Contacts of the helix formed by residues 700 - 707 (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 ASP 700 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669A CYS* 3.3 17.2 - - - -
670A GLY 4.6 4.7 - - - +
672A ILE* 3.5 29.4 + - + +
698A ALA 3.3 0.6 + - - -
699A GLY* 1.3 67.3 - - - -
701A ALA* 1.3 63.4 + - - +
702A ARG* 3.1 3.3 + - - -
703A LYS* 3.2 31.0 + - + +
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Residues in contact with ALA 701 (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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667A VAL* 3.2 44.2 - - + +
668A PRO 3.9 0.7 - - - +
672A ILE* 3.6 16.5 - - + +
697A LEU* 3.7 8.4 - - - +
698A ALA 3.0 20.0 + - - +
700A ASP* 1.3 77.2 - - - +
702A ARG* 1.3 54.1 + - - +
703A LYS 3.1 1.1 - - - -
704A PHE* 3.0 34.5 + - - +
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Residues in contact with ARG 702 (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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697A LEU* 3.4 27.1 - - + +
699A GLY* 2.8 33.4 + - - +
700A ASP* 3.1 1.8 + - - -
701A ALA* 1.3 76.4 - - - +
703A LYS* 1.3 56.2 + - + +
704A PHE 3.1 1.3 - - - -
705A LYS* 3.0 37.5 + - + +
720A GLU* 3.8 33.8 + - + +
721A ALA* 3.4 14.3 + - - +
722A ASP* 2.7 41.3 + - - +
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Residues in contact with LYS 703 (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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672A ILE* 5.2 6.7 - - + -
676A ALA* 6.3 2.5 - - + -
700A ASP* 3.2 23.3 + - + +
701A ALA 3.1 0.6 - - - -
702A ARG* 1.3 77.3 - - + +
704A PHE* 1.3 59.6 + - - +
705A LYS 3.2 1.3 + - - -
706A ALA* 3.6 17.0 + - - +
707A THR* 5.0 0.3 + - - -
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Residues in contact with PHE 704 (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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606A LEU* 6.0 1.6 - - + -
667A VAL* 4.1 15.5 - - + -
672A ILE* 4.3 15.5 - - + -
675A ILE* 3.7 42.8 - - + -
676A ALA* 3.9 12.6 - - - -
681A ALA* 4.6 4.5 - - + -
682A ASN* 3.6 41.3 - - - -
685A LEU* 3.5 33.2 - - + +
697A LEU* 4.3 6.3 - - + -
701A ALA* 3.0 26.8 + - - +
703A LYS* 1.3 74.2 - - - +
705A LYS* 1.3 63.6 + - - +
706A ALA 3.1 2.7 - - - -
707A THR* 3.0 24.7 + - - -
708A ILE* 3.7 6.5 + - - +
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Residues in contact with LYS 705 (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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697A LEU* 3.7 18.5 - - + +
702A ARG* 3.0 30.3 + - + +
704A PHE* 1.3 76.7 - - - +
706A ALA* 1.3 60.0 + - - +
708A ILE* 3.3 23.5 + - + +
709A LYS 3.3 7.1 + - - -
710A ILE 3.7 16.4 + - - +
711A ALA* 3.5 22.2 - - - +
712A ASP* 3.1 28.0 + - - +
714A GLY* 3.8 3.8 - - - +
718A ILE* 5.0 7.6 - - + -
720A GLU* 2.6 43.2 + - - +
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Residues in contact with ALA 706 (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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703A LYS 3.6 12.6 + - - +
704A PHE 3.1 1.0 - - - -
705A LYS* 1.3 77.7 - - - +
707A THR* 1.3 61.0 + - - +
709A LYS* 3.0 48.4 + - - +
710A ILE 5.3 0.2 - - - +
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Residues in contact with THR 707 (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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682A ASN* 2.6 45.3 + - + +
685A LEU* 5.5 2.2 - - - -
686A MET* 3.5 44.7 - - + +
703A LYS 5.0 0.3 + - - -
704A PHE* 3.0 22.1 + - - -
706A ALA* 1.3 76.9 - - - +
708A ILE* 1.3 60.7 + - - +
709A LYS* 3.1 6.7 + - - +
751A ILE* 5.9 0.9 - - - +
752D PRO* 4.7 3.8 - - + -
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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