Contacts of the helix formed by residues 143 - 159 (chain A) in PDB entry 3NA0
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 LYS 143 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLU* 3.6 34.9 + - + +
122A LEU* 6.3 3.4 - - + -
142A LYS* 1.3 75.2 - - - +
144A SER* 1.3 85.6 + - - +
146A ALA* 3.5 8.2 + - - +
147A TRP* 3.2 12.7 + - - -
460A ARG* 4.7 4.3 - - - +
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Residues in contact with SER 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASN* 3.5 39.2 + - - +
118A PRO 5.9 0.2 + - - -
119A GLU* 5.3 1.0 - - - +
143A LYS* 1.3 94.0 + - - +
145A ALA* 1.3 66.2 + - - +
146A ALA 4.5 0.9 + - - -
147A TRP* 2.9 16.6 + - - +
148A LYS 3.1 9.5 + - - -
460A ARG* 5.7 0.2 - - - +
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Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 4.3 2.8 + - - +
144A SER* 1.3 84.5 + - - +
146A ALA* 1.3 59.7 + - - +
148A LYS* 3.4 8.3 + - - +
149A LYS* 3.1 25.1 + - - +
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Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 3.6 30.2 + - + +
143A LYS 3.5 6.9 + - - +
144A SER* 3.3 1.8 + - - -
145A ALA* 1.3 74.5 - - - +
147A TRP* 1.3 64.5 + - - +
149A LYS* 3.8 8.0 + - - +
150A ASP* 3.5 16.3 + - - +
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Residues in contact with TRP 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PRO 4.1 12.8 - - - -
117A ASN* 3.8 27.6 - - + -
118A PRO* 4.3 1.8 - - + -
139A VAL* 3.2 39.9 - - + +
142A LYS* 3.8 15.8 - - - +
143A LYS* 3.2 18.4 + - - +
144A SER 2.9 9.2 + - - +
146A ALA* 1.3 74.0 - - - +
148A LYS* 1.3 89.1 + - + +
150A ASP* 3.3 4.2 + - - +
151A ARG* 2.8 49.7 + - + +
459A VAL* 3.5 38.1 - - + -
460A ARG* 3.2 36.9 - - + +
601A HEM 2.9 20.3 + - - -
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Residues in contact with LYS 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PRO* 4.0 20.0 + - - +
117A ASN* 3.4 21.5 - - - +
144A SER 3.1 2.4 + - - +
145A ALA* 3.6 11.0 - - - +
147A TRP* 1.3 95.5 - - + +
149A LYS* 1.3 57.2 + - - +
151A ARG* 3.2 2.5 + - + +
152A VAL* 2.8 50.0 + - + +
459A VAL* 4.6 5.5 - - - +
45C ALA* 2.8 40.2 + - - +
47C GLU* 4.2 13.9 - - - +
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Residues in contact with LYS 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ALA 3.1 14.3 + - - +
146A ALA* 3.9 8.3 - - - +
147A TRP 3.2 0.4 - - - -
148A LYS* 1.3 80.4 - - - +
150A ASP* 1.3 66.0 + - - +
152A VAL* 4.2 3.7 - - - +
153A ALA* 3.3 22.7 + - - +
310A LYS* 4.6 27.8 + - + -
311A MET* 5.1 4.1 - - + +
312A SER 6.0 1.0 - - - +
315A ASP* 5.1 9.2 + - - +
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Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ILE 4.8 0.2 - - - +
139A VAL* 3.9 15.7 + - + -
142A LYS* 3.1 35.8 + - - +
146A ALA 3.5 6.8 + - - +
147A TRP 3.3 7.7 + - - +
149A LYS* 1.3 79.1 - - - +
151A ARG* 1.3 60.4 + - - +
153A ALA* 3.2 7.0 + - - +
154A LEU* 2.8 35.2 + - + +
311A MET* 3.7 16.1 - - - +
315A ASP* 3.9 8.7 - - - +
319A ASN* 2.7 31.2 + - - +
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Residues in contact with ARG 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 3.8 8.0 - - + +
147A TRP* 2.8 48.9 + - + +
148A LYS* 3.7 4.7 - - + +
150A ASP* 1.3 72.9 - - - +
152A VAL* 1.3 53.5 + - + +
154A LEU* 3.2 2.6 + - - -
155A ASN* 2.7 72.9 + - - +
159A MET* 4.2 6.9 - - - +
459A VAL 3.4 21.2 + - - +
460A ARG* 3.9 1.8 - - - +
