Contacts of the helix formed by residues 120 - 136 (chain F) in PDB entry 1NZX
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 VAL 120 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F ILE* 2.7 44.8 + - + +
119F LEU* 1.3 79.2 - - + +
121F ASP* 1.3 64.6 + - - +
122F LEU 3.5 0.4 - - - -
123F ASP* 3.3 2.5 + - - +
124F MET* 2.9 54.6 + - + +
170F PHE* 6.0 1.6 - - + -
292F PHE* 6.5 0.2 - - + -
296F PHE* 4.0 25.1 - - + -
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Residues in contact with ASP 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F GLU* 4.4 12.3 - - + +
112F LYS* 2.7 45.3 + - - +
116F ILE* 3.2 18.6 + - - +
117F SER* 3.5 11.4 - - - +
120F VAL* 1.3 76.9 - - - +
122F LEU* 1.3 63.3 + - + +
124F MET* 3.2 5.0 + - - +
125F VAL* 2.8 36.5 + - + +
170F PHE* 3.4 21.8 - - - +
172F LEU* 5.6 0.2 - - + -
173F LEU* 4.4 11.7 - - + +
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Residues in contact with LEU 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F ILE* 3.8 29.6 - - + -
99F ARG* 3.9 35.4 - - + +
102F LEU* 4.1 14.4 - - + -
103F ALA* 4.0 17.3 - - + +
106F GLU* 5.2 0.7 - - + -
117F SER* 2.9 26.2 + - - +
118F TYR 3.5 9.4 - - - +
121F ASP* 1.3 76.8 - - + +
123F ASP* 1.3 62.6 + - - +
125F VAL* 3.2 6.9 + - + +
126F LEU* 3.0 30.9 + - + +
172F LEU* 3.6 27.6 - - + -
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Residues in contact with ASP 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F ARG* 3.9 19.9 + - - +
118F TYR 3.8 3.2 + - - -
119F LEU 3.2 25.5 - - - +
120F VAL* 3.3 1.9 + - - +
121F ASP 3.3 0.6 - - - -
122F LEU* 1.3 77.3 - - - +
124F MET* 1.3 62.0 + - - +
126F LEU* 3.3 10.3 + - - +
127F LYS* 3.0 63.8 + - - +
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Residues in contact with MET 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F VAL* 2.9 39.9 + - + +
121F ASP 3.6 3.4 - - - +
123F ASP* 1.3 78.3 - - - +
125F VAL* 1.3 67.1 + - - +
127F LYS* 3.9 8.8 - - + +
128F CYS* 3.0 26.2 + - - +
170F PHE* 6.6 0.2 - - - -
173F LEU* 3.7 35.2 - - + +
177F TRP* 4.8 6.1 - - + +
459F PHE* 3.5 43.7 - - + +
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Residues in contact with VAL 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F ILE* 4.0 35.2 - - + -
121F ASP 2.8 20.1 + - - +
122F LEU* 3.2 11.2 + - + +
124F MET* 1.3 76.6 - - - +
126F LEU* 1.3 64.1 + - - +
128F CYS* 3.3 2.1 + - - +
129F LEU* 3.1 26.9 + - + +
172F LEU* 3.6 19.5 - - + +
173F LEU* 3.6 38.6 - - - +
176F ALA* 4.1 13.9 - - + -
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Residues in contact with LEU 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F ALA* 3.1 38.8 - - + +
95F ILE* 4.0 14.8 - - + -
96F GLU* 3.8 42.8 - - + +
99F ARG* 4.6 17.0 - - - +
122F LEU* 3.0 21.1 + - + +
123F ASP* 3.5 10.8 - - - +
124F MET 3.3 0.2 - - - -
125F VAL* 1.3 78.8 - - + +
127F LYS* 1.3 58.0 + - + +
129F LEU* 3.5 2.2 + - - +
130F ARG* 3.0 50.9 + - - +
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Residues in contact with LYS 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E ASP* 3.6 28.5 + - - +
123F ASP* 3.0 51.4 + - - +
124F MET* 3.9 8.7 - - + +
126F LEU* 1.3 76.7 - - + +
128F CYS* 1.3 58.3 + - - +
130F ARG* 3.8 6.5 - - - +
131F TYR* 2.9 31.2 + - - +
461F ALA* 4.1 7.9 - - + +
462F GLN* 6.3 0.9 - - - +
80H ASP* 5.4 2.6 + - - -
82H SER* 5.5 4.9 - - - +
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Residues in contact with CYS 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F MET 3.0 17.8 + - - +
125F VAL 3.6 5.4 - - - +
126F LEU 3.3 0.2 - - - -
127F LYS* 1.3 75.6 - - - +
129F LEU* 1.3 63.7 + - - +
131F TYR* 3.1 4.2 + - - +
132F TYR* 3.0 37.2 + - - -
176F ALA* 3.7 26.0 - - + -
177F TRP* 3.6 34.3 - - + +
180F GLY* 5.2 0.2 - - - -
461F ALA* 3.9 14.5 - - + +
477F LEU* 4.2 7.9 - - - -
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Residues in contact with LEU 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F LEU* 4.2 23.1 - - + +
