Contacts of the helix formed by residues 319 - 332 (chain A) in PDB entry 4H0N
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 ASN 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLU* 4.7 2.0 + - - -
149A PRO* 3.7 27.8 - - + +
154A VAL* 4.0 1.6 - - - +
156A ASN* 5.4 2.4 + - - -
158A ARG* 4.3 12.7 - - - +
162A TYR* 5.2 5.3 + - - +
292A ILE 3.8 12.1 + - - -
293A MET* 3.6 13.3 - - - +
294A CYS* 3.8 17.4 - - - -
318A VAL* 1.3 72.5 - - - +
320A VAL* 1.3 62.9 + - - +
321A LYS* 2.9 30.9 + - - +
322A VAL* 3.0 36.1 + - + +
323A ILE* 3.5 16.3 + - - +
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Residues in contact with VAL 320 (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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14A GLY* 3.6 10.5 - - - +
17A CYS* 3.6 31.6 - - + +
18A ALA* 3.4 30.2 - - - +
21A GLU* 4.5 12.6 - - + -
293A MET 3.0 7.8 + - - +
294A CYS 3.2 22.0 - - - +
295A PHE* 3.7 33.2 - - + -
296A PRO* 5.0 2.0 - - + -
318A VAL* 4.4 2.0 - - - +
319A ASN* 1.3 71.7 - - - +
321A LYS* 1.3 60.6 + - - +
324A SER* 3.2 19.6 + - - -
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Residues in contact with LYS 321 (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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21A GLU* 5.4 9.9 - - - +
152A VAL* 3.1 43.8 + - + -
153A GLY* 5.7 0.8 + - - -
154A VAL* 4.1 11.4 - - + -
188A PHE* 3.9 19.4 - - - -
294A CYS* 3.7 22.1 - - + +
319A ASN* 2.9 11.5 + - - +
320A VAL* 1.3 78.3 - - - +
322A VAL* 1.3 64.9 + - - +
324A SER* 3.3 7.2 + - - -
325A GLU* 3.0 27.1 + - + +
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 3.9 30.1 - - + -
148A CYS 4.8 0.7 - - - -
149A PRO* 3.9 19.7 - - + -
152A VAL* 3.9 24.9 - - + -
162A TYR* 3.9 28.0 - - + +
184A LEU* 5.6 0.7 - - + -
319A ASN* 3.0 26.5 + - + +
321A LYS* 1.3 76.3 - - + +
323A ILE* 1.3 57.9 + - - +
325A GLU* 3.2 8.7 + - - +
326A LEU* 3.0 27.7 + - + +
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Residues in contact with ILE 323 (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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15A MET* 3.5 37.5 - - + -
18A ALA* 3.6 21.3 - - + -
73A LEU* 5.7 0.4 - - + -
115A LEU* 4.1 15.5 - - + -
117A GLU* 4.0 5.6 - - - +
162A TYR* 4.2 19.5 - - + +
318A VAL* 3.5 35.0 - - + -
319A ASN 3.5 8.8 + - - +
321A LYS 3.2 0.6 - - - -
322A VAL* 1.3 73.2 - - - +
324A SER* 1.3 56.2 + - - +
326A LEU* 3.1 7.0 + - - +
327A LEU* 2.8 45.2 + - + +
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Residues in contact with SER 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 3.6 16.5 - - - +
21A GLU* 3.1 18.4 + - - +
22A SER* 3.0 29.5 + - - -
320A VAL 3.2 19.5 + - - -
321A LYS* 3.5 7.4 - - - -
323A ILE* 1.3 76.4 - - - +
325A GLU* 1.3 64.1 + - - +
327A LEU* 3.4 5.9 + - - +
328A LYS* 3.1 33.9 + - - +
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Residues in contact with GLU 325 (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* 4.2 8.3 - - + -
184A LEU* 4.3 19.2 - - + +
186A LYS* 3.8 14.5 - - - +
188A PHE* 3.3 37.2 - - + -
321A LYS* 3.0 21.4 + - + +
322A VAL* 3.5 8.5 - - - +
323A ILE 3.2 0.2 - - - -
324A SER* 1.3 80.1 + - - +
326A LEU* 1.3 59.7 + - - +
328A LYS* 3.4 39.2 + - - +
329A ILE* 3.3 25.7 + - + +
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Residues in contact with LEU 326 (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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115A LEU* 3.8 17.5 - - + -
145A PHE* 3.6 35.4 - - + -
147A LEU* 3.9 7.2 - - + -
162A TYR* 3.4 50.0 - - + -
164A THR* 4.0 6.5 - - + +
184A LEU* 3.8 21.8 - - + -
322A VAL* 3.0 20.7 + - + +
323A ILE* 3.1 9.4 + - - +
325A GLU* 1.3 73.3 - - - +
327A LEU* 1.3 56.2 + - - +
329A ILE* 3.1 6.5 + - + +
330A LEU* 2.7 36.7 + - - +
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Residues in contact with LEU 327 (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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18A ALA 3.9 8.1 - - - +
19A TRP* 3.6 49.6 - - + +
22A SER* 4.2 8.5 - - - +
24A LEU* 3.7 6.3 - - + +
73A LEU* 3.9 26.0 - - + -
115A LEU* 3.9 13.5 - - + -
323A ILE* 2.8 28.6 + - + +
324A SER 3.6 4.9 - - - +
326A LEU* 1.3 77.3 - - - +
328A LYS* 1.3 60.5 + - - +
330A LEU* 4.3 2.7 - - - -
331A PHE* 3.0 52.8 + - + +
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Residues in contact with LYS 328 (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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21A GLU* 4.5 5.2 + - - -
22A SER* 4.1 26.1 + - - +
24A LEU* 4.7 9.2 - - + +
186A LYS* 6.2 1.2 - - - +
324A SER* 3.1 25.2 + - - +
325A GLU* 3.4 39.8 + - - +
326A LEU 3.2 0.2 - - - -
327A LEU* 1.3 76.1 - - - +
329A ILE* 1.3 63.5 + - + +
331A PHE* 3.5 1.8 + - - +
332A GLU* 3.2 25.3 + - - +
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Residues in contact with ILE 329 (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 PHE* 4.7 11.9 - - + -
164A THR* 5.1 2.9 - - + +
172A TRP* 3.0 24.6 + - + -
174A PHE* 3.7 37.5 - - + -
184A LEU* 3.7 30.5 - - + -
185A PRO* 4.1 21.3 - - + -
325A GLU 3.3 9.8 + - - +
326A LEU* 3.1 12.4 + - + +
328A LYS* 1.3 78.9 - - + +
330A LEU* 1.3 63.5 + - - +
331A PHE 3.2 1.2 + - - -
332A GLU* 3.3 23.0 + - - +
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Residues in contact with LEU 330 (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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71A THR* 5.8 0.4 - - + -
73A LEU* 5.8 0.9 - - + -
113A TYR* 4.1 10.9 - - + -
114A ILE 3.6 25.1 - - - +
115A LEU* 4.0 16.2 - - + -
164A THR* 3.7 24.9 - - + -
165A ALA 3.5 20.0 - - - +
166A ARG* 2.9 37.9 + - + -
172A TRP* 3.7 9.1 + - + -
326A LEU 2.7 20.8 + - - +
327A LEU* 3.4 1.8 + - + +
329A ILE* 1.3 73.4 - - - +
331A PHE* 1.3 83.6 + - + +
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Residues in contact with PHE 331 (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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3A HIS* 3.4 39.5 - + - -
19A TRP* 3.7 15.5 - + - -
24A LEU* 3.7 21.3 - - + -
71A THR* 3.8 12.8 - - + -
113A TYR* 3.6 40.2 - + + -
166A ARG* 3.9 7.5 + - - +
327A LEU* 3.0 42.7 + - + +
328A LYS 3.9 2.0 - - - +
330A LEU* 1.3 101.2 - - + +
332A GLU* 1.3 67.1 + - - +
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Residues in contact with GLU 332 (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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166A ARG* 4.3 3.8 + - - -
171A THR 4.2 5.2 - - - +
172A TRP* 4.1 11.0 - - - +
173A PRO* 3.4 41.2 - - + +
174A PHE* 3.4 34.0 + - - +
328A LYS 3.2 12.0 + - - +
329A ILE* 3.3 32.6 + - - +
330A LEU 3.5 0.4 - - - -
331A PHE* 1.3 82.4 - - - +
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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