Contacts of the helix formed by residues 299 - 310 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300B ASP* 1.3 73.1 + - - +
301B VAL* 3.1 31.9 + - - +
302B ARG* 3.1 35.6 + - - +
303B GLU* 3.1 26.3 + - - +
442B GLU* 5.0 5.7 - - - +
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Residues in contact with ASP 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ASP* 1.3 77.5 - - - +
301B VAL* 1.3 85.1 + - + +
303B GLU* 3.0 31.8 - - - +
304B ARG* 3.4 17.1 + - - +
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ASP* 3.1 17.5 + - - +
300B ASP* 1.3 90.9 + - + +
302B ARG* 1.3 64.4 + - - +
304B ARG* 3.4 20.8 - - - +
305B ILE* 3.2 27.2 + - - +
442B GLU* 4.1 30.7 - - + +
472B GLU* 3.7 28.1 - - + +
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ASP* 3.1 36.3 + - - +
301B VAL* 1.3 76.9 - - + +
303B GLU* 1.3 65.9 + - - +
304B ARG 3.2 0.2 + - - -
305B ILE* 3.3 10.5 + - - +
306B ILE* 3.0 31.0 + - + +
324B GLY* 4.0 18.6 - - - -
325B ILE* 4.1 27.4 - - + +
328B LEU* 3.7 28.8 - - - +
442B GLU* 5.1 8.5 - - - +
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ASP 3.1 12.2 + - - +
300B ASP* 3.0 30.6 + - - +
302B ARG* 1.3 77.6 - - - +
304B ARG* 1.3 55.9 + - - +
306B ILE* 3.3 10.7 + - - +
307B LYS* 2.8 69.2 + - + +
332B PHE* 6.4 2.0 - - + -
517B GLN* 5.3 0.7 - - - +
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ASP* 3.4 15.4 + - - +
301B VAL* 3.4 25.7 - - - +
302B ARG 3.1 0.4 - - - -
303B GLU* 1.3 81.2 - - + +
305B ILE* 1.3 65.7 + - - +
308B ARG 3.1 6.6 + - - -
472B GLU* 3.2 43.7 + - + +
473B LYS* 5.3 2.2 - - - +
490B TRP* 3.4 56.3 - - + +
493B LEU* 5.5 1.2 - - - +
515B MET* 3.6 19.0 - - + +
517B GLN* 3.0 37.1 + - - +
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Residues in contact with ILE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B VAL 3.2 17.8 + - - +
302B ARG* 3.3 5.6 + - - +
304B ARG* 1