Contacts of the helix formed by residues 299 - 308 (chain A) in PDB entry 1UN0
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 ARG 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A ALA* 5.7 0.7 - - - -
267A TYR* 5.6 1.9 + - - -
296A ILE 3.0 17.7 + - - -
297A ASP* 3.3 21.4 + - - +
298A VAL* 1.3 80.1 - - - +
300A ILE* 1.3 66.0 + - - +
301A PRO* 3.4 4.2 - - - -
302A LYS* 3.8 19.5 + - + +
303A ARG* 4.3 3.1 + - - +
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Residues in contact with ILE 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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259A LEU* 4.0 16.8 - - + +
262A LEU* 4.9 0.2 - - + -
263A ALA* 4.0 26.5 - - + +
266A ILE* 4.2 11.0 - - + -
281A ILE* 3.9 28.5 - - + -
295A VAL* 3.4 20.6 + - + +
298A VAL* 3.6 23.6 - - + -
299A ARG* 1.3 78.3 - - - +
301A PRO* 1.3 73.0 - - + +
303A ARG* 2.9 18.2 + - - +
304A LEU* 3.2 37.3 + - + +
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Residues in contact with PRO 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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295A VAL* 3.5 13.9 - - + +
296A ILE* 3.8 28.7 - - + +
299A ARG* 3.4 4.3 - - - -
300A ILE* 1.3 99.4 - - + +
302A LYS* 1.3 59.7 + - - +
304A LEU* 3.8 9.5 - - + +
305A VAL* 3.2 29.5 + - - +
323A VAL* 5.4 0.8 - - + +
326A ILE* 4.3 14.1 - - + -
336A VAL* 4.1 21.1 - - + +
337A VAL* 4.4 12.3 - - + -
340A ALA* 4.6 1.6 - - + -
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Residues in contact with LYS 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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267A TYR* 4.4 13.9 + - - +
299A ARG* 3.8 15.2 + - + +
300A ILE 3.0 0.8 + - - -
301A PRO* 1.3 81.9 - - - +
303A ARG* 1.3 62.8 + - - +
305A VAL* 3.3 10.6 + - - +
306A GLU* 3.4 40.0 + - + +
340A ALA* 4.2 17.6 - - + +
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Residues in contact with ARG 303 (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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266A ILE* 2.9 51.4 + - + +
267A TYR* 3.6 53.0 + - + +
268A SER 5.5 2.0 + - - -
269A MET* 6.0 3.6 - - - -
274A LEU* 5.6 2.4 - - - +
299A ARG 4.3 3.3 + - - +
300A ILE 2.9 9.4 + - - +
302A LYS* 1.3 78.7 - - - +
304A LEU* 1.3 65.8 + - - +
306A GLU* 2.8 36.2 + - - +
307A LEU* 3.0 46.0 + - + +
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Residues in contact with LEU 304 (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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266A ILE* 4.7 4.7 - - + -
278A CYS* 4.5 15.0 - - + -
281A ILE* 4.3 14.6 - - + -
300A ILE* 3.2 38.1 + - + +
301A PRO* 3.9 8.7 - - + +
302A LYS 3.3 0.2 - - - -
303A ARG* 1.3 76.4 - - - +
305A VAL* 1.3 62.5 + - - +
307A LEU* 3.1 17.3 + - + +
308A LEU* 3.2 17.2 + - - +
319A ALA* 4.3 23.6 - - + +
322A ALA* 3.8 26.0 - - + -
323A VAL* 3.9 13.9 - - + -
326A ILE* 4.2 18.8 - - + -
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Residues in contact with VAL 305 (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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301A PRO 3.2 15.0 + - - +
302A LYS 3.6 8.3 - - - +
303A ARG 3.2 0.2 - - - -
304A LEU* 1.3 76.8 - - - +
306A GLU* 1.3 63.7 - - + +
308A LEU* 3.3 23.8 + - - +
309A SER* 4.4 1.4 + - - -
323A VAL* 4.8 4.9 - - + -
337A VAL* 4.1 8.1 - - + +
340A ALA* 3.2 36.3 - - + +
341A GLY* 3.6 20.4 - - - +
342A VAL* 3.6 25.6 - - + +
345A ALA* 4.1 8.2 - - + +
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Residues in contact with GLU 306 (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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267A TYR* 4.4 2.3 + - - -
302A LYS* 3.4 38.7 + - + +
303A ARG* 2.8 51.7 + - - +
305A VAL* 1.3 80.2 - - + +
307A LEU* 1.3 58.7 + - - +
309A SER* 3.1 26.0 + - - -
310A HIS* 4.2 1.7 + - - -
340A ALA 6.1 0.2 - - - +
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Residues in contact with LEU 307 (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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266A ILE* 3.8 24.0 - - + +
274A LEU* 4.0 20.4 - - + -
278A CYS* 3.9 25.4 - - - -
303A ARG* 3.0 43.0 + - + +
304A LEU* 3.1 13.4 + - + +
306A GLU* 1.3 72.7 - - - +
308A LEU* 1.3 64.4 + - - +
309A SER 3.0 3.7 + - - -
310A HIS* 3.1 27.5 + - + +
315A VAL* 4.1 18.8 - - + +
316A GLN* 4.3 5.5 - - - +
319A ALA* 4.3 6.3 - - + -
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Residues in contact with LEU 308 (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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304A LEU 3.2 10.8 + - - +
305A VAL* 3.4 15.7 - - - +
306A GLU 3.3 0.8 - - - -
307A LEU* 1.3 75.4 - - - +
309A SER* 1.3 55.7 + - - +
310A HIS 3.4 0.7 - - - -
316A GLN* 3.6 21.0 - - - +
319A ALA* 3.7 12.3 - - + +
320A LEU* 3.4 44.0 - - + +
323A VAL* 4.4 8.5 - - + -
342A VAL* 3.8 25.6 - - + +
345A ALA* 3.7 28.0 - - + -
346A LEU* 5.0 0.9 - - + -
348A LEU* 4.2 4.0 - - - +
349A LEU* 3.7 28.2 - - + +
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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