Contacts of the helix formed by residues 690 - 702 (chain D) in PDB entry 1UES
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 LYS 690 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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688D ALA 3.8 6.0 + - - +
689D PRO* 1.3 78.1 - - - +
691D GLY* 1.3 63.9 + - - +
693D LEU 3.8 0.5 + - - -
694D GLY* 3.0 19.3 + - - -
788D GLU* 2.7 29.6 + - - +
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Residues in contact with GLY 691 (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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690D LYS* 1.3 77.4 - - - +
692D LYS* 1.3 65.8 + - - -
695D GLU* 3.1 30.0 + - - +
788D GLU* 5.4 1.3 - - - -
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Residues in contact with LYS 692 (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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691D GLY* 1.3 68.7 - - - -
693D LEU* 1.3 60.6 + - - +
695D GLU* 3.2 11.9 + - - +
696D ALA* 2.8 30.3 + - - +
791D TYR* 3.9 17.8 - - + -
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Residues in contact with LEU 693 (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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689D PRO* 4.8 1.3 - - + -
690D LYS 3.8 0.2 + - - -
691D GLY 3.3 0.4 - - - -
692D LYS* 1.3 79.4 - - - +
694D GLY* 1.3 58.9 + - - +
696D ALA* 3.1 2.8 + - - +
697D ILE* 2.9 48.8 + - + +
726D LEU* 4.8 3.1 - - + -
734D LEU* 4.0 22.9 - - + -
753D LEU* 4.2 8.1 - - + -
784D TRP* 4.2 9.2 - - + -
787D VAL* 3.7 25.8 - - + +
788D GLU* 3.7 41.7 - - + +
791D TYR* 3.6 32.5 - - + -
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Residues in contact with GLY 694 (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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689D PRO* 3.8 30.6 - - - +
690D LYS* 3.0 22.0 + - - -
691D GLY 3.8 0.7 - - - -
693D LEU* 1.3 76.8 - - - +
695D GLU* 1.3 60.8 + - - +
697D ILE* 3.5 2.6 + - - +
698D ASP* 3.2 28.4 + - - +
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Residues in contact with GLU 695 (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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691D GLY 3.1 22.4 + - - +
692D LYS* 3.6 11.4 - - - +
694D GLY* 1.3 74.3 - - - +
696D ALA* 1.3 65.0 + - - +
698D ASP* 3.7 6.1 - - + +
699D LYS* 3.0 41.4 + - - +
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Residues in contact with ALA 696 (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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692D LYS 2.8 16.3 + - - +
693D LEU* 3.1 4.9 + - - +
695D GLU* 1.3 77.9 - - - +
697D ILE* 1.3 56.2 + - - +
699D LYS* 4.7 4.0 - - - +
700D GLN* 2.9 44.5 + - - +
734D LEU* 3.6 14.6 - - + -
791D TYR* 3.3 28.9 - - + +
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Residues in contact with ILE 697 (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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689D PRO* 3.7 26.7 - - + -
693D LEU* 2.9 31.1 + - + +
694D GLY* 3.8 5.2 - - - +
695D GLU 3.3 0.2 - - - -
696D ALA* 1.3 78.7 - - - +
698D ASP* 1.3 56.5 - - - +
701D PHE* 2.7 38.6 + - + +
702D GLY 3.7 0.2 + - - -
703D SER 4.0 0.8 + - - +
704D PHE* 4.0 20.2 - - + -
707D PHE* 3.7 41.1 - - + -
726D LEU* 4.7 5.8 - - + -
734D LEU* 3.8 18.8 - - + -
784D TRP* 4.3 11.0 - - + -
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Residues in contact with ASP 698 (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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694D GLY 3.2 17.8 + - - +
695D GLU* 3.7 7.6 - - + +
697D ILE* 1.3 79.8 - - - +
699D LYS* 1.3 58.9 + - + +
702D GLY* 2.8 39.5 + - - +
703D SER* 3.7 5.5 - - - +
704D PHE* 3.6 22.7 + - - +
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Residues in contact with LYS 699 (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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695D GLU* 3.0 33.1 + - + +
696D ALA* 4.1 4.5 - - - +
698D ASP* 1.3 81.1 - - - +
700D GLN* 1.3 65.5 + - + +
702D GLY* 4.1 2.6 + - - -
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Residues in contact with GLN 700 (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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696D ALA* 2.9 37.3 + - - +
699D LYS* 1.3 84.6 - - + +
701D PHE* 1.3 71.4 + - + +
702D GLY 3.6 0.4 - - - -
732D GLY 3.8 8.3 - - - +
733D LYS* 3.4 18.0 - - + +
734D LEU* 2.5 42.7 + - - +
791D TYR* 4.6 0.2 + - - -
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Residues in contact with PHE 701 (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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697D ILE* 2.7 31.2 + - + +
700D GLN* 1.3 81.8 - - + +
702D GLY* 1.3 55.4 + - - +
703D SER 3.2 4.7 - - - +
706D LYS* 3.2 24.1 - - - +
707D PHE* 3.8 45.5 - + + +
710D GLU* 3.7 37.5 - - - +
726D LEU* 4.7 1.3 - - + -
734D LEU* 3.9 41.7 - - + -
735D SER* 4.7 2.5 - - - -
736D ILE* 3.7 21.8 - - + -
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Residues in contact with GLY 702 (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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698D ASP* 2.8 24.9 + - - +
699D LYS 4.1 2.3 + - - -
700D GLN 3.6 1.6 - - - -
701D PHE* 1.3 77.7 - - - +
703D SER* 1.3 60.4 + - - +
706D LYS* 3.8 12.6 - - - -
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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