Contacts of the helix formed by residues 120 - 136 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116G ILE* 2.7 44.9 + - + +
118G TYR 3.4 0.2 - - - -
119G LEU* 1.3 79.9 - - + +
121G ASP* 1.3 64.6 + - - +
122G LEU 3.4 0.4 - - - -
123G ASP* 3.2 2.0 + - - +
124G MET* 2.8 56.7 + - - +
170G PHE* 6.0 1.3 - - + -
292G PHE* 6.5 0.2 - - + -
296G PHE* 4.2 23.6 - - + -
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Residues in contact with ASP 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G GLU* 4.5 12.0 - - + +
112G LYS* 2.6 45.6 + - - +
116G ILE* 3.1 21.2 + - - +
117G SER* 3.4 11.2 - - - +
120G VAL* 1.3 76.5 - - - +
122G LEU* 1.3 63.7 + - + +
124G MET* 3.3 4.4 + - - +
125G VAL* 2.9 35.9 + - + +
170G PHE* 3.3 21.7 - - - +
172G LEU* 5.6 1.1 - - + -
173G LEU* 4.4 11.0 - - + +
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Residues in contact with LEU 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G ILE* 3.8 29.4 - - + -
99G ARG* 3.8 33.2 - - + +
102G LEU* 4.1 15.7 - - + -
103G ALA* 3.7 22.2 - - + +
106G GLU* 5.1 0.9 - - + -
117G SER* 2.9 31.2 + - - +
118G TYR 3.6 9.2 - - - +
120G VAL 3.4 0.2 - - - -
121G ASP* 1.3 73.5 - - + +
123G ASP* 1.3 65.8 + - - +
125G VAL* 3.3 6.8 + - + +
126G LEU* 3.0 30.8 + - + +
172G LEU* 3.8 24.0 - - + -
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Residues in contact with ASP 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G ARG* 3.7 19.0 + - - +
118G TYR 3.9 3.0 + - - -
119G LEU 3.3 25.7 - - - +
120G VAL* 3.2 2.4 + - - +
122G LEU* 1.3 77.6 - - - +
124G MET* 1.3 61.4 + - - +
126G LEU* 3.3 11.8 + - - +
127G LYS* 2.9 62.0 + - - +
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Residues in contact with MET 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G VAL* 2.8 40.2 + - + +
121G ASP 3.8 1.3 - - - +
123G ASP* 1.3 78.7 - - + +
125G VAL* 1.3 59.8 + - - +
127G LYS* 3.9 10.6 - - + +
128G CYS* 3.0 30.3 + - - +
173G LEU* 3.7 36.1 - - + +
177G TRP* 4.8 6.0 + - + +
459G PHE* 3.6 44.2 - - + +
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Residues in contact with VAL 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G ILE* 4.0 35.4 - - + -
121G ASP 2.9 22.4 + - - +
122G LEU* 3.4 11.9 - - + +
123G ASP 3.2 0.2 - - - -
124G MET* 1.3 77.1 - - - +
126G LEU* 1.3 62.8 + - - +
128G CYS* 3.3 2.4 + - - +
129G LEU* 3.1 26.9 + - + +
172G LEU* 3.6 22.0 - - + +
173G LEU* 3.6 35.7 - - - +
176G ALA* 4.2 13.4 - - + +
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Residues in contact with LEU 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G ALA* 3.1 36.8 - - + +
95G ILE* 3.8 14.8 - - + -
96G GLU* 3.7 41.3 - - + +
99G ARG* 4.8 14.6 - - + +
122G LEU 3.0 22.0 + - - +
123G ASP* 3.6 13.9 - - - +
125G VAL* 1.3 78.3 - - + +
127G LYS* 1.3 63.9 + - + +
129G LEU* 3.9 4.1 - - - +
130G ARG* 3.0 46.5 + - - +
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Residues in contact with LYS 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E ASP* 5.4 1.8 + - - -
82E SER* 5.5 6.1 - - - +
123G ASP* 2.9 51.0 + - - +
124G MET* 4.0 9.8 - - + +
126G LEU* 1.3 77.8 - - + +
128G CYS* 1.3 57.5 + - - +
130G ARG* 4.1 6.1 - - - +
131G TYR* 3.0 31.2 + - - +
461G ALA* 4.0 7.2 - - + +
462G GLN* 6.4 0.4 - - - +
147H ASP* 3.6 29.7 + - - +
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Residues in contact with CYS 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G MET 3.0 18.8 + - - +
125G VAL 3.6 4.7 - - - +
126G LEU 3.2 0.2 - - - -
127G LYS* 1.3 76.8 - - - +
129G LEU* 1.3 63.1 + - - +
131G TYR* 3.3 2.8 + - - +
132G TYR* 3.0 42.3 + - - -
176G ALA* 3.6 29.6 - - + -
177G TRP* 3.8 30.7 - - + +
180G GLY* 5.1 0.2 - - - -
461G ALA* 4.0 13.9 - - + +
477G LEU* 4.4 4.7 - - + -
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Residues in contact with LEU 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G LEU* 4.1 19.6 - - + +
