Contacts of the helix formed by residues 744 - 749 (chain A) in PDB entry 1GGE
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 744 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689A TYR* 2.9 78.6 + - + +
692A LEU* 3.4 4.8 - - + -
693A LYS 2.8 40.6 + - - +
695A ILE* 4.7 0.2 - - - +
715A GLU* 4.1 5.7 + - - +
716A GLU 5.1 1.7 + - - +
717A GLY* 3.2 33.1 + - - -
718A ILE* 3.6 9.5 - - - +
741A VAL* 3.0 29.2 + - + +
743A SER* 1.3 77.2 + - - +
745A ILE* 1.3 67.2 + - - +
746A PRO 3.3 1.3 - - - -
747A LYS* 2.8 23.1 + - + -
748A ILE* 3.3 11.9 + - + +
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Residues in contact with ILE 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A PHE* 3.5 33.4 - - + -
521A ARG* 3.5 38.8 - - - +
522A HIS* 3.9 17.5 - - - +
692A LEU* 3.7 32.0 - - + +
742A TRP* 3.0 22.8 + - + +
744A ARG* 1.3 76.2 - - - +
746A PRO* 1.3 69.2 - - + +
748A ILE* 3.1 25.3 + - + +
749A ASP* 4.3 5.9 + - - +
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Residues in contact with PRO 746 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ARG* 5.4 7.4 - - - +
742A TRP 4.2 1.3 - - - +
743A SER* 3.4 18.8 - - - +
744A ARG 3.4 0.9 - - - -
745A ILE* 1.3 99.9 - - + +
747A LYS* 1.3 61.8 + - + +
748A ILE 3.6 0.3 + - - -
749A ASP* 4.4 5.4 + - - +
750A LYS 5.6 0.3 + - - -
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Residues in contact with LYS 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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689A TYR* 3.9 24.2 - - - +
710A ILE* 3.4 25.0 - - + +
711A ALA* 5.6 1.4 - - - +
715A GLU* 3.3 31.2 + - - +
743A SER 4.7 4.7 - - - +
744A ARG* 2.8 28.0 + - + +
746A PRO* 1.3 75.7 - - + +
748A ILE* 1.3 60.5 + - - +
749A ASP 3.6 1.1 + - - -
750A LYS* 4.3 8.4 + - - +
751A ILE* 4.2 13.2 + - - +
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Residues in contact with ILE 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A TYR* 4.0 10.8 - - + +
690A LYS* 3.3 38.1 - - + +
692A LEU* 3.9 18.4 - - + -
744A ARG* 3.4 30.5 - - + +
745A ILE* 3.1 21.2 + - + +
747A LYS* 1.3 74.3 - - - +
749A ASP* 1.3 76.9 + - - +
750A LYS 3.2 5.2 - - - -
751A ILE* 2.8 40.2 + - + +
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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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521A ARG* 5.2 7.1 + - - -
690A LYS* 5.2 6.4 - - - -
745A ILE* 4.3 6.0 + - - +
746A PRO 4.4 4.5 + - - +
747A LYS 3.6 1.2 - - - -
748A ILE* 1.3 95.4 - - - +
750A LYS* 1.3 55.5 + - - +
751A ILE 4.8 0.4 - - - -
677D ASP 4.3 1.4 - - - +
678D ASN* 4.6 1.4 - - - -
679D GLY* 3.1 22.4 + - - -
680D ASP* 4.7 10.7 + - - +
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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
------------------------------------------------------------
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