Contacts of the helix formed by residues 329 - 342 (chain A) in PDB entry 1N0U
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 PRO 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ARG* 5.7 3.6 - - - +
217A GLY 4.0 4.9 - - - +
219A ALA 3.9 3.3 - - - +
224A GLN* 4.9 2.2 + - - +
325A ARG* 3.0 23.9 - - - +
326A LYS* 4.1 6.5 - - - +
327A PHE 3.8 6.1 - - - +
328A LEU* 1.3 82.5 - - - +
330A ALA* 1.3 66.5 + - - +
331A ALA* 3.4 2.2 - - + +
332A ASP* 3.3 41.0 + - + +
333A ALA 3.7 2.9 + - - -
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Residues in contact with ALA 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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35A LEU* 5.3 10.5 - - + -
38A SER* 4.0 13.0 - - - +
213A SER 5.1 1.6 - - - +
214A GLY* 5.7 1.6 - - - +
217A GLY* 3.3 19.7 + - - +
218A TRP 3.6 19.5 - - - +
219A ALA* 3.6 17.4 - - + +
328A LEU 2.9 3.6 + - - -
329A PRO* 1.3 67.6 - - - +
331A ALA* 1.3 68.2 + - - +
333A ALA* 2.9 15.6 + - - +
334A LEU* 3.2 16.3 + - + +
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Residues in contact with ALA 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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38A SER* 3.5 24.9 + - - +
39A LEU* 4.4 11.7 - - - -
42A ARG* 3.4 37.2 - - + -
329A PRO* 3.4 2.2 - - + -
330A ALA* 1.3 76.4 - - - +
332A ASP* 1.3 58.4 + - - +
334A LEU* 3.0 5.1 + - - +
335A LEU* 2.8 36.8 + - + +
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Residues in contact with ASP 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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42A ARG* 2.8 41.0 + - - +
224A GLN* 3.7 13.1 + - - +
329A PRO* 3.3 33.3 + - + +
330A ALA 3.1 0.6 - - - -
331A ALA* 1.3 74.9 - - - +
333A ALA* 1.3 62.3 + - - +
335A LEU* 4.1 7.1 - - - +
336A GLU* 3.2 23.4 + - - +
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Residues in contact with ALA 333 (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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210A ALA* 4.7 3.8 - - + -
219A ALA* 3.6 26.9 - - + +
220A PHE* 3.7 9.2 - - - +
221A THR* 3.7 5.7 - - + +
224A GLN* 3.5 28.5 - - - +
329A PRO 3.7 1.4 + - - -
330A ALA 2.9 10.4 + - - +
332A ASP* 1.3 79.5 - - - +
334A LEU* 1.3 64.6 + - + +
336A GLU* 3.5 4.1 + - - +
337A MET* 3.4 26.1 + - - +
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Residues in contact with LEU 334 (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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35A LEU* 4.2 29.6 - - + +
38A SER* 5.3 1.6 - - - +
39A LEU* 3.7 28.0 - - + -
126A LEU* 4.2 19.7 - - + +
156A VAL* 3.1 43.1 - - + -
210A ALA* 4.5 3.8 - - + -
219A ALA* 5.1 4.3 - - + -
330A ALA* 3.5 15.5 - - + +
331A ALA* 3.0 9.1 + - - +
333A ALA* 1.3 77.5 - - + +
335A LEU* 1.3 65.2 + - - +
337A MET* 3.3 10.7 + - + +
338A ILE* 3.1 28.3 + - + +
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Residues in contact with LEU 335 (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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39A LEU* 3.8 21.1 - - + -
42A ARG* 4.0 29.4 - - + +
43A ALA* 4.0 17.0 - - + -
77A LEU* 4.3 11.2 - - + -
79A SER* 4.3 20.2 - - - +
81A MET* 4.8 4.0 - - + -
100A ILE* 3.8 25.1 - - + -
331A ALA* 2.8 26.2 + - + +
332A ASP* 4.2 6.7 - - - +
334A LEU* 1.3 72.3 - - - +
336A GLU* 1.3 58.7 + - - +
338A ILE* 3.3 5.2 + - + +
339A VAL* 2.9 35.4 + - - +
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Residues in contact with GLU 336 (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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81A MET* 4.5 16.3 - - + +
85A ASP* 6.1 0.4 - - - +
207A GLY* 5.0 3.1 - - - +
221A THR* 2.7 31.9 + - - +
223A ARG* 3.5 35.5 + - - +
224A GLN* 3.4 20.7 + - - +
332A ASP 3.2 19.1 + - - +
333A ALA 3.5 4.9 - - - +
334A LEU 3.2 0.2 - - - -
335A LEU* 1.3 77.6 - - - +
337A MET* 1.3 57.3 + - - +
340A LEU* 3.0 52.9 + - + +
341A HIS* 6.3 0.2 - - + -
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Residues in contact with MET 337 (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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126A LEU* 3.9 4.3 - - + -
154A VAL* 3.1 39.0 - - + -
155A VAL 3.4 16.2 - - - +
156A VAL* 3.5 14.6 - - + -
207A GLY 3.3 15.3 - - - +
208A THR 3.6 22.2 - - - -
209A VAL 3.7 5.6 - - - -
210A ALA* 3.5 22.4 - - + -
221A THR* 3.8 8.5 - - + -
333A ALA 3.4 10.0 + - - +
334A LEU* 3.3 11.5 + - + +
336A GLU* 1.3 79.5 - - - +
338A ILE* 1.3 59.7 + - + +
341A HIS* 2.9 40.0 + - - +
342A LEU* 3.4 4.7 + - - +
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Residues in contact with ILE 338 (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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20A ARG* 3.4 22.9 + - + -
22A MET* 3.9 25.8 - - + -
39A LEU* 4.5 19.3 - - + -
77A LEU* 5.4 0.7 - - + -
100A ILE* 3.6 28.3 - - + -
126A LEU* 5.0 8.7 - - + -
154A VAL* 6.0 0.4 - - + -
334A LEU* 3.1 22.9 + - + +
335A LEU* 3.6 14.6 - - + +
336A GLU 3.3 0.4 - - - -
337A MET* 1.3 77.1 - - + +
339A VAL* 1.3 59.5 + - - +
342A LEU* 3.1 54.1 + - + +
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Residues in contact with VAL 339 (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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20A ARG* 2.7 34.1 + - + +
79A SER* 4.1 14.8 - - - +
81A MET* 3.5 32.5 - - + -
89A ILE* 3.9 8.0 - - + +
91A GLN* 4.7 0.2 - - - +
98A PHE* 3.6 41.5 - - + -
100A ILE* 4.1 21.1 - - + -
335A LEU 2.9 20.5 + - - +
338A ILE* 1.3 77.4 - - - +
340A LEU* 1.3 60.9 + - + +
342A LEU 4.2 0.7 - - - +
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Residues in contact with LEU 340 (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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81A MET* 4.6 9.6 - - - -
85A ASP* 3.5 34.1 - - + +
88A GLU* 4.6 7.2 - - + +
89A ILE* 3.5 37.8 - - + +
90A LYS 5.0 2.1 + - - -
91A GLN* 5.5 1.1 - - - +
223A ARG* 3.4 41.7 - - - +
336A GLU* 3.0 32.4 + - + +
339A VAL* 1.3 77.7 - - - +
341A HIS* 1.3 79.3 + - + +
342A LEU 5.0 0.2 - - - -
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Residues in contact with HIS 341 (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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90A LYS* 6.4 1.8 - - - -
91A GLN* 5.6 0.4 - - - -
152A LYS* 2.9 36.1 + - - +
154A VAL* 3.9 8.7 - - + -
206A ARG* 3.1 29.1 + - + -
207A GLY* 3.5 21.6 + - - -
208A THR* 3.4 24.0 - - + +
223A ARG* 5.6 3.6 - - - -
336A GLU* 6.3 0.4 - - + -
337A MET* 2.9 21.9 + - - +
340A LEU* 1.3 100.4 + - + +
342A LEU* 1.3 64.7 + - - +
343A PRO* 3.6 0.5 - - - +
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Residues in contact with LEU 342 (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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20A ARG* 3.0 28.1 + - + -
21A ASN 6.0 0.2 - - - +
22A MET* 4.1 23.6 - - + -
91A GLN* 3.4 7.3 - - - +
124A GLY* 4.1 4.7 - - - -
125A ALA 4.0 15.9 - - - +
126A LEU* 4.9 0.9 - - + +
152A LYS* 3.5 28.3 - - + +
154A VAL* 3.7 26.5 - - + -
337A MET 3.4 2.0 + - - +
338A ILE* 3.1 48.5 + - + +
339A VAL 4.2 0.7 - - - +
341A HIS* 1.3 80.2 - - - +
343A PRO* 1.3 66.8 - - + +
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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