Contacts of the helix formed by residues 299 - 310 (chain C) in PDB entry 3DLX
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 ASP 299 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300C ASP* 1.3 58.7 + - - +
301C VAL* 2.8 31.2 + - - +
302C ARG* 2.6 58.9 + - - +
303C GLU* 2.9 32.1 + - - +
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Residues in contact with ASP 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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299C ASP* 1.3 73.1 - - - +
301C VAL* 1.3 66.1 + - + +
303C GLU* 3.3 5.6 + - - +
304C ARG* 3.2 36.1 + - - +
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Residues in contact with VAL 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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299C ASP* 2.8 30.6 + - - +
300C ASP* 1.3 74.6 - - + +
302C ARG* 1.3 57.6 + - + +
304C ARG* 3.5 23.1 + - - +
305C ILE* 3.3 32.1 + - - +
442C GLU* 3.8 33.2 - - + +
472C GLU* 3.6 22.8 - - + +
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Residues in contact with ARG 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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299C ASP* 2.6 57.6 + - - +
301C VAL* 1.3 73.7 - - + +
303C GLU* 1.3 60.2 + - - +
305C ILE* 4.0 11.0 - - - +
306C ILE* 2.9 49.2 + - + +
325C ILE* 4.2 24.8 - - + +
328C LEU* 3.3 28.3 - - + +
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Residues in contact with GLU 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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299C ASP 2.9 18.9 + - - +
300C ASP* 3.8 5.8 - - - +
302C ARG* 1.3 75.5 - - - +
304C ARG* 1.3 55.9 - - + +
306C ILE* 4.3 7.6 - - - -
307C LYS* 2.8 54.1 + - + +
332C PHE* 5.7 6.7 - - + -
517C GLN* 4.5 0.4 - - - -
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Residues in contact with ARG 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 ASP* 3.2 26.8 + - - +
301C VAL* 3.7 27.2 - - - +
302C ARG 3.4 0.2 - - - -
303C GLU* 1.3 75.8 - - - +
305C ILE* 1.3 60.7 + - - +
308C ARG 3.2 4.3 + - - -
472C GLU* 3.0 41.6 + - + +
473C LYS* 4.8 4.9 - - - +
490C TRP* 3.7 56.6 - - + +
493C LEU* 5.0 2.6 - - - +
515C MET* 3.2 12.2 - - + +
517C GLN* 2.8 33.6 + - - +
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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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301C VAL* 3.3 22.6 + - + +
302C ARG* 4.0 9.2 - - - +
304C ARG* 1.3 79.9 - - - +
306C ILE* 1.3 52.2 + - - +
308C ARG* 3.2 4.2 + - - +
309C ALA* 2.7 31.9 + - - +
325C ILE* 4.2 19.7 - - + -
440C THR* 3.7 32.5 - - + -
441C MET 3.8 23.8 - - - +
442C GLU* 3.8 11.7 - - + +
470C ILE* 3.9 12.7 - - + +
471C THR* 3.6 9.4 - - - -
472C GLU* 3.5 24.5 - - - +
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Residues in contact with ILE 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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302C ARG* 2.9 43.0 + - + +
303C GLU* 3.8 6.1 - - - +
305C ILE* 1.3 75.9 - - - +
307C LYS* 1.3 61.0 + - - +
308C ARG 3.1 2.2 - - - -
309C ALA* 3.8 7.6 - - - +
310C ALA* 2.9 28.8 + - - +
325C ILE* 4.2 18.2 - - + +
328C LEU* 3.6 27.6 - - + +
329C ALA* 3.8 14.8 - - + +
332C PHE* 3.2 42.8 - - + -
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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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303C GLU* 2.8 38.5 + - - +
306C ILE* 1.3 74.8 - - - +
308C ARG* 1.3 58.0 + - - +
310C ALA* 4.1 1.4 - - - +
311C LEU* 3.9 4.5 - - - +
332C PHE* 4.3 24.0 - - + -
517C GLN* 3.2 30.6 - - + +
518C ILE* 2.9 62.0 + - + +
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Residues in contact with ARG 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 ARG 3.2 15.8 + - - +
305C ILE 3.2 4.4 + - - +
306C ILE 3.1 0.8 - - - -
307C LYS* 1.3 77.0 - - - +
309C ALA* 1.3 64.6 + - - +
310C ALA 3.2 1.1 - - - -
311C LEU* 3.2 18.3 + - - +
312C GLU* 2.7 32.7 + - - +
468C ARG* 3.6 12.7 - - - +
470C ILE* 3.7 23.0 - - + +
475C VAL* 4.0 20.1 - - + +
487C ILE* 4.9 1.8 - - - +
488C GLU* 3.0 38.1 + - - -
515C MET* 3.7 8.7 - - + -
516C GLN* 3.5 39.6 - - - +
517C GLN* 3.6 1.1 - - - +
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Residues in contact with ALA 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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305C ILE 2.7 20.3 + - - +
306C ILE* 3.8 8.5 - - - +
308C ARG* 1.3 73.1 - - - +
310C ALA* 1.3 54.0 + - - +
312C GLU* 2.8 31.5 + - - +
313C PHE* 3.8 4.7 - - - -
325C ILE* 6.5 0.2 - - + -
329C ALA* 4.3 6.3 - - + -
398C MET* 3.6 19.8 - - + +
440C THR* 3.7 27.4 - - + -
470C ILE* 3.6 11.9 - - - +
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Residues in contact with ALA 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 ILE 2.9 18.5 + - - +
307C LYS 4.1 0.9 - - - +
308C ARG 3.2 0.2 - - - -
309C ALA* 1.3 77.1 - - - +
311C LEU* 1.3 57.3 - - - +
312C GLU 3.2 0.4 - - - -
313C PHE* 3.4 31.5 + - - +
329C ALA* 4.7 3.9 - - - +
332C PHE* 3.8 19.1 - - + +
333C ILE* 4.8 2.1 - - - +
334C SER 5.4 0.7 + - - -
337C ILE* 6.0 0.2 - - - +
518C ILE* 3.6 42.8 - - + +
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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