Contacts of the helix formed by residues 300 - 307 (chain C) in PDB entry 5UHO
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 SER 300 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259C ILE 4.7 3.4 + - - -
261C VAL* 4.8 7.0 - - - -
298C GLY 4.1 2.2 + - - -
299C ARG* 1.3 74.6 - - - +
301C THR* 1.3 65.7 + - - +
302C GLU* 3.1 29.6 + - - +
303C LEU* 3.3 23.3 + - - +
331C TRP* 3.3 14.9 - - - -
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Residues in contact with THR 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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300C SER* 1.3 72.8 + - - +
302C GLU* 1.4 74.4 + - - +
303C LEU 3.1 7.2 + - - -
304C ILE* 3.3 22.6 + - - +
305C PRO* 3.9 1.0 - - - +
331C TRP* 3.7 17.9 - - + +
334C SER* 3.4 24.9 - - - +
335C ASN* 3.2 25.7 + - - -
373C LEU* 3.4 12.9 + - + +
374C TYR* 3.6 26.2 - - + +
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Residues in contact with GLU 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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261C VAL* 3.8 13.9 - - + +
300C SER* 3.1 15.8 + - - +
301C THR* 1.4 94.0 + - - +
303C LEU* 1.3 59.7 + - - +
304C ILE 3.5 0.4 - - - -
305C PRO* 3.6 9.0 - - - +
306C ARG* 3.3 32.5 + - - +
335C ASN* 3.6 11.6 + - - +
372C VAL 5.5 2.3 + - - -
373C LEU* 4.0 9.8 - - - +
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Residues in contact with LEU 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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259C ILE* 3.5 32.5 - - + +
261C VAL* 3.8 23.3 - - + +
264C ILE* 3.7 30.7 - - + -
277C ILE* 6.3 0.4 - - + -
299C ARG* 3.7 19.5 - - + -
300C SER 3.3 28.5 - - - +
301C THR 3.1 0.4 - - - -
302C GLU* 1.3 79.3 - - - +
304C ILE* 1.4 54.6 + - - +
305C PRO 3.4 0.2 - - - -
306C ARG* 2.8 30.2 + - - +
307C LEU* 3.2 28.4 + - + +
331C TRP* 4.5 4.7 - - + -
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Residues in contact with ILE 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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58C ARG* 3.3 6.9 + - - +
60C PHE* 3.4 25.6 - - + -
301C THR* 3.4 19.1 - - - +
303C LEU* 1.4 74.1 - - - +
305C PRO* 1.4 63.0 - - + +
306C ARG 3.2 1.2 + - - -
307C LEU* 3.2 19.6 + - - +
331C TRP* 3.7 31.6 - - + +
332C TYR* 3.7 38.6 - - + +
335C ASN* 3.8 19.7 - - + +
336C MET* 3.8 27.4 - - - +
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Residues in contact with PRO 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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58C ARG* 3.8 21.2 + - - +
301C THR 3.9 3.1 - - - +
302C GLU* 3.6 17.3 - - - +
303C LEU 3.6 3.6 - - - -
304C ILE* 1.4 94.3 - - + +
306C ARG* 1.4 66.7 + - + +
307C LEU 3.6 0.4 - - - -
335C ASN* 5.2 4.0 - - - +
336C MET 5.6 0.9 - - - +
338C GLY* 3.8 33.9 - - - +
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Residues in contact with ARG 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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261C VAL* 3.4 27.0 - - - +
264C ILE* 3.6 26.3 - - + +
265C GLU* 3.2 30.7 + - - +
268C SER* 4.1 2.6 + - - +
274C ALA* 3.5 18.6 - - - +
275C PRO* 3.7 1.7 - - - +
302C GLU* 3.3 32.1 + - - +
303C LEU* 2.8 14.1 + - - +
305C PRO* 1.4 82.1 - - + +
307C LEU* 1.3 58.8 + - - +
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Residues in contact with LEU 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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58C ARG* 2.8 32.1 + - - -
60C PHE* 3.6 6.4 - - + -
264C ILE* 3.6 33.7 - - + -
274C ALA* 3.9 2.9 - - - -
275C PRO* 3.5 12.1 - - + +
277C ILE* 3.6 40.4 - - + -
303C LEU* 3.2 38.5 + - + +
304C ILE* 3.2 6.5 + - - +
306C ARG* 1.3 77.1 - - - +
308C LYS* 1.3 57.4 - - - +
309C GLY 3.3 7.9 - - - +
310C VAL* 3.8 18.6 - - + -
331C TRP* 4.8 2.2 - - + -
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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