - - +
725C ALA* 1.3 77.0 - - - +
727C THR* 1.3 81.0 + - - +
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Residues in contact with THR 727 (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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640C MET* 3.9 14.5 - - - +
643C MET* 4.3 3.3 - - - +
723C GLU* 3.1 18.2 + - + +
726C ARG* 1.3 110.6 - - - +
728C GLY* 1.3 61.9 + - - +
729C LYS* 2.9 56.4 + - - +
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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