Contacts of the helix formed by residues 718 - 727 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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632A PRO* 5.3 5.2 - - + -
633A LEU* 5.7 2.0 - - + -
656A CYS* 4.2 8.5 - - - -
660A GLU* 4.1 5.4 - - - +
664A LEU* 3.6 45.8 - - + -
696A ILE* 3.9 22.0 - - + +
697A LEU 4.1 7.2 + - - +
698A LYS* 3.8 29.8 - - + +
717A THR* 1.3 73.6 - - - +
719A ALA* 1.3 62.7 + - - +
721A LEU* 2.9 16.4 + - + +
722A LEU* 3.1 26.0 + - + +
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Residues in contact with ALA 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717A THR* 3.1 12.6 + - - +
718A ILE* 1.3 79.7 - - - +
720A TRP* 1.3 56.2 + - - +
722A LEU* 3.8 11.0 - - - +
723A GLU* 2.8 32.7 + - - +
736A PHE* 3.8 15.4 - - + -
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Residues in contact with TRP 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646A LEU* 3.5 37.2 - - + -
651A ILE* 4.2 19.3 - - + -
694A HIS* 3.5 23.1 - + - -
696A ILE* 4.2 10.3 - - + -
716A VAL* 3.7 22.2 - - + -
717A THR 3.1 13.1 + - - +
718A ILE 3.0 0.6 + - - -
719A ALA* 1.3 78.0 - - - +
721A LEU* 1.3 78.2 + - + +
723A GLU* 3.2 2.8 + - - +
724A THR* 3.0 33.3 + - - -
730A ARG* 4.4 2.2 - - + -
731A ALA* 2.8 40.2 + - + +
733A GLU* 3.4 37.0 - - + +
736A PHE* 3.5 34.4 - + + -
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Residues in contact with LEU 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646A LEU* 3.9 16.4 - - + -
651A ILE* 5.0 0.2 - - + -
653A PHE* 4.6 2.0 - - + -
664A LEU* 3.9 46.7 - - + +
667A LEU* 4.0 14.8 - - + -
668A ALA* 4.1 13.0 - - + +
671A LEU* 3.7 21.5 - - + -
696A ILE* 4.1 26.2 - - + -
717A THR 4.1 0.2 + - - -
718A ILE* 2.9 11.6 + - + +
720A TRP* 1.3 87.7 - - + +
722A LEU* 1.3 62.0 + - + +
724A THR* 3.3 6.2 + - - -
725A ALA* 3.1 19.6 + - - +
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Residues in contact with LEU 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632A PRO* 3.4 40.4 - - + -
633A LEU* 4.2 13.0 - - + -
637A VAL* 4.3 16.0 - - + +
638A PRO 4.7 1.2 - - - +
664A LEU* 5.0 0.2 - - + -
667A LEU* 3.6 30.7 - - + -
718A ILE* 3.1 24.2 + - + +
719A ALA* 4.0 9.9 - - - +
721A LEU* 1.3 76.4 - - + +
723A GLU* 1.3 60.8 + - - +
725A ALA* 3.3 4.5 + - + +
726A ARG* 3.0 28.9 + - - +
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Residues in contact with GLU 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A ALA 2.8 18.5 + - - +
720A TRP 3.8 3.4 - - - +
722A LEU* 1.3 73.9 - - - +
724A THR* 1.3 64.5 + - - +
726A ARG* 2.5 42.3 + - - +
727A THR* 3.1 33.1 + - + +
731A ALA* 4.3 10.5 - - + -
736A PHE* 3.9 23.8 - - + -
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Residues in contact with THR 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A PRO* 3.6 25.8 - - + +
646A LEU* 3.8 18.4 - - + -
671A LEU* 3.8 14.6 - - + -
720A TRP* 3.0 23.7 + - - -
721A LEU* 3.4 11.7 - - - -
723A GLU* 1.3 78.7 - - - +
725A ALA* 1.3 60.7 + - - +
727A THR* 3.5 1.0 + - - -
728A GLY* 3.1 21.1 + - - -
729A LYS 3.4 14.4 + - - +
730A ARG* 3.8 2.0 - - - -
731A ALA* 3.0 23.4 + - - +
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Residues in contact with ALA 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A VAL* 5.1 3.1 - - + -
638A PRO 3.8 3.8 - - - +
639A VAL* 3.3 24.3 - - + +
640A MET* 2.8 24.6 + - - +
667A LEU* 5.1 8.7 - - + -
671A LEU* 3.8 24.0 - - + +
721A LEU 3.1 12.9 + - - +
722A LEU* 3.7 10.5 - - - +
723A GLU 3.2 0.2 - - - -
724A THR* 1.3 78.0 - - - +
726A ARG* 1.3 63.9 + - - +
727A THR 3.4 0.2 + - - -
728A GLY* 3.6 4.0 + - - -
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Residues in contact with ARG 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A PRO* 3.3 38.5 + - + +
640A MET* 3.4 19.2 + - - +
722A LEU 3.0 15.9 + - - +
723A GLU* 2.5 42.0 + - - +
724A THR 3.4 0.2 - - - -
725A ALA* 1.3 79.6 - - - +
727A THR* 1.3 73.3 + - - +
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Residues in contact with THR 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640A MET* 3.3 23.6 - - - +
723A GLU* 3.1 22.3 + - + +
725A ALA 3.3 0.2 - - - -
726A ARG* 1.3 103.7 - - - +
728A GLY* 1.3 58.4 + - - +
729A LYS* 2.9 50.6 + - - +
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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