Contacts of the helix formed by residues 304 - 317 (chain C) in PDB entry 3UDB
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 304 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C ARG* 3.5 6.3 - - - +
302C GLY 3.8 0.6 + - - -
303C GLN* 1.3 76.3 - - - +
305C ILE* 1.3 65.1 + - - +
306C GLU* 3.4 17.3 + - - +
307C GLU* 2.5 40.6 + - - +
308C ILE* 3.0 22.8 + - - +
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Residues in contact with ILE 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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67C ILE* 4.2 27.4 - - + -
70C ARG* 3.5 32.4 - - - +
304C SER* 1.3 74.3 - - - +
306C GLU* 1.3 64.6 + - + +
308C ILE* 3.9 8.6 - - - +
309C MET* 3.0 39.9 + - + +
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Residues in contact with GLU 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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304C SER* 3.4 20.9 - - - +
305C ILE* 1.3 85.5 + - + +
307C GLU* 1.3 63.9 + - + +
309C MET* 3.4 6.3 + - - +
310C GLN* 3.0 25.5 + - - +
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Residues in contact with GLU 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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303C GLN* 3.3 19.9 - - + +
304C SER* 2.5 44.5 + - - +
306C GLU* 1.3 77.1 - - + +
308C ILE* 1.3 62.1 + - - +
310C GLN* 3.6 5.4 + - - +
311C ILE* 3.2 32.1 + - + +
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Residues in contact with ILE 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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66C ILE* 4.1 13.2 - - + -
67C ILE* 4.4 11.2 - - + -
70C ARG* 3.6 42.2 - - + +
80C PHE* 3.8 12.3 - - + -
83C VAL* 3.6 19.3 - - + -
303C GLN* 3.5 29.4 - - + +
304C SER 3.0 18.9 + - - +
305C ILE* 3.9 5.2 - - - +
307C GLU* 1.3 75.9 - - - +
309C MET* 1.3 64.5 + - - +
311C ILE* 3.3 2.8 + - - +
312C ILE* 3.0 40.7 + - + +
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Residues in contact with MET 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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63C LYS* 3.5 38.4 - - + +
67C ILE* 4.2 21.3 - - - -
305C ILE* 3.0 34.0 + - + +
306C GLU* 3.4 7.8 + - - +
308C ILE* 1.3 76.6 - - - +
310C GLN* 1.3 63.4 + - - +
312C ILE* 3.3 14.5 + - + +
313C ALA* 3.1 22.0 + - - +
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Residues in contact with GLN 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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306C GLU 3.0 16.8 + - - +
307C GLU* 3.8 7.2 - - - +
309C MET* 1.3 77.2 - - - +
311C ILE* 1.3 64.6 + - + +
313C ALA* 3.2 18.6 + - - +
314C GLU* 3.3 37.8 + - - +
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Residues in contact with ILE 311 (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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83C VAL* 3.5 29.2 - - + +
84C ILE* 4.2 4.5 - - - -
85C LEU* 3.7 31.9 - - + +
90C LEU* 4.1 14.1 - - + +
303C GLN* 4.0 11.4 - - - +
307C GLU* 3.2 20.2 + - + +
308C ILE 3.3 4.2 + - - +
310C GLN* 1.3 80.0 - - + +
312C ILE* 1.3 60.1 + - - +
314C GLU* 4.2 11.5 - - - +
315C ALA* 3.5 20.3 + - - +
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Residues in contact with ILE 312 (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 ILE* 3.8 17.6 - - + +
62C VAL* 5.8 1.1 - - + -
63C LYS* 4.4 33.2 - - + +
66C ILE* 3.8 31.6 - - + -
67C ILE* 5.5 0.9 - - + -
83C VAL* 5.1 1.8 - - + -
90C LEU* 4.6 11.0 - - + -
308C ILE* 3.0 34.6 + - + +
309C MET* 3.6 16.6 - - + +
310C GLN 3.1 0.2 - - - -
311C ILE* 1.3 78.8 - - - +
313C ALA* 1.3 61.3 + - - +
315C ALA* 3.5 6.7 + - - +
316C THR* 2.9 31.8 + - + +
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Residues in contact with ALA 313 (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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309C MET 3.1 12.4 + - - +
310C GLN* 3.2 19.5 + - - +
312C ILE* 1.3 75.7 - - - +
314C GLU* 1.3 65.5 + - + +
316C THR* 2.3 36.6 + - - +
317C VAL* 3.6 4.0 + - - +
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Residues in contact with GLU 314 (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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54C ARG* 3.6 3.0 + - - +
85C LEU* 3.9 28.0 - - + +
310C GLN* 3.3 39.7 + - - +
311C ILE* 4.3 10.1 - - - +
313C ALA* 1.3 76.4 - - + +
315C ALA* 1.3 57.9 + - - +
317C VAL* 2.4 45.8 + - + +
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Residues in contact with ALA 315 (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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54C ARG* 2.9 44.5 - - + +
58C ILE* 3.3 26.2 - - + +
85C LEU* 4.2 11.4 - - + +
90C LEU* 4.2 14.1 - - + -
311C ILE 3.5 16.5 + - - +
312C ILE* 3.6 6.3 - - - +
313C ALA 3.1 0.6 - - - -
314C GLU* 1.3 78.6 - - - +
316C THR* 1.3 58.9 + - - +
317C VAL 3.0 2.0 + - - +
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Residues in contact with THR 316 (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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54C ARG 3.8 6.3 - - - +
55C GLY 4.0 16.6 - - - +
56C GLU* 4.9 3.4 + - - -
58C ILE* 3.6 22.9 - - + +
312C ILE* 2.9 28.9 - - + +
313C ALA* 2.3 28.2 + - - +
315C ALA* 1.3 75.1 - - - +
317C VAL* 1.3 64.9 + - - +
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Residues in contact with VAL 317 (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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54C ARG* 2.5 49.3 + - - +
313C ALA 3.8 9.6 - - - +
314C GLU* 2.4 39.3 + - + +
315C ALA 3.4 3.8 - - - +
316C THR* 1.3 85.8 - - - +
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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