Contacts of the helix formed by residues 298 - 310 (chain C) in PDB entry 1USK
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 GLU 298 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296C SER* 3.3 14.4 + - - +
297C ASP* 1.3 85.8 - - - +
299C PRO* 1.3 71.6 - - + +
300C LEU* 3.3 2.9 - - + +
301C ALA* 3.1 23.5 + - + +
302C LEU* 3.2 14.2 + - - +
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Residues in contact with PRO 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C LYS* 4.0 27.8 - - + +
72C TYR* 4.5 1.3 - - + -
93C GLY 3.3 28.3 - - - +
95C LEU* 3.8 23.2 - - + +
113C HIS* 4.5 2.5 - - + -
297C ASP 3.4 8.7 - - - +
298C GLU* 1.3 82.5 - - + +
300C LEU* 1.3 62.3 + - - +
302C LEU* 3.3 14.0 + - + +
303C VAL* 3.3 27.0 + - - +
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Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C GLN* 4.1 41.1 - - + +
113C HIS* 4.0 26.5 - - + +
298C GLU* 3.3 3.0 - - + +
299C PRO* 1.3 79.0 - - - +
301C ALA* 1.3 63.3 + - - +
303C VAL* 3.3 4.6 + - + +
304C LYS* 3.0 29.7 + - + +
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Residues in contact with ALA 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C THR* 4.6 4.9 - - + +
296C SER* 3.9 20.6 - - - +
298C GLU* 3.1 22.3 + - + +
300C LEU* 1.3 78.4 - - - +
302C LEU* 1.3 58.2 + - - +
304C LYS* 4.0 11.4 - - + +
305C ASP* 3.1 27.5 + - - +
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Residues in contact with LEU 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C TYR* 3.4 41.7 - - + +
95C LEU* 3.9 11.9 - - + -
287C LEU* 4.7 3.1 - - + -
290C ALA* 3.5 41.9 - - + +
291C LEU* 3.7 12.3 - - + +
294C THR* 3.6 12.1 - - - +
296C SER* 3.6 15.7 - - - +
298C GLU 3.2 16.8 + - - +
299C PRO* 3.6 6.7 - - + +
300C LEU 3.2 0.8 - - - -
301C ALA* 1.3 76.1 - - + +
303C VAL* 1.3 64.6 + - - +
305C ASP* 3.3 4.6 + - - +
306C LEU* 3.1 29.0 + - - +
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Residues in contact with VAL 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C LEU* 3.6 25.4 - - + -
112C GLN 3.2 22.7 - - - +
113C HIS* 3.8 26.2 - - - +
114C ILE 4.8 0.2 - - - +
115C MET* 4.0 24.4 - - + +
299C PRO 3.3 8.6 + - - +
300C LEU* 3.3 6.5 + - + +
302C LEU* 1.3 75.4 - - - +
304C LYS* 1.3 64.2 + - - +
306C LEU* 3.2 3.9 + - - +
307C LYS* 3.1 45.9 + - + +
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Residues in contact with LYS 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C LEU* 3.0 25.2 + - + +
301C ALA* 4.0 10.8 - - + +
303C VAL* 1.3 79.1 - - - +
305C ASP* 1.3 67.8 + - + +
307C LYS* 3.5 9.8 + - - +
308C ALA* 3.2 36.3 + - - +
309C ASN* 5.5 2.0 - - - +
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Residues in contact with ASP 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C ALA* 3.5 18.9 - - - -
293C ARG* 2.9 33.8 + - - +
294C THR* 3.2 27.3 - - + +
301C ALA 3.1 19.9 + - - +
302C LEU* 3.6 6.1 - - - +
303C VAL 3.2 0.2 - - - -
304C LYS* 1.3 89.1 + - + +
306C LEU* 1.3 56.9 + - - +
308C ALA* 4.7 1.1 - - - -
309C ASN* 3.1 43.5 + - - +
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Residues in contact with LEU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C LEU* 5.6 2.5 - - + -
97C ILE* 4.3 11.0 - - + -
115C MET* 3.7 27.8 - - + -
286C SER* 3.4 39.7 - - - +
287C LEU* 4.6 0.9 - - - +
289C THR* 4.7 0.2 - - + -
290C ALA* 3.9 11.9 - - + +
293C ARG* 4.1 7.2 - - - +
302C LEU 3.1 19.5 + - - +
303C VAL* 3.2 6.9 + - - +
305C ASP* 1.3 73.5 - - - +
307C LYS* 1.3 62.0 + - - +
310C GLY* 3.1 41.0 + - - +
311C ALA* 4.1 4.9 - - + -
320C TRP* 3.2 30.2 + - + +
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Residues in contact with LYS 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C TYR 4.4 8.9 + - - -
112C GLN* 4.3 10.1 + - - +
114C ILE 4.6 2.7 + - - -
115C MET* 4.0 10.5 - - + -
303C VAL* 3.1 38.3 + - + +
304C LYS* 3.5 8.5 + - - +
305C ASP 3.4 0.2 - - - -
306C LEU* 1.3 76.3 - - - +
308C ALA* 1.3 59.4 + - - +
320C TRP* 3.7 21.2 + - + +
321C ASP 3.7 14.6 - - - +
322C GLU* 2.6 33.4 + - - +
323C LYS 4.0 6.5 + - - -
324C GLY* 3.8 18.6 - - - +
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Residues in contact with ALA 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C LYS* 3.2 29.6 + - - +
305C ASP 4.1 2.0 - - - +
306C LEU 3.2 0.6 - - - -
307C LYS* 1.3 80.9 - - - +
309C ASN* 1.3 77.1 + - - +
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Residues in contact with ASN 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C ARG* 3.6 31.8 + - - +
304C LYS* 5.5 3.4 - - - +
305C ASP* 3.1 29.3 + - - +
308C ALA* 1.3 90.7 - - - +
310C GLY* 1.3 64.0 + - - +
319C ASN* 4.8 4.5 - - - +
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Residues in contact with GLY 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C THR* 4.0 0.3 - - - +
293C ARG* 3.0 26.7 + - - +
306C LEU* 3.1 22.8 + - - +
308C ALA 3.9 0.2 - - - -
309C ASN* 1.3 78.2 - - - +
311C ALA* 1.3 64.0 + - - +
318C LEU 3.4 14.8 - - - -
319C ASN* 4.3 7.2 - - - -
320C TRP* 3.9 6.3 - - - -
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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