Contacts of the helix formed by residues 743 - 753 (chain A) in PDB entry 1GM5
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 VAL 743 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530A SER* 4.3 24.2 - - - -
741A PHE* 4.6 13.5 - - + -
742A LYS* 1.3 80.2 - - - +
744A ALA* 1.3 54.8 + - - +
745A ASP 2.2 22.7 + - - +
746A LEU* 2.3 36.9 + - + +
747A TYR* 2.5 52.4 - - + +
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Residues in contact with ALA 744 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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742A LYS* 5.2 1.7 - - + +
743A VAL* 1.3 75.7 - - - +
745A ASP* 1.3 59.6 + - - +
747A TYR* 3.7 12.3 - - - +
748A ARG* 2.8 40.5 + - - +
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Residues in contact with ASP 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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322A GLU* 4.6 13.3 - - - +
325A ALA* 4.5 3.6 - - - +
326A TYR* 4.1 29.8 + - + +
329A LEU* 4.2 17.4 - - + +
739A SER* 5.4 1.5 - - - -
742A LYS* 4.3 28.4 - - - +
743A VAL* 2.2 18.1 + - - +
744A ALA* 1.3 71.1 - - - +
746A LEU* 1.3 50.0 + - - +
747A TYR 2.9 4.5 - - - -
748A ARG* 2.8 11.4 + - - +
749A ASP* 2.5 44.8 + - - +
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Residues in contact with LEU 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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329A LEU* 3.7 28.5 - - + -
333A GLN* 3.8 15.0 + - + +
530A SER* 4.0 19.3 - - - +
533A LEU* 4.2 11.0 - - + +
534A ALA* 3.1 35.4 - - + +
741A PHE* 5.0 9.6 - - + -
742A LYS 6.0 0.4 - - - +
743A VAL* 2.3 38.3 + - + +
745A ASP* 1.3 62.9 - - - +
747A TYR* 1.3 58.4 - - + +
749A ASP* 2.1 66.0 - - - +
750A LEU* 3.5 15.2 - - - +
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Residues in contact with TYR 747 (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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529A ARG* 5.0 14.3 + - - -
533A LEU* 5.4 11.0 - - + -
743A VAL* 2.5 47.9 - - + +
744A ALA* 3.7 9.0 - - - +
745A ASP 2.9 0.2 - - - -
746A LEU* 1.3 81.8 - - + +
748A ARG* 1.3 55.6 + - - +
749A ASP 2.5 17.0 + - - -
750A LEU* 2.8 25.4 + - + +
751A LYS* 3.4 27.6 + - - +
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Residues in contact with ARG 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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296A ARG* 1.5 76.3 - - - +
326A TYR* 4.4 9.2 - - + -
744A ALA* 2.8 30.1 + - - +
745A ASP* 3.2 13.9 - - - +
747A TYR* 1.3 75.4 - - - +
749A ASP* 1.3 52.8 - - - +
751A LYS* 3.9 5.7 + - - +
752A LEU* 2.0 52.2 + - + +
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Residues in contact with ASP 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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326A TYR* 4.2 9.0 - - - -
329A LEU* 4.0 13.2 - - - +
330A PHE 4.9 0.5 + - - -
333A GLN* 3.9 17.4 - - + +
745A ASP 2.5 22.7 + - - +
746A LEU* 2.1 54.8 - - - +
747A TYR 2.5 3.4 + - - -
748A ARG* 1.3 66.0 - - - +
750A LEU* 1.3 65.7 + - - +
751A LYS 2.6 4.7 + - - -
752A LEU 2.9 0.7 + - - -
753A LEU* 1.5 101.5 + - + +
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Residues in contact with LEU 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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333A GLN* 4.5 16.8 - - - +
337A GLN* 4.7 18.2 - - - +
340A ARG* 5.2 7.4 - - - +
533A LEU* 5.1 15.3 - - + +
746A LEU 3.5 20.6 + - - +
747A TYR* 2.8 22.5 + - + +
749A ASP* 1.3 82.4 - - - +
751A LYS* 1.3 69.9 + - + +
753A LEU* 3.2 17.1 + - - +
754A GLU* 3.9 7.3 + - - +
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Residues in contact with LYS 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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295A LYS* 4.4 15.2 + - - +
296A ARG* 5.1 2.5 - - - +
747A TYR* 3.4 28.3 - - - +
748A ARG* 4.2 9.9 - - - +
749A ASP 2.6 4.8 + - - -
750A LEU* 1.3 76.7 - - + +
752A LEU* 1.3 59.5 + - + +
753A LEU 2.9 4.9 + - - -
754A GLU* 4.3 11.5 + - - +
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Residues in contact with LEU 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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291A ARG* 6.0 4.3 - - - +
292A ILE* 4.9 7.9 - - + -
295A LYS* 3.6 17.9 - - + +
296A ARG* 3.0 48.5 - - + +
326A TYR* 2.9 27.1 - - + +
330A PHE* 4.6 2.8 - - - -
748A ARG* 2.0 41.3 - - - +
749A ASP 2.9 0.6 + - - -
751A LYS* 1.3 71.1 - - + +
753A LEU* 1.3 95.7 + - + +
754A GLU 3.1 9.5 + - - -
755A TRP 3.4 18.5 + - - +
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Residues in contact with LEU 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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326A TYR* 3.0 16.8 - - + +
330A PHE* 3.6 23.1 - - + -
333A GLN* 4.1 21.2 - - + +
334A LEU* 4.5 5.4 - - + +
337A GLN* 3.4 20.3 - - - +
749A ASP* 1.5 100.0 + - + +
750A LEU* 3.5 8.4 - - - +
751A LYS 2.9 1.2 - - - -
752A LEU* 1.3 119.0 - - + +
754A GLU* 1.3 61.9 + - - +
755A TRP* 4.8 0.2 - - - -
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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