Contacts of the helix formed by residues 743 - 755 (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 743 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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708A ILE 3.1 14.3 + - - -
709A GLY* 4.6 1.4 + - - -
741A HIS* 2.9 3.5 + - - -
742A ASP* 1.3 72.9 - - - +
744A GLY* 1.4 64.5 + - - +
745A LYS 3.3 2.6 + - - -
746A GLN* 3.6 13.6 + - - +
747A ALA* 3.9 8.5 + - - +
776A GLY 4.9 2.1 - - - +
778A GLY 6.0 0.3 + - - -
13B A 3.6 34.8 - - - +
14B C 4.4 4.0 + - - -
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Residues in contact with GLY 744 (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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709A GLY 4.6 3.6 + - - -
713A ALA* 3.9 10.4 - - - +
738A ILE 4.8 0.7 - - - -
739A ALA* 3.3 30.1 - - - -
741A HIS 3.1 10.4 + - - -
743A GLY* 1.4 70.8 - - - +
745A LYS* 1.3 71.3 + - - +
747A ALA* 3.3 16.3 + - - +
748A LEU* 3.2 17.8 - - - +
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Residues in contact with LYS 745 (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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712A GLN* 2.8 50.5 + - + +
713A ALA* 4.0 3.6 - - - +
716A THR* 3.3 27.9 + - - +
744A GLY* 1.3 77.5 - - - +
746A GLN* 1.3 94.5 + - - +
747A ALA 3.1 0.2 + - - -
748A LEU* 3.1 9.1 + - - -
749A GLU* 2.6 42.1 + - - +
13B A 3.8 10.3 - - - +
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Residues in contact with GLN 746 (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 3.6 4.2 + - - +
744A GLY 3.4 1.2 - - - -
745A LYS* 1.3 100.5 - - - +
747A ALA* 1.3 61.7 + - - +
749A GLU* 3.4 14.5 + - + +
750A THR* 2.3 33.9 + - - -
779A LYS* 3.5 37.0 - - + +
13B A 2.4 41.1 + - - +
14B C 3.6 21.5 - - - +
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Residues in contact with ALA 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A ILE* 3.8 18.4 - - + +
743A GLY 3.9 6.7 + - - +
744A GLY 3.3 12.0 + - - +
746A GLN* 1.3 83.4 - - - +
748A LEU* 1.3 61.3 + - - +
750A THR* 3.0 10.6 + - - -
751A VAL* 3.3 10.9 + - - +
773A ALA 3.8 22.2 - - - +
775A ASN 6.0 0.2 - - - +
778A GLY* 4.6 4.7 - - - -
779A LYS 4.0 17.2 - - - +
782A LEU* 3.9 6.9 - - - +
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Residues in contact with LEU 748 (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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713A ALA* 4.7 3.1 - - + +
716A THR* 3.8 22.0 - - + +
717A VAL* 3.6 24.7 - - + -
720A LEU* 3.9 17.7 - - + +
735A VAL* 3.6 31.9 - - + -
738A ILE* 3.5 28.5 - - + -
739A ALA* 3.8 8.3 - - + -
744A GLY 3.2 26.5 - - - +
745A LYS 3.1 3.8 + - - +
747A ALA* 1.3 72.8 - - - +
749A GLU* 1.3 54.5 + - - +
751A VAL* 2.9 28.7 + - - +
752A GLN* 3.1 14.2 + - - +
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Residues in contact with GLU 749 (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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716A THR* 4.8 4.6 + - + +
720A LEU* 3.7 20.5 - - + +
745A LYS* 2.6 49.4 + - + +
746A GLN* 3.5 17.3 + - - +
748A LEU* 1.3 78.8 - - - +
750A THR* 1.3 57.3 + - - +
751A VAL 3.1 0.2 - - - -
752A GLN* 3.2 26.2 + - - +
753A ARG* 3.1 41.9 + - - +
779A LYS* 5.1 1.0 + - - +
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Residues in contact with THR 750 (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 2.3 27.3 + - - -
747A ALA 3.0 5.1 + - - -
749A GLU* 1.3 73.4 - - - +
751A VAL* 1.3 59.0 + - - +
753A ARG* 3.6 6.3 - - - +
754A LEU* 3.2 32.6 - - + +
779A LYS* 2.9 55.5 + - - +
782A LEU* 3.6 21.6 - - + +
783A GLU* 3.7 15.7 - - + -
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Residues in contact with VAL 751 (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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724A LEU* 5.6 5.2 - - + -
728A HIS* 5.7 0.7 - - - +
730A LEU* 4.8 11.9 - - + -
738A ILE* 4.1 20.0 - - + -
747A ALA 3.3 10.3 + - - +
748A LEU* 2.9 13.2 + - - +
750A THR* 1.3 76.4 - - - +
752A GLN* 1.3 58.4 + - + +
753A ARG 2.6 15.9 + - - -
754A LEU 2.6 0.9 + - - -
755A LEU* 2.3 64.2 + - + +
769A VAL* 4.6 15.5 - - + +
770A VAL* 5.6 1.3 - - - -
773A ALA* 4.9 0.2 - - + -
782A LEU* 4.1 13.9 - - + -
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Residues in contact with GLN 752 (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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720A LEU* 3.1 49.3 - - + +
723A VAL* 4.8 11.9 - - + -
728A HIS* 4.6 15.5 - - - -
748A LEU 3.1 5.8 + - - +
749A GLU* 3.2 19.2 + - - +
751A VAL* 1.3 84.0 - - + +
753A ARG* 1.3 96.9 + - - +
756A PRO* 4.5 7.6 - - - +
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Residues in contact with ARG 753 (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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749A GLU* 3.1 55.4 + - - +
750A THR* 3.5 5.6 - - - +
751A VAL 2.6 6.6 + - - -
752A GLN* 1.3 107.1 - - - +
754A LEU* 1.3 71.2 + - + +
755A LEU 3.9 0.3 + - - -
756A PRO* 4.1 3.5 - - - +
757A VAL* 3.8 12.3 - - - +
779A LYS* 2.9 31.4 - - - +
783A GLU* 5.6 1.6 + - - -
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Residues in contact with LEU 754 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A THR* 3.2 22.8 + - + +
751A VAL 2.6 6.5 + - - -
753A ARG* 1.3 88.9 - - + +
755A LEU* 1.3 65.1 + - - +
756A PRO* 3.6 2.0 - - - -
757A VAL* 3.7 16.6 - - + +
758A LEU* 3.3 29.8 + - + +
782A LEU* 5.5 2.7 - - + +
783A GLU* 4.1 34.1 - - + +
786A GLN* 3.3 44.9 - - + +
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Residues in contact with LEU 755 (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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724A LEU* 5.6 0.4 - - + -
728A HIS* 3.6 37.0 - - + +
730A LEU* 4.5 18.6 - - + -
751A VAL* 2.3 59.1 + - + +
754A LEU 1.3 69.8 - - - +
756A PRO* 1.4 75.1 - - + +
758A LEU* 3.1 22.5 + - - +
759A CYS* 4.0 16.4 + - - -
766A PRO* 4.6 15.9 - - + +
769A VAL* 4.4 16.2 - - + -
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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