Contacts of the helix formed by residues 770 - 779 (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 ARG 770 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASN* 4.2 19.7 - - - +
426C PHE* 6.3 0.6 - - - -
766D THR* 3.7 21.0 + - - +
767D TYR* 2.9 41.2 + - + +
768D GLN* 3.2 7.2 + - - -
769D ASN* 1.3 86.4 - - - +
771D ARG* 1.3 65.2 + - - +
772D ALA 3.2 2.5 - - - +
773D ASP* 2.9 39.8 + - + +
774D HIS 3.2 15.9 + - - -
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Residues in contact with ARG 771 (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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49A GLU* 5.9 0.4 - - - +
559C TRP* 5.5 3.6 - - - -
715D GLY 2.9 27.1 + - - -
716D THR* 3.7 19.5 + - + +
718D LEU 2.7 25.4 + - - -
720D GLY* 2.9 28.5 + - - +
758D VAL* 3.3 30.4 + - + +
760D GLU* 5.2 4.0 - - - +
763D TYR* 3.0 48.3 + - + +
769D ASN 2.9 12.4 + - - +
770D ARG* 1.3 71.6 - - - +
772D ALA* 1.3 64.4 + - - +
774D HIS* 3.0 13.0 + - - +
775D LEU* 3.0 21.8 + - + +
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Residues in contact with ALA 772 (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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46A THR 3.8 22.4 - - - +
47A GLU* 4.0 16.4 - - - +
49A GLU* 4.2 11.0 + - + +
50A ASN* 4.4 12.3 + - - +
716D THR* 3.9 21.3 + - + +
770D ARG* 3.2 0.8 - - - +
771D ARG* 1.3 79.9 - - - +
773D ASP* 1.3 64.0 + - - +
775D LEU* 3.4 2.5 + - - +
776D LYS* 3.1 27.2 + - - +
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Residues in contact with ASP 773 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU 5.1 2.4 - - - +
50A ASN* 4.5 13.8 - - - +
767D TYR* 3.7 7.4 - - + -
770D ARG* 2.9 53.4 + - - +
772D ALA* 1.3 81.1 - - - +
774D HIS* 1.3 63.9 + - - +
776D LYS* 3.3 15.0 + - - +
777D ASP* 3.0 31.2 + - - +
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Residues in contact with HIS 774 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618D VAL* 4.0 13.2 + - - +
619D ILE* 4.5 4.9 - - + -
677D TYR* 4.3 6.8 + - - -
757D ASP 4.5 6.7 + - - -
762D ALA 4.0 12.1 + - - -
763D TYR* 3.4 40.7 - + + +
767D TYR* 3.3 30.8 + - + -
770D ARG 3.2 10.0 + - - +
771D ARG 3.0 9.9 + - - +
773D ASP* 1.3 77.8 - - - +
775D LEU* 1.3 74.4 + - + +
777D ASP* 3.2 2.9 + - - +
778D LEU* 3.0 61.1 + - + +
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Residues in contact with LEU 775 (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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712D ASN* 3.8 19.0 - - + +
715D GLY* 3.6 29.6 - - - +
716D THR* 3.5 23.6 - - - +
724D VAL* 5.3 0.2 - - + -
756D PHE* 3.8 33.7 - - + -
757D ASP 4.7 0.7 - - - +
758D VAL* 3.9 19.5 - - + -
771D ARG* 3.0 20.2 + - + +
772D ALA 4.0 4.0 - - - +
774D HIS* 1.3 91.7 - - + +
776D LYS* 1.3 63.0 + - - +
778D LEU* 3.3 11.6 + - + -
779D TRP* 3.3 15.8 + - - -
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Residues in contact with LYS 776 (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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47A GLU* 2.9 62.5 + - + +
48A PHE* 4.2 4.4 - - - -
55A THR* 5.2 3.0 - - - +
59A LYS* 4.0 32.1 - - - +
712D ASN* 4.1 10.1 - - - +
772D ALA 3.1 16.9 + - - +
773D ASP* 3.7 16.8 - - - +
775D LEU* 1.3 76.2 - - - +
777D ASP* 1.3 66.4 + - - +
779D TRP* 3.3 24.2 + - - +
780D SER 5.0 0.2 + - - -
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Residues in contact with ASP 777 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618D VAL* 4.0 16.2 - - + +
767D TYR* 2.7 36.7 + - - +
773D ASP* 3.0 16.3 + - - +
774D HIS 3.2 2.2 + - - +
776D LYS* 1.3 84.1 - - - +
778D LEU* 1.3 64.4 + - - +
779D TRP 3.1 0.9 + - - -
780D SER* 3.0 24.1 + - - -
781D ILE* 4.5 0.3 + - - +
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Residues in contact with LEU 778 (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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618D VAL* 3.7 14.4 - - + -
619D ILE* 4.1 7.2 - - + -
677D TYR* 4.8 4.0 - - + +
681D PHE* 4.1 14.5 - - + -
756D PHE* 3.6 48.5 - - + -
757D ASP 5.2 0.7 - - - +
774D HIS* 3.0 54.8 + - + +
775D LEU* 3.3 11.3 + - + +
777D ASP* 1.3 76.0 - - - +
779D TRP* 1.3 61.4 + - - +
781D ILE* 3.1 34.0 + - + +
782D VAL* 3.5 10.2 - - - +
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Residues in contact with TRP 779 (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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686D GLY* 3.5 11.4 - - - -
687D GLY 4.5 2.9 + - - +
704D PHE* 4.3 4.5 - + + -
707D PHE* 3.5 25.8 - + - -
708D LYS* 3.8 43.7 - - + +
711D PHE* 3.5 36.3 - + + -
712D ASN* 2.8 29.7 + - - +
754D LEU* 3.8 11.4 - - + -
756D PHE* 3.5 14.6 - + - -
775D LEU 3.3 10.9 + - - -
776D LYS* 3.3 25.6 - - - +
777D ASP 3.1 0.8 + - - -
778D LEU* 1.3 77.6 - - - +
780D SER* 1.3 61.4 + - - +
781D ILE 3.2 1.0 + - - -
782D VAL* 3.4 18.6 + - + +
784D TRP* 3.7 33.3 + + - -
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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