Contacts of the helix formed by residues 125 - 135 (chain X) in PDB entry 3NZ9
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 GLY 125 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61X THR* 2.9 17.0 + - - -
124X GLY* 1.3 69.8 + - - -
126X ALA* 1.3 60.3 + - - -
127X GLN 3.2 2.9 - - - -
128X LEU 3.1 1.2 + - - -
129X TYR* 2.8 38.0 + - - -
208X NDP 3.0 32.5 + - - -
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Residues in contact with ALA 126 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X ILE* 3.8 10.7 - - + +
125X GLY* 1.3 72.1 - - - -
127X GLN* 1.3 59.4 + - + +
129X TYR* 3.6 6.8 - - - +
130X LYS* 2.9 28.8 + - - +
154X VAL* 3.5 18.2 - - + -
155X PHE 3.4 26.2 - - - +
157X PRO* 3.9 6.7 - - + +
208X NDP 3.0 16.9 + - - +
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Residues in contact with GLN 127 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X LYS* 3.9 20.8 - - - +
82X ARG* 5.6 3.6 + - - -
125X GLY 3.2 0.4 - - - -
126X ALA* 1.3 78.8 - - + +
128X LEU* 1.3 61.8 + - - +
130X LYS* 3.2 11.6 + - + +
131X ALA* 3.2 18.5 + - - +
208X NDP 2.8 68.0 + - + +
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Residues in contact with LEU 128 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X LEU* 3.5 31.2 - - + +
57X MET* 3.6 19.3 - - - +
58X GLY 4.1 4.3 - - - +
80X ILE* 3.9 24.9 - - + -
98X LEU* 3.4 28.9 - - + -
122X VAL* 3.7 15.3 - - + -
124X GLY 3.7 15.9 - - - +
125X GLY 3.1 2.7 + - - +
127X GLN* 1.3 77.5 - - - +
129X TYR* 1.3 58.7 - - - +
131X ALA* 3.2 8.2 + - + +
132X ALA* 2.9 27.2 + - - +
208X NDP 3.3 22.9 + - + +
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Residues in contact with TYR 129 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X LEU* 3.5 28.3 - - + -
10X ILE 2.6 29.0 + - - -
11X VAL* 3.4 25.6 - - + +
19X ILE* 3.9 17.7 - - + -
122X VAL* 3.8 10.5 - - + -
123X ILE 3.2 11.8 + - - -
124X GLY* 3.4 26.0 - - - -
125X GLY* 2.8 25.6 + - - +
126X ALA* 3.6 5.4 - - - +
128X LEU* 1.3 68.3 - - - +
130X LYS* 1.4 60.9 + - - +
132X ALA* 3.1 5.1 + - - +
133X MET* 2.8 33.8 + - - +
156X PHE* 3.5 24.9 - + + -
157X PRO* 3.9 7.0 - - + -
208X NDP 3.4 11.9 - + - -
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Residues in contact with LYS 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126X ALA 2.9 14.4 + - - +
127X GLN* 3.4 12.8 - - + +
128X LEU 3.2 0.4 - - - -
129X TYR* 1.4 76.5 - - - +
131X ALA* 1.3 61.4 + - - +
133X MET* 3.3 5.7 + - + +
134X ASP* 3.2 47.1 + - - +
157X PRO* 3.6 24.4 - - + +
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Residues in contact with ALA 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98X LEU* 3.8 15.9 - - + +
127X GLN 3.2 8.2 + - - +
128X LEU* 3.5 10.5 - - + +
130X LYS* 1.3 75.8 - - - +
132X ALA* 1.3 64.4 + - - +
134X ASP* 3.3 10.1 + - - +
135X HIS* 3.1 20.8 + - - +
208X NDP 3.6 26.9 - - - +
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Residues in contact with ALA 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X LEU* 5.5 1.1 - - + -
9X LEU* 4.3 11.4 - - + -
98X LEU* 3.5 19.0 - - + +
122X VAL* 4.1 24.5 - - + -
128X LEU 2.9 17.5 + - - +
129X TYR 3.1 5.1 + - - +
131X ALA* 1.3 76.9 - - - +
133X MET* 1.3 58.3 + - - +
135X HIS* 3.0 17.0 + - - +
138X LEU* 3.2 28.5 - - + +
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Residues in contact with MET 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X LEU* 3.9 12.6 - - + -
129X TYR 2.8 20.9 + - - +
130X LYS* 3.6 7.6 - - + +
131X ALA 3.2 0.2 - - - -
132X ALA* 1.3 78.2 - - - +
134X ASP* 1.3 61.1 + - - +
138X LEU* 3.5 20.9 - - - -
141X ILE* 3.9 13.7 - - + -
156X PHE* 4.0 17.7 - - + -
157X PRO* 4.7 2.7 - - + -
158X LEU* 3.5 51.6 - - + +
160X PHE* 4.5 2.2 - - + -
169X TRP* 3.6 26.7 - - + +
204X ARG* 2.6 30.7 + - - +
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Residues in contact with ASP 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130X LYS* 3.2 39.1 + - - +
131X ALA* 3.6 11.7 - - - +
132X ALA 3.2 0.4 - - - -
133X MET* 1.3 79.3 - - - +
135X HIS* 1.3 59.4 + - - +
136X PRO* 3.7 6.1 - - - +
158X LEU* 5.7 2.9 - - - +
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Residues in contact with HIS 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X GLN* 3.7 11.1 + - - -
7X LEU* 3.7 16.1 - - + +
98X LEU* 4.2 13.4 - - + +
99X ASP* 2.8 43.0 + - - -
102X LEU* 4.0 10.4 - - + +
131X ALA 3.1 11.4 + - - +
132X ALA* 3.0 18.2 + - - +
134X ASP* 1.3 76.8 - - - +
136X PRO* 1.3 70.9 - - + +
137X LYS* 2.9 56.1 + - + +
138X LEU 3.2 5.4 + - - -
204X ARG* 2.9 23.1 + - - -
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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