461A GLN* 2.9 38.2 + - - +
462A CYS 3.5 12.3 + - - -
463A LEU* 3.5 19.6 - - - +
601A HEM 2.7 40.8 + - - +
51C ALA* 4.8 1.4 - - - +
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LYS* 2.8 42.1 + - + +
149A LYS* 4.2 4.0 - - - +
151A ARG* 1.3 74.1 - - + +
153A ALA* 1.3 64.1 + - - +
155A ASN* 3.4 8.6 + - - +
156A GLN* 3.2 37.8 + - - +
310A LYS* 6.5 0.7 - - + -
45C ALA 4.8 1.8 - - - +
46C CYS* 4.7 9.4 - - - +
47C GLU* 3.4 42.2 - - + +
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LYS 3.3 13.9 + - - +
150A ASP 3.2 8.6 + - - +
152A VAL* 1.3 82.0 - - - +
154A LEU* 1.3 61.1 - - - +
156A GLN* 3.4 18.4 + - - +
157A GLU* 3.9 3.5 + - - +
305A LEU* 4.2 14.8 - - + +
309A SER* 5.2 6.9 - - - -
310A LYS* 5.3 6.7 - - + +
311A MET* 3.6 32.5 - - + +
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A VAL* 4.1 8.3 - - + -
150A ASP 2.8 26.8 + - - +
151A ARG* 3.8 2.5 - - - +
153A ALA* 1.3 71.2 - - - +
155A ASN* 1.3 60.9 + - - +
157A GLU* 3.0 4.6 + - - +
158A VAL* 2.9 37.2 + - + +
305A LEU* 4.0 28.5 - - + -
311A MET* 4.2 10.1 - - - -
316A ILE* 6.3 0.2 - - - -
319A ASN* 3.6 43.7 - - + +
323A MET* 4.4 15.3 - - - -
463A LEU* 3.8 29.8 - - + -
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Residues in contact with ASN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG* 2.7 57.9 + - - +
152A VAL* 3.7 8.5 - - - +
153A ALA 3.3 0.2 - - - -
154A LEU* 1.3 73.4 - - - +
156A GLN* 1.3 61.1 + - - +
159A MET* 3.1 17.7 + - - +
160A ALA* 3.0 26.0 + - - +
459A VAL 4.9 2.0 + - - -
463A LEU* 3.4 8.8 - - - +
46C CYS* 4.1 20.2 + - - +
49C THR* 3.6 21.2 - - + +
51C ALA* 3.9 16.2 - - - +
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Residues in contact with GLN 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A VAL* 3.2 29.3 + - + +
153A ALA* 3.7 9.4 - - - +
154A LEU 3.2 0.8 - - - -
155A ASN* 1.3 77.3 - - - +
157A GLU* 1.3 71.5 + - + +
160A ALA* 3.5 12.9 - - - +
163A ALA* 3.4 17.3 + - - +
304A ARG* 5.4 0.3 + - - -
47C GLU* 4.7 15.4 + - - +
48C GLY 5.3 1.9 - - - +
49C THR* 3.9 12.4 + - - -
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Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ALA 4.4 3.6 - - - +
154A LEU 3.0 7.5 + - - +
156A GLN* 1.3 92.1 - - + +
158A VAL* 1.3 65.3 + - + +
163A ALA* 3.6 13.9 - - - +
167A PHE* 3.5 19.1 - - - -
298A TYR* 4.9 3.8 + - - -
301A ILE* 4.0 14.3 - - + +
304A ARG* 3.2 56.2 + - + +
305A LEU* 3.8 29.6 - - + +
308A ASP 5.1 5.8 - - - +
309A SER* 5.9 0.9 - - - -
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A LEU* 2.9 21.4 + - + +
155A ASN 3.6 0.2 + - - -
157A GLU* 1.3 86.9 - - + +
159A MET* 1.3 60.6 + - - +
160A ALA 3.8 0.4 - - - -
164A THR* 3.3 17.0 - - - +
167A PHE* 4.0 8.2 - - - -
301A ILE* 3.9 19.3 - - + -
323A MET* 3.6 29.8 - - + -
463A LEU* 3.4 31.3 - - + +
464A GLY* 4.8 0.4 - - - -
466A ARG* 3.8 9.9 - - - +
467A ILE* 3.9 22.4 + - + +
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Residues in contact with MET 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG* 4.2 1.8 - - - +
155A ASN* 3.1 24.1 + - - +
158A VAL* 1.3 76.0 - - - +
160A ALA* 1.3 65.2 + - - +
161A PRO* 3.6 2.9 - - - +
164A THR* 3.7 3.9 - - - +
461A GLN* 3.7 28.9 - - + +
462A CYS 3.8 11.9 - - - +
463A LEU* 3.5 29.2 - - + +
465A ARG* 4.2 1.8 - - + -
466A ARG* 3.7 52.5 + - - +
49C THR* 3.3 29.6 - - + +
50C LEU* 5.2 0.3 - - - +
51C ALA* 3.4 27.6 - - + -
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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