Contacts of the helix formed by residues 79 - 90 (chain P) in PDB entry 4G7Z
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 79 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77P THR 4.1 4.9 - - - +
78P SER* 1.3 85.9 + - - +
80P PRO* 1.3 60.6 - - - +
81P VAL* 2.3 36.9 + - - +
82P ARG* 2.4 35.8 + - + +
83P GLN 3.3 1.7 + - - -
8R G 2.2 47.6 + - - +
9R G 5.8 0.4 - - - -
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Residues in contact with PRO 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572N ARG* 3.4 24.3 + - + +
576N GLU* 3.2 36.1 - - - +
587N ARG* 4.7 3.1 - - - +
78P SER* 2.7 11.1 - - - +
79P ASP* 1.3 84.8 - - - +
81P VAL* 1.3 57.0 + - + +
82P ARG 3.5 0.2 - - - -
83P GLN* 3.8 10.3 - - + +
84P TYR* 2.9 30.1 + - - +
210P LEU* 3.8 21.9 - - + +
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Residues in contact with VAL 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79P ASP* 2.3 23.9 + - - +
80P PRO* 1.3 68.9 - - + +
82P ARG* 1.3 56.2 - - - -
84P TYR* 3.3 5.3 + - + +
85P LEU* 2.9 43.3 + - + +
209P PHE* 4.3 28.5 - - + -
210P LEU* 3.8 27.1 - - + -
213P ILE* 5.8 2.7 - - + -
8R G 3.4 36.8 - - + +
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Residues in contact with ARG 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243M ARG* 2.9 41.2 - - - +
244M PRO* 4.1 24.6 + - - +
245M GLY* 6.0 3.1 - - - -
246M ASP* 6.1 0.8 - - - +
77P THR* 4.2 30.1 + - - +
78P SER 4.8 1.1 - - - +
79P ASP* 2.4 55.9 + - + +
81P VAL* 1.3 68.5 - - - +
83P GLN* 1.3 54.9 + - - +
85P LEU* 3.6 6.4 + - - +
86P HIS* 3.0 27.6 + - + +
7R G 4.6 7.9 + - - +
8R G 3.2 20.3 + - - +
9R G 4.1 4.0 + - - +
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Residues in contact with GLN 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128N TYR* 3.5 6.0 + - - +
129N PHE 2.8 38.0 + - - -
130N SER* 3.3 16.1 - - - +
572N ARG* 3.3 26.6 + - - +
77P THR* 6.2 0.7 - - - -
78P SER* 4.1 13.6 + - - +
79P ASP 3.3 2.4 + - - -
80P PRO* 3.7 8.5 - - - +
81P VAL 3.1 0.4 - - - -
82P ARG* 1.3 77.6 - - - +
84P TYR* 1.3 59.6 + - - +
86P HIS* 3.2 11.1 + - + +
87P GLU* 2.9 49.1 + - + +
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Residues in contact with TYR 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565N ILE* 4.4 12.3 - - + -
569N ASN* 3.2 38.6 - - + +
572N ARG* 4.0 8.7 - - - +
80P PRO 2.9 18.7 + - - +
81P VAL* 3.8 5.2 - - + +
83P GLN* 1.3 76.2 - - - +
85P LEU* 1.3 67.9 + - + +
87P GLU* 3.1 15.3 + - - +
88P ILE* 2.9 59.5 + - + +
192P LEU* 4.2 5.0 + - + +
196P VAL* 3.6 21.3 - - + +
210P LEU* 4.6 4.3 - - + -
213P ILE* 3.5 31.9 - - + +
217P ASN* 3.1 28.2 + - - -
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Residues in contact with LEU 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81P VAL* 2.9 37.4 + - + +
82P ARG* 3.9 6.1 - - - +
84P TYR* 1.3 79.4 - - + +
86P HIS* 1.3 60.9 + - - +
88P ILE* 3.5 5.7 + - + +
89P GLY 3.1 20.1 + - - -
196P VAL* 3.7 37.0 - - + -
209P PHE* 5.6 0.2 - - + -
213P ILE* 5.3 1.6 - - + -
7R G 3.2 55.3 - - + +
8R G 4.3 29.2 - - + +
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Residues in contact with HIS 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245M GLY 5.9 0.8 + - - -
155N ASP* 5.2 9.7 + - - -
82P ARG* 3.0 17.1 + - + +
83P GLN* 3.2 16.8 + - + +
85P LEU* 1.3 76.8 - - - +
87P GLU* 1.3 65.8 + - + +
89P GLY* 3.1 16.8 + - - -
90P GLN* 3.3 39.9 + - + +
7R G 4.1 15.3 + - - +
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Residues in contact with GLU 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N PHE 3.5 3.1 - - - +
155N ASP* 4.9 4.5 - - - +
159N ARG* 4.7 3.0 + - - +
565N ILE* 3.7 35.9 - - + +
568N ARG* 3.3 39.0 + - - +
572N ARG* 3.0 24.2 + - - -
83P GLN* 2.9 44.2 + - + +
84P TYR* 3.5 11.2 - - - +
86P HIS* 1.3 82.8 - - + +
88P ILE* 1.3 61.0 + - - +
90P GLN* 3.8 18.6 - - - +
91P VAL 4.5 0.2 + - - -
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Residues in contact with ILE 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565N ILE* 3.7 7.9 - - + -
84P TYR* 2.9 54.1 + - + +
85P LEU* 3.7 12.3 - - + +
86P HIS 3.1 0.2 - - - -
87P GLU* 1.3 74.7 - - - +
89P GLY* 1.3 57.6 + - - +
90P GLN 3.0 10.2 + - - -
91P VAL* 3.1 23.3 + - - +
189P GLU 5.3 1.5 - - - +
192P LEU* 3.4 37.7 - - + -
193P ARG* 3.5 40.5 + - + +
196P VAL* 4.8 3.4 - - + -
7R G 4.6 6.5 - - - +
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Residues in contact with GLY 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85P LEU 3.1 7.7 + - - -
86P HIS 3.1 9.3 + - - -
88P ILE* 1.3 75.5 - - - +
90P GLN* 1.3 64.7 + - - +
91P VAL 3.2 2.0 + - - -
92P PRO* 5.1 0.5 - - - +
193P ARG* 3.6 20.5 + - - -
7R G 3.7 29.2 - - - +
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Residues in contact with GLN 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155N ASP* 4.5 5.8 + - - +
156N GLU* 4.9 15.4 + - - +
159N ARG* 4.2 33.8 + - - +
86P HIS* 3.4 40.8 + - + +
87P GLU* 3.8 16.6 - - - +
88P ILE 3.0 1.6 - - - -
89P GLY* 1.3 80.9 - - - +
91P VAL* 1.3 61.0 + - + +
92P PRO* 3.7 7.6 - - - +
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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