91F LEU* 4.0 24.0 - - + -
92F ALA* 4.3 17.5 - - + +
95F ILE* 3.7 28.9 - - + -
125F VAL* 3.1 19.5 + - + +
126F LEU* 4.0 3.1 - - - +
128F CYS* 1.3 79.2 - - - +
130F ARG* 1.3 59.1 + - - +
132F TYR* 3.4 4.4 + - - +
133F ALA* 2.8 29.0 + - - +
176F ALA* 4.2 29.4 - - + +
179F LEU* 4.9 4.5 - - + -
180F GLY* 4.2 14.8 - - - +
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Residues in contact with ARG 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F LEU 5.6 0.2 - - - -
89F ASN* 3.9 19.0 + - - +
92F ALA* 3.6 21.3 + - + +
93F ASP* 2.9 35.8 + - - +
96F GLU* 2.9 29.3 + - - -
126F LEU* 3.0 41.0 + - - +
127F LYS* 4.0 6.0 - - - +
129F LEU* 1.3 72.8 - - - +
131F TYR* 1.3 66.4 + - - +
133F ALA* 3.5 3.6 + - - +
134F GLY* 3.5 12.6 + - - -
86H ARG* 3.4 50.5 - - - +
134H GLY* 6.0 0.2 - - - -
138H LYS* 5.1 0.3 + - - -
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Residues in contact with TYR 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127F LYS 2.9 19.3 + - - +
128F CYS 3.1 4.0 + - - +
130F ARG* 1.3 77.6 - - - +
132F TYR* 1.3 78.3 + + - +
134F GLY 3.1 6.9 + - - -
135F TRP* 3.0 35.1 + + - -
461F ALA* 3.1 32.1 - - + -
462F GLN* 3.4 32.1 + - + +
478F GLY* 3.3 24.1 - - - -
479F GLU 3.6 1.9 + - - -
137H ASP* 3.3 25.1 - - - +
138H LYS* 2.9 48.1 + - + +
140H HIS* 4.4 5.0 + - - -
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Residues in contact with TYR 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F LEU* 4.0 2.7 - - + -
128F CYS* 3.0 31.7 + - - +
129F LEU 4.1 1.6 - - - +
131F TYR* 1.3 85.0 - + - +
133F ALA* 1.3 67.2 + - - +
134F GLY 3.0 1.8 - - - -
135F TRP* 3.0 29.2 + + + +
136F ALA 3.3 7.6 + - - -
177F TRP 5.2 0.4 - - - -
180F GLY* 3.6 25.1 - - - +
181F PRO* 3.8 40.7 - - + +
184F ALA* 3.4 9.8 - - + +
461F ALA* 5.6 0.2 - - + -
477F LEU* 2.9 35.5 + - + -
478F GLY 2.7 29.5 + - - -
481F GLY* 3.6 6.1 - - - -
482F LEU* 3.9 17.0 - - + -
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Residues in contact with ALA 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F GLY* 3.4 28.5 - - - +
88F LEU* 3.5 20.4 - - + +
89F ASN* 3.7 21.3 - - - +
129F LEU 2.8 19.1 + - - +
130F ARG 3.6 8.1 - - - +
131F TYR 3.2 0.2 - - - -
132F TYR* 1.3 76.6 - - - +
134F GLY* 1.3 62.7 + - - +
136F ALA* 3.3 18.9 + - - +
137F ASP* 5.0 1.2 - - - +
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Residues in contact with GLY 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F ASN* 5.4 0.6 - - - +
130F ARG 3.5 4.9 + - - -
131F TYR 3.1 9.3 + - - -
132F TYR 3.0 0.8 - - - -
133F ALA* 1.3 81.2 - - - +
135F TRP* 1.3 57.0 + - - +
136F ALA 3.6 0.3 + - - -
137F ASP* 3.8 1.3 - - - +
138F LYS* 2.8 35.2 + - - +
130H ARG 6.0 0.4 - - - -
134H GLY* 3.8 23.6 - - - -
138H LYS* 3.8 7.6 - - - -
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Residues in contact with TRP 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F TYR* 3.0 37.7 + + - -
132F TYR* 3.0 28.4 + + + +
134F GLY* 1.3 73.8 - - - +
136F ALA* 1.3 68.7 + - - +
137F ASP 3.2 2.7 - - - -
138F LYS* 2.9 50.7 + - + -
139F TYR* 3.6 16.4 + + - +
184F ALA* 4.8 2.2 - - + -
479F GLU* 3.5 50.5 - - + +
482F LEU* 3.6 25.5 - - + +
135H TRP* 4.7 11.2 - + - -
138H LYS* 3.3 41.9 - - + +
140H HIS* 4.1 5.8 - + - -
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Residues in contact with ALA 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F ALA* 3.3 23.8 - - - +
84F ARG* 3.3 24.6 + - + -
85F GLY* 3.7 13.5 - - - +
132F TYR 3.3 3.2 + - - +
133F ALA* 3.3 18.8 + - - +
134F GLY 3.3 0.2 - - - -
135F TRP* 1.3 77.2 - - - +
137F ASP* 1.3 59.1 + - - +
138F LYS 3.8 0.7 + - - -
139F TYR* 5.0 2.6 + - - +
184F ALA* 3.4 25.9 - - - +
145G PRO* 4.8 2.1 - - - +
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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
------------------------------------------------------------
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