91G LEU* 4.2 24.7 - - + -
92G ALA* 4.2 18.2 - - + +
95G ILE* 3.6 32.1 - - + -
125G VAL* 3.1 19.8 + - + +
126G LEU* 3.9 3.6 - - - +
128G CYS* 1.3 79.3 - - - +
130G ARG* 1.3 56.6 + - - +
132G TYR* 3.6 4.0 + - - +
133G ALA* 3.0 27.7 + - - +
176G ALA* 4.2 29.2 - - + +
179G LEU* 4.9 5.2 - - + -
180G GLY* 4.3 14.4 - - - +
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Residues in contact with ARG 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E ARG* 3.4 49.9 - - - +
89E ASN* 6.2 0.7 - - - +
134E GLY* 6.0 0.2 - - - -
138E LYS* 4.9 0.5 + - - -
88G LEU 5.6 0.2 - - - -
89G ASN* 3.6 17.4 + - - +
92G ALA* 3.8 20.8 + - + +
93G ASP* 3.1 33.9 + - - +
96G GLU* 2.8 30.5 + - - -
126G LEU* 3.0 40.3 + - - +
127G LYS* 4.1 4.7 - - - +
129G LEU* 1.3 73.0 - - - +
131G TYR* 1.3 67.3 + - - +
133G ALA* 3.3 19.4 - - - +
134G GLY* 3.4 4.7 + - - -
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Residues in contact with TYR 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E ASP* 3.5 21.5 - - - +
138E LYS* 2.9 51.2 + - + +
140E HIS* 4.5 5.4 + - - -
127G LYS 3.0 20.1 + - - +
128G CYS 3.3 3.6 + - - +
130G ARG* 1.3 75.9 - - - +
132G TYR* 1.3 79.5 + + - +
134G GLY 3.1 6.4 + - - -
135G TRP* 2.9 35.1 + + - -
461G ALA* 3.0 33.0 - - + -
462G GLN* 3.5 30.7 + - + +
478G GLY* 3.3 24.6 - - - -
479G GLU 3.5 1.9 + - - -
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Residues in contact with TYR 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G LEU* 4.1 2.2 - - + -
128G CYS* 3.0 33.7 + - - +
129G LEU 4.2 1.8 - - - +
131G TYR* 1.3 93.5 - + - +
133G ALA* 1.3 66.0 + - - +
135G TRP* 2.9 22.9 + + + +
136G ALA 3.3 8.5 + - - -
177G TRP 5.2 0.2 - - - -
180G GLY* 3.5 24.0 - - - +
181G PRO* 3.8 29.6 - - + -
184G ALA* 3.4 10.2 - - + +
461G ALA* 5.6 0.2 - - + -
477G LEU* 2.9 34.2 + - + -
478G GLY 2.7 28.6 + - - -
481G GLY* 3.6 5.0 - - - -
482G LEU* 3.6 31.4 - - + -
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Residues in contact with ALA 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G GLY* 3.4 28.4 - - - +
88G LEU* 3.7 19.1 - - + -
89G ASN* 3.5 30.7 - - - +
129G LEU 3.0 19.9 + - - +
130G ARG 3.3 9.4 - - - +
131G TYR 3.2 0.2 - - - -
132G TYR* 1.3 77.4 - - - +
134G GLY* 1.3 60.9 + - - +
135G TRP 3.4 0.2 + - - -
136G ALA* 3.4 8.3 - - - +
137G ASP* 5.1 1.0 - - - +
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Residues in contact with GLY 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ARG 6.0 0.4 - - - -
134E GLY* 3.8 22.9 - - - -
138E LYS* 3.9 7.4 - - - -
89G ASN* 5.3 0.9 - - - +
130G ARG 3.4 4.1 + - - -
131G TYR 3.1 9.1 + - - -
132G TYR 3.1 1.0 - - - -
133G ALA* 1.3 80.2 - - - +
135G TRP* 1.3 57.9 + - - +
137G ASP* 3.7 1.6 - - - +
138G LYS* 2.8 35.7 + - - +
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Residues in contact with TRP 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E TRP* 4.6 11.2 - + - -
138E LYS* 3.2 41.2 - - + +
140E HIS* 4.1 5.4 - + - -
131G TYR* 2.9 38.7 + + - -
132G TYR* 2.9 27.3 + + + +
134G GLY* 1.3 76.8 - - - +
136G ALA* 1.3 65.4 + - - +
137G ASP 3.2 1.3 - - - -
138G LYS* 2.9 48.9 + - + -
139G TYR* 3.6 15.9 + + - +
184G ALA* 4.7 1.6 - - + -
479G GLU* 3.5 50.8 - - + +
482G LEU* 3.7 26.6 - - + +
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Residues in contact with ALA 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F PRO* 4.8 1.9 - - - +
81G ALA* 3.2 25.2 - - - +
82G SER* 5.2 0.2 - - - -
84G ARG* 3.3 21.5 + - + -
85G GLY* 3.7 13.2 - - - +
88G LEU* 5.3 0.2 - - + -
132G TYR 3.3 4.0 + - - -
133G ALA 3.4 16.4 - - - +
134G GLY 3.4 0.8 - - - -
135G TRP* 1.3 78.0 - - - +
137G ASP* 1.3 59.1 + - - +
138G LYS 3.8 0.3 + - - -
139G TYR* 4.9 2.8 + - - +
184G ALA* 3.4 28.0 - - - +
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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