Contacts of the helix formed by residues 777 - 789 (chain A) in PDB entry 3UGM
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 GLY 777 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775A ASN* 3.0 4.1 + - - +
776A GLY* 1.3 75.4 - - - +
778A GLY* 1.3 60.7 + - - +
779A LYS 3.7 1.1 - - - -
780A GLN* 3.2 10.6 + - - +
781A ALA* 3.1 22.9 + - - +
809A ASN 5.6 1.5 + - - -
810A ASN* 4.6 9.5 + - - +
812A GLY* 5.6 0.9 - - - -
813A LYS 5.6 0.3 + - - -
14B C 4.2 14.8 - - - -
15B T 3.6 26.0 + - - +
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Residues in contact with GLY 778 (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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743A GLY 6.0 0.2 + - - -
747A ALA* 4.6 7.2 - - - -
772A ILE 4.0 2.0 - - - +
773A ALA* 4.3 19.5 - - - -
775A ASN* 3.1 13.4 + - - -
776A GLY 3.2 4.8 + - - -
777A GLY* 1.3 70.3 - - - +
779A LYS* 1.3 67.9 + - - +
780A GLN 2.8 2.9 + - - -
781A ALA* 2.9 14.0 + - - +
782A LEU* 3.0 20.3 + - - +
14B C 4.8 1.2 + - - -
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Residues in contact with LYS 779 (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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746A GLN* 3.5 40.8 + - + +
747A ALA* 4.0 7.9 - - - +
749A GLU* 5.1 0.8 + - - +
750A THR* 2.9 50.7 + - - +
753A ARG* 2.9 26.9 - - - +
777A GLY 3.7 0.2 - - - -
778A GLY* 1.3 72.8 - - - +
780A GLN* 1.3 63.8 + - - +
782A LEU* 3.6 3.3 + - - +
783A GLU* 3.2 57.5 + - - +
14B C 3.7 14.0 + - - +
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Residues in contact with GLN 780 (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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777A GLY 3.3 13.0 - - - +
778A GLY 2.9 0.6 - - - -
779A LYS* 1.3 85.9 - - - +
781A ALA* 1.3 58.6 + - - +
783A GLU* 4.1 15.2 + - - +
784A THR* 2.6 31.7 + - - -
813A LYS* 2.7 52.6 - - + +
14B C 2.7 55.9 + - - +
15B T 4.5 0.9 - - - +
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Residues in contact with ALA 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A ILE* 3.6 21.1 - - + +
775A ASN* 5.7 1.8 - - - +
777A GLY 3.1 10.4 + - - +
778A GLY* 2.9 5.3 + - - +
780A GLN* 1.3 74.3 - - - +
782A LEU* 1.4 68.9 + - - +
784A THR* 2.9 13.5 + - - -
785A VAL* 2.9 16.1 + - - +
807A ALA* 3.7 21.5 - - + +
809A ASN 5.4 0.7 - - - +
812A GLY* 3.9 15.0 - - - -
813A LYS 4.3 7.6 - - - +
816A LEU* 4.8 1.2 - - - +
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Residues in contact with LEU 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A ALA 3.9 7.6 - - - +
750A THR* 3.6 43.1 - - + +
751A VAL* 4.1 6.1 - - + -
754A LEU* 5.5 3.4 - - + -
758A LEU* 4.0 19.4 - - + +
769A VAL* 3.9 28.9 - - + +
772A ILE* 3.9 12.9 + - + +
773A ALA* 3.8 31.2 - - + -
778A GLY 3.0 11.1 + - - +
779A LYS* 3.6 6.5 - - - +
781A ALA* 1.4 74.1 - - - +
783A GLU* 1.3 55.6 + - - +
785A VAL* 2.8 30.1 + - - +
786A GLN* 3.0 12.4 + - - +
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Residues in contact with GLU 783 (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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750A THR* 3.7 13.5 - - + +
753A ARG* 5.6 1.4 + - - -
754A LEU* 4.1 15.0 - - + +
779A LYS* 3.2 49.6 + - - +
780A GLN* 4.1 16.6 + - - +
782A LEU* 1.3 78.4 - - - +
784A THR* 1.3 59.0 + - - +
786A GLN* 3.3 9.3 + - - +
787A ARG* 2.9 29.8 + - - +
813A LYS* 5.3 2.0 + - - +
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Residues in contact with THR 784 (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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780A GLN 2.6 23.3 + - - -
781A ALA 2.9 6.6 + - - -
783A GLU* 1.3 76.8 - - - +
785A VAL* 1.3 60.8 + - - +
787A ARG* 3.5 29.8 + - - +
788A LEU* 3.2 37.9 + - + +
789A LEU 4.4 0.2 + - - -
813A LYS* 3.2 32.8 - - + +
816A LEU* 4.0 21.9 - - + +
817A GLU* 5.1 1.1 - - + +
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Residues in contact with VAL 785 (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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758A LEU* 3.8 18.8 - - + -
764A LEU* 3.9 11.0 - - + -
772A ILE* 4.2 15.7 - - + -
781A ALA 2.9 10.8 + - - +
782A LEU* 2.8 10.6 + - - +
784A THR* 1.3 77.6 - - - +
786A GLN* 1.3 70.8 + - - +
787A ARG 3.1 0.2 + - - -
789A LEU* 2.9 51.3 + - + +
803A VAL* 4.2 18.4 - - + +
804A VAL* 5.6 0.4 - - - +
807A ALA* 4.1 22.4 - - + -
816A LEU* 4.7 3.8 - - + -
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Residues in contact with GLN 786 (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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754A LEU* 3.3 37.8 - - + +
757A VAL* 4.0 17.9 - - - +
758A LEU* 4.2 15.9 - - + +
761A ALA* 6.1 0.2 - - - +
762A HIS* 5.8 1.6 - - - +
782A LEU 3.0 9.9 + - - +
783A GLU* 3.4 11.9 - - - +
785A VAL* 1.3 78.2 - - - +
787A ARG* 1.3 70.1 + - + +
789A LEU* 4.4 2.3 + - - +
790A PRO* 5.0 2.8 - - - +
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Residues in contact with ARG 787 (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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783A GLU 2.9 17.4 + - - +
784A THR* 3.5 35.1 + - - +
786A GLN* 1.3 84.3 - - - +
788A LEU* 1.3 78.7 + - + +
789A LEU 3.7 0.3 + - - -
790A PRO* 4.6 8.7 - - - +
813A LYS* 4.1 16.8 - - - +
817A GLU* 4.1 21.6 + - - +
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Residues in contact with LEU 788 (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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784A THR* 3.2 25.8 + - + +
787A ARG* 1.3 92.2 - - + +
789A LEU* 1.3 66.1 + - - +
790A PRO* 2.8 17.8 - - - +
816A LEU* 3.9 19.7 - - + +
817A GLU* 3.8 39.0 - - + +
820A GLN* 4.2 24.9 - - + +
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Residues in contact with LEU 789 (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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762A HIS* 4.4 17.9 - - + -
764A LEU* 4.4 19.1 - - + -
784A THR 4.4 0.4 + - - -
785A VAL* 2.9 42.2 + - + +
786A GLN* 4.9 0.9 - - - +
788A LEU* 1.3 69.3 - - - +
790A PRO* 1.4 81.9 - - + +
798A LEU* 6.1 1.2 - - - +
799A THR 5.3 4.7 - - - +
800A GLN* 4.7 21.5 - - + +
803A VAL* 4.3 27.8 - - + +
816A LEU* 6.0 1.9 - - - +
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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