Contacts of the helix formed by residues 302 - 311 (chain A) in PDB entry 5UM9
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 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A LEU* 3.0 22.8 + - + +
300A GLU 3.7 2.1 + - - +
301A PRO* 1.3 69.1 - - - +
303A GLU* 1.3 63.1 + - - +
304A GLU* 3.2 18.4 - - - +
305A GLU* 3.2 36.5 + - + +
306A LEU* 3.1 26.0 + - - +
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Residues in contact with GLU 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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301A PRO 3.5 5.5 + - - +
302A ASN* 1.3 74.3 + - - +
304A GLU* 1.3 77.1 + - - +
306A LEU* 3.1 5.1 + - - +
307A ILE* 2.9 41.2 + - + +
322A ARG* 3.2 39.5 + - + +
325A VAL* 3.8 33.7 - - + +
326A LYS* 4.2 20.8 - - - +
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Residues in contact with GLU 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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302A ASN* 3.2 13.5 - - - +
303A GLU* 1.3 85.4 + - + +
305A GLU* 1.3 63.8 + - - +
307A ILE* 3.2 11.8 + - + +
308A LYS* 2.9 35.4 + - + +
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Residues in contact with GLU 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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147A LEU* 3.6 26.4 - - + +
302A ASN* 3.2 29.5 + - - +
303A GLU 3.4 0.2 - - - -
304A GLU* 1.3 80.0 - - + +
306A LEU* 1.3 58.1 + - - +
308A LYS* 3.1 38.7 + - - +
309A PHE* 2.9 31.9 + - - +
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Residues in contact with LEU 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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68A PHE* 4.6 7.4 - - + -
144A LEU* 3.5 32.3 - - + -
147A LEU* 3.8 34.1 - - + +
148A MET* 4.1 16.4 - - + -
301A PRO* 4.5 7.2 - - + -
302A ASN 3.1 23.9 + - - +
303A GLU* 3.1 5.6 + - - +
305A GLU* 1.3 77.3 - - - +
307A ILE* 1.3 58.4 + - - +
309A PHE* 4.6 0.4 - - - -
310A MET* 2.9 44.1 + - + +
321A ILE* 4.5 4.1 - - + +
325A VAL* 3.8 27.6 - - + -
328A LEU* 5.6 1.3 - - + -
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Residues in contact with ILE 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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303A GLU* 2.9 36.2 + - + +
304A GLU* 3.6 10.5 - - + +
306A LEU* 1.3 75.5 - - + +
308A LYS* 1.3 66.0 + - + +
311A CYS* 3.0 42.0 + - + +
312A GLY 3.1 6.2 + - - -
318A GLU* 4.3 11.4 - - + +
321A ILE* 4.6 12.8 - - + -
322A ARG* 3.3 51.1 - - + +
325A VAL* 5.8 0.7 - - + -
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Residues in contact with LYS 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 GLU* 2.9 19.7 + - + +
305A GLU* 3.1 42.7 + - - +
307A ILE* 1.3 78.1 - - + +
309A PHE* 1.3 61.8 + - - +
312A GLY* 3.3 22.4 + - - +
313A GLU* 3.3 5.7 + - - +
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Residues in contact with PHE 309 (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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64A LEU* 4.2 11.7 - - + -
140A GLU* 4.5 17.9 - - + -
143A HIS* 4.0 28.0 - + + -
144A LEU* 4.4 16.2 - - + -
147A LEU* 3.9 19.3 - - + -
305A GLU 2.9 18.6 + - - +
306A LEU 4.1 0.9 - - - +
308A LYS* 1.3 76.7 - - - +
310A MET* 1.3 91.6 + - + +
313A GLU* 3.3 18.2 + - + +
314A LYS* 3.1 46.7 + - + +
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Residues in contact with MET 310 (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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64A LEU* 4.1 25.4 - - + +
68A PHE* 4.4 13.0 - - + -
144A LEU* 3.7 17.3 - - + -
306A LEU* 2.9 34.9 + - + +
309A PHE* 1.3 90.0 - - + +
311A CYS* 1.3 59.0 + - - +
314A LYS* 3.1 9.7 - - - +
315A GLN 2.9 21.0 + - - -
316A PHE* 3.0 46.7 + - + -
321A ILE* 3.7 28.9 - - + -
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Residues in contact with CYS 311 (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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307A ILE* 3.0 26.4 + - + +
310A MET* 1.3 76.4 - - - +
312A GLY* 1.3 66.9 + - - +
315A GLN* 3.1 20.1 + - - +
316A PHE 3.6 24.1 - - - +
318A GLU* 3.7 30.1 - - + -
321A ILE* 3.9 27.6 - - - -
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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