Contacts of the helix formed by residues 295 - 302 (chain A) in PDB entry 2NUN
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 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ALA* 3.7 27.8 - - + +
49A ARG 4.0 1.1 - - - +
50A TRP* 3.6 52.7 - - + -
51A PRO* 4.6 0.4 - - + -
293A GLY 3.6 6.2 + - - +
294A ASN* 1.3 70.5 - - - +
296A SER* 1.3 64.9 + - - +
297A ASP* 3.3 18.8 - - - +
298A ILE* 3.0 23.9 + - + +
299A GLU* 2.9 25.3 + - - +
600A ADP 5.6 3.4 - - - +
1503A TRS 5.6 0.4 - - - +
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Residues in contact with SER 296 (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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255A HIS* 3.6 31.6 + - - -
269A ALA* 5.2 2.4 + - - +
273A GLU* 3.6 18.0 + - - +
290A PHE* 3.8 25.3 - - - -
294A ASN 3.5 6.3 + - - -
295A VAL* 1.3 69.2 - - - +
297A ASP* 1.3 73.3 + - - +
299A GLU* 3.1 10.0 + - - +
300A ALA* 2.9 22.8 + - - +
308A PHE* 4.2 5.9 - - - -
315A LEU* 5.8 0.2 - - - -
600A ADP 5.2 2.6 + - - -
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Residues in contact with ASP 297 (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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255A HIS* 4.8 1.2 + - - +
259A ALA* 3.9 26.9 - - + +
269A ALA* 3.4 25.0 - - + +
295A VAL* 3.3 19.3 - - - +
296A SER* 1.3 79.9 + - - +
298A ILE* 1.3 62.8 + - - +
300A ALA* 3.1 3.1 + - - +
301A MET* 2.8 41.1 + - + +
600A ADP 4.7 4.0 + - - +
1503A TRS 2.5 46.2 + - - +
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Residues in contact with ILE 298 (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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50A TRP* 3.6 31.2 - - + -
127A LEU* 6.0 0.7 - - + -
131A TYR* 4.8 8.5 - - + -
134A VAL* 4.1 22.9 - - + -
137A ARG* 5.6 1.3 - - + +
178A PHE* 5.1 8.3 - - + -
215A ILE* 5.7 6.1 - - + -
295A VAL* 3.0 15.3 + - + +
297A ASP* 1.3 84.7 - - - +
299A GLU* 1.3 70.8 + - - +
301A MET* 3.3 17.7 + - - +
302A LEU* 3.0 45.6 + - + +
1503A TRS 5.2 4.5 - - - -
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Residues in contact with GLU 299 (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 ARG* 3.0 42.0 + - - -
293A GLY 4.3 4.0 - - - +
294A ASN* 3.9 19.7 + - + -
295A VAL 2.9 26.7 + - - +
296A SER* 3.1 8.5 + - - +
298A ILE* 1.3 80.4 - - - +
300A ALA* 1.3 59.6 + - - +
302A LEU* 3.6 9.3 + - - +
303A SER* 2.9 21.3 + - - -
308A PHE* 3.9 3.5 - - + -
311A LYS* 4.2 13.5 + - - -
315A LEU* 4.2 38.4 - - + +
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Residues in contact with ALA 300 (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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164A GLN* 3.2 11.3 - - - +
255A HIS* 5.8 0.4 - - + -
256A TRP* 3.3 19.0 + - + -
259A ALA* 4.2 14.1 - - + -
260A SER* 3.9 7.2 - - - +
296A SER 2.9 14.1 + - - +
297A ASP 3.3 9.2 - - - +
298A ILE 3.1 0.2 - - - -
299A GLU* 1.3 76.5 - - - +
301A MET* 1.3 65.6 + - - +
303A SER* 3.0 16.8 + - - +
308A PHE* 3.5 25.5 - - + -
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Residues in contact with MET 301 (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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162A TYR* 3.5 5.2 - - - -
164A GLN* 3.3 23.8 - - - +
176A ASN* 3.2 38.6 - - - +
178A PHE* 3.2 31.9 - - + -
215A ILE* 4.8 1.8 - - - -
217A HIS* 3.3 28.3 - - + +
259A ALA 3.8 17.0 - - - +
260A SER* 4.2 8.7 - - - +
262A MET* 4.6 5.4 - - + -
297A ASP 2.8 24.2 + - - +
298A ILE* 3.3 16.4 + - - +
300A ALA* 1.3 72.3 - - - +
302A LEU* 1.3 58.4 + - - +
303A SER 3.2 0.7 - - - -
1503A TRS 4.3 19.7 - - - +
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Residues in contact with LEU 302 (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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134A VAL* 4.7 3.4 - - + -
137A ARG* 4.0 46.4 - - + +
138A VAL* 4.3 12.1 - - + -
141A HIS* 2.8 38.8 + - + -
162A TYR* 3.6 12.8 - - + -
178A PHE* 3.3 37.9 - - + -
298A ILE* 3.0 38.1 + - + +
299A GLU* 4.0 5.2 - - - +
300A ALA 3.1 0.4 - - - -
301A MET* 1.3 76.8 - - - +
303A SER* 1.3 60.5 + - - +
307A GLU* 4.7 0.3 - - - +
311A LYS* 5.4 1.1 + - - +
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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