Contacts of the helix formed by residues 143 - 159 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119B GLU* 3.2 33.2 + - + +
122B LEU* 5.7 7.8 - - + +
141B LEU 5.6 0.7 - - - +
142B LYS* 1.3 74.6 - - - +
144B SER* 1.3 83.2 + - - +
146B ALA* 3.5 8.7 + - - +
147B TRP* 3.0 16.4 + - - -
460B ARG* 4.5 4.5 - - - +
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Residues in contact with SER 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ASN* 3.6 39.3 + - - +
118B PRO 5.8 0.4 + - - -
119B GLU* 4.8 1.6 + - - -
143B LYS* 1.3 90.8 - - - +
145B ALA* 1.3 73.0 + - - +
146B ALA 4.7 0.2 - - - -
147B TRP* 3.1 13.6 + - - +
148B LYS 3.2 9.0 + - - -
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASN* 3.9 5.8 - - - +
144B SER* 1.3 85.1 + - - +
146B ALA* 1.3 56.5 + - - +
148B LYS* 3.0 9.2 + - - +
149B LYS* 2.9 31.1 + - - +
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Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LYS* 3.6 29.2 + - + +
143B LYS 3.5 7.1 + - - +
144B SER* 3.3 0.6 - - - -
145B ALA* 1.3 77.4 - - - +
147B TRP* 1.3 61.8 + - - +
149B LYS* 3.9 8.1 + - - +
150B ASP* 3.6 16.1 + - - +
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Residues in contact with TRP 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B PRO 4.1 2.5 - - - -
117B ASN* 3.7 24.9 - - + -
118B PRO* 4.0 13.2 - - + -
139B VAL* 3.3 37.7 - - + +
142B LYS* 3.9 6.7 - - - +
143B LYS* 3.0 28.4 + - - +
144B SER 3.1 6.9 + - - +
146B ALA* 1.3 77.7 - - - +
148B LYS* 1.3 87.1 + - + +
150B ASP* 3.3 4.1 + - - +
151B ARG* 2.8 49.3 + - + +
459B VAL* 3.6 33.7 - - + -
460B ARG* 3.1 40.4 - - + +
601B HEM 2.9 21.0 + - - -
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Residues in contact with LYS 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PRO* 3.8 19.9 + - - +
117B ASN* 3.8 16.8 - - - +
144B SER 3.2 2.9 + - - +
145B ALA* 3.0 12.0 + - - +
147B TRP* 1.3 96.0 - - + +
149B LYS* 1.3 61.0 + - - +
151B ARG* 3.9 2.2 - - + +
152B VAL* 2.9 51.1 + - + +
459B VAL* 4.7 4.4 - - - +
45D ALA* 3.0 46.7 + - - +
47D GLU* 5.4 3.8 - - - -
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Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ALA 2.9 15.8 + - - +
146B ALA* 4.0 9.6 - - - +
148B LYS* 1.3 78.5 - - - +
150B ASP* 1.3 66.1 + - - +
152B VAL* 4.3 3.8 - - - +
153B ALA* 3.3 22.0 + - - +
310B LYS* 4.6 20.5 + - + +
311B MET* 5.1 5.5 - - + +
312B SER 5.8 1.0 - - - +
315B ASP* 5.1 9.6 + - - +
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Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 4.1 14.8 + - + -
142B LYS* 3.1 35.7 + - + +
146B ALA 3.6 7.9 + - - +
147B TRP 3.3 7.9 + - - +
148B LYS 3.3 0.2 - - - -
149B LYS* 1.3 85.4 - - - +
151B ARG* 1.3 59.8 + - - +
153B ALA 3.2 1.2 + - - -
154B LEU* 2.9 34.4 + - - +
311B MET* 3.3 26.8 - - + +
315B ASP* 4.0 12.3 - - - +
319B ASN* 2.9 21.5 + - - +
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Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 4.0 6.7 - - + +
147B TRP* 2.8 48.8 + - + +
148B LYS* 3.9 4.5 - - + +
150B ASP* 1.3 74.2 - - - +
152B VAL* 1.3 55.3 + - + +
154B LEU* 3.3 1.7 + - - -
155B ASN* 2.7 74.4 + - - +
159B MET* 4.1 6.9 - - - +
459B VAL 3.4 21.8 + - - +
460B ARG* 3.9 3.0 - - - +
461B GLN* 3.0 39.4 + - - +
462B CYS 3.7 11.3 + - - -
463B LEU* 3.4 20.0 - - - +
601B HEM 3.0 32.3 + - - +
51D ALA* 4.9 1.4 - - - +
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B LYS* 2.9 44.1 + - + +
149B LYS* 4.3 3.6 - - - +
151B ARG* 1.3 78.0 - - + +
153B ALA* 1.3 62.7 + - - +
154B LEU 3.3 0.2 + - - -
155B ASN* 3.4 13.8 + - - +
156B GLN* 3.4 17.2 + - - +
45D ALA 4.6 1.1 - - - +
46D CYS* 4.6 8.3 - - - +
47D GLU* 3.6 39.9 - - + +
49D THR* 5.3 0.9 - - - +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LYS 3.3 15.8 + - - +
150B ASP 3.2 3.2 + - - +
152B VAL* 1.3 79.3 - - - +
154B LEU* 1.3 61.8 + - - +
156B GLN* 3.5 23.8 - - - +
157B GLU 4.0 2.4 + - - -
305B LEU* 4.1 11.5 - - - +
309B SER* 4.0 10.7 + - - +
310B LYS* 5.0 9.9 - - + +
311B MET* 3.8 30.1 - - + +
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 4.3 9.4 - - + -
150B ASP 2.9 18.5 + - - +
151B ARG* 3.8 2.7 - - - +
153B ALA* 1.3 76.8 - - - +
155B ASN* 1.3 64.8 + - - +
156B GLN 3.2 0.2 - - - -
157B GLU* 3.1 5.0 + - + +
158B VAL* 3.0 28.8 + - + +
301B ILE* 5.7 1.3 - - + -
305B LEU* 4.0 29.8 - - + -
311B MET* 3.5 12.3 - - + -
319B ASN* 3.4 44.0 - - + +
323B MET* 4.4 14.6 - - + -
463B LEU* 3.8 29.8 - - + -
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Residues in contact with ASN 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ARG* 2.7 59.7 + - - +
152B VAL* 3.8 7.1 - - - +
154B LEU* 1.3 73.8 - - - +
156B GLN* 1.3 58.1 + - - +
159B MET* 2.9 44.9 + - - +
160B ALA* 2.9 12.1 + - - +
459B VAL 4.9 2.0 + - - -
463B LEU* 3.5 2.4 - - - +
46D CYS* 3.9 22.9 + - - +
49D THR* 3.4 27.3 + - + +
51D ALA* 3.9 5.8 - - - +
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Residues in contact with GLN 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B VAL* 3.4 12.2 + - - +
153B ALA* 3.5 18.2 - - - +
154B LEU 3.2 1.0 - - - -
155B ASN* 1.3 78.9 - - - +
157B GLU* 1.3 79.0 + - + +
160B ALA* 3.6 8.4 - - + +
163B ALA* 3.2 18.2 - - - +
304B ARG* 5.1 0.2 + - - -
308B ASP 4.6 12.7 + - - -
309B SER* 6.1 0.6 - - - +
49D THR* 3.8 16.4 - - + +
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ALA 4.4 3.8 - - - +
154B LEU* 3.1 8.2 + - + +
156B GLN* 1.3 103.5 + - + +
158B VAL* 1.3 59.8 + - - +
163B ALA* 3.7 11.0 - - - +
167B PHE* 3.6 17.8 - - - -
298B TYR* 4.9 2.8 + - - -
301B ILE* 3.9 23.4 - - + +
304B ARG* 2.8 62.5 + - + +
305B LEU* 3.8 25.1 - - + +
308B ASP 5.4 1.9 - - - +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 3.0 12.8 + - + +
157B GLU* 1.3 78.3 - - - +
159B MET* 1.3 62.6 + - + +
164B THR* 3.3 17.8 - - - +
167B PHE* 3.8 7.3 - - - -
301B ILE* 3.8 31.4 - - + -
323B MET* 4.1 20.4 - - + -
463B LEU* 3.2 51.0 - - + +
464B GLY* 5.1 0.2 - - - -
466B ARG* 3.8 9.7 - - - +
467B ILE* 3.8 19.1 - - + +
601B HEM 5.8 0.4 - - + -
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Residues in contact with MET 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ARG* 4.1 2.0 - - - +
155B ASN* 2.9 35.1 + - - +
158B VAL* 1.3 77.8 - - + +
160B ALA* 1.3 66.4 + - - +
161B PRO* 3.5 3.1 - - - +
164B THR* 3.6 4.3 + - - +
461B GLN* 3.9 22.9 - - + +
462B CYS 3.9 17.0 - - - +
463B LEU* 3.4 26.9 - - + +
465B ARG* 4.2 2.5 - - + -
466B ARG* 3.5 51.8 + - - +
49D THR 3.4 15.4 - - - +
50D LEU* 5.1 0.6 - - - +
51D ALA* 3.6 27.4 - - + -
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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