Contacts of the helix formed by residues 152 - 164 (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 152 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141P VAL* 4.7 1.3 - - - -
150P THR* 3.4 17.1 + - - +
151P LEU* 1.3 76.0 - - - +
153P PRO* 1.3 67.2 - - + +
154P LYS* 3.7 27.5 + - - +
155P THR* 2.7 45.2 + - - -
156P VAL* 3.3 11.4 + - - +
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Residues in contact with PRO 153 (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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138P SER* 6.1 0.4 - - - +
141P VAL* 4.5 20.6 - - + -
152P ASP* 1.3 87.0 - - + +
154P LYS* 1.3 61.1 + - - +
155P THR 3.2 0.2 - - - -
156P VAL* 3.1 34.9 - - + +
157P GLU* 3.3 12.5 + - - +
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Residues in contact with LYS 154 (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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152P ASP* 2.9 18.0 + - - +
153P PRO* 1.3 79.1 - - - +
155P THR* 1.3 63.1 + - - +
157P GLU* 3.6 4.2 + - - +
158P GLU* 3.1 33.3 + - + +
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Residues in contact with THR 155 (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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126P LEU* 5.7 7.0 - - + -
130P VAL* 5.2 2.4 - - + +
149P GLU* 4.5 16.8 - - + +
150P THR* 3.9 10.4 + - - +
151P LEU* 5.0 5.6 - - + -
152P ASP* 2.7 36.6 + - - -
154P LYS* 1.3 75.3 - - - +
156P VAL* 1.3 58.8 + - - -
157P GLU 3.3 0.7 - - - -
158P GLU* 3.8 17.5 + - - +
159P ILE* 3.0 44.3 + - + +
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Residues in contact with VAL 156 (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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130P VAL* 4.0 20.5 - - + +
133P ALA* 4.8 14.6 - - + -
134P LYS* 4.5 17.4 - - + +
141P VAL* 4.6 6.1 - - + -
151P LEU* 4.0 24.0 - - + -
152P ASP 3.6 13.5 - - - +
153P PRO* 3.1 25.6 - - + +
155P THR* 1.3 77.3 - - - +
157P GLU* 1.3 68.1 + - + +
160P ASP* 2.9 29.5 + - - +
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Residues in contact with GLU 157 (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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134P LYS* 3.0 32.2 + - - -
153P PRO 3.3 13.6 + - - +
154P LYS* 4.1 4.5 - - - +
156P VAL* 1.3 84.6 - - + +
158P GLU* 1.3 59.4 + - - +
159P ILE 3.3 0.4 - - - -
160P ASP* 4.3 0.9 - - - -
161P GLN* 3.0 65.1 + - + +
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Residues in contact with GLU 158 (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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154P LYS* 3.1 24.6 + - + +
155P THR* 3.8 20.9 + - - +
157P GLU* 1.3 78.0 - - - +
159P ILE* 1.3 67.7 + - + +
161P GLN* 4.3 2.6 - - - +
162P LYS* 3.2 45.2 + - - +
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Residues in contact with ILE 159 (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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122P LEU* 4.3 28.0 - - + -
126P LEU* 5.2 12.6 - - + -
127P ILE* 5.5 3.8 - - + -
130P VAL* 4.1 31.0 - - + -
155P THR* 3.0 32.4 + - + +
158P GLU* 1.3 82.9 - - + +
160P ASP* 1.3 61.2 + - - +
162P LYS* 3.4 27.1 + - + +
163P LEU* 2.9 38.1 + - + +
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Residues in contact with ASP 160 (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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130P VAL* 4.5 8.9 - - + +
134P LYS* 2.8 33.7 + - + +
156P VAL 2.9 23.0 + - - +
157P GLU* 4.1 2.7 - - - +
159P ILE* 1.3 76.8 - - - +
161P GLN* 1.3 58.5 + - - +
163P LEU* 3.3 5.4 + - - +
164P LYS* 2.8 58.9 + - - +
174P LEU* 4.5 8.3 - - - +
178P ARG* 3.3 20.4 + - - -
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Residues in contact with GLN 161 (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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157P GLU* 3.0 43.2 + - + +
158P GLU* 4.3 2.2 - - - +
160P ASP* 1.3 74.5 + - - +
162P LYS* 1.3 60.8 + - - +
164P LYS* 3.6 33.8 - - - +
165P SER* 3.0 28.6 + - - -
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Residues in contact with LYS 162 (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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120P THR* 4.6 22.5 - - + +
122P LEU* 4.8 8.4 - - + +
158P GLU* 3.2 37.4 + - - +
159P ILE* 3.5 28.0 - - + +
160P ASP 3.2 0.2 - - - -
161P GLN* 1.3 77.8 - - - +
163P LEU* 1.3 61.0 + - + +
165P SER* 3.3 18.9 + - - -
166P LEU* 3.8 9.9 + - - +
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Residues in contact with LEU 163 (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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116P LEU* 4.1 26.5 - - + -
120P THR* 4.1 24.5 - - + +
122P LEU* 6.0 1.1 - - + -
127P ILE* 4.3 26.9 - - + +
130P VAL* 5.3 5.6 - - + -
131P VAL* 4.7 5.2 - - + -
159P ILE* 2.9 32.0 + - + +
160P ASP* 3.6 8.7 - - - +
162P LYS* 1.3 73.0 - - + +
164P LYS* 1.3 57.2 + - - +
165P SER 2.9 9.4 + - - -
166P LEU* 3.0 27.9 + - + +
171P LYS* 4.3 6.4 - - - +
174P LEU* 3.8 32.5 - - + +
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Residues in contact with LYS 164 (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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408N GLU* 4.1 16.3 + - - +
409N VAL* 4.9 5.5 - - - +
410N SER* 4.2 11.0 - - - +
413N ASP* 3.2 29.3 + - - -
134P LYS* 4.3 3.6 - - - +
160P ASP* 2.8 50.1 + - - +
161P GLN* 3.6 31.0 - - - +
162P LYS 3.4 0.4 - - - -
163P LEU* 1.3 71.8 - - - +
165P SER* 1.3 58.6 + - - +
166P LEU 3.3 1.4 - - - +
171P LYS* 2.7 42.4 + - - +
174P LEU* 3.8 14.6 - - + -
178P ARG* 4.2 2.9 - - - +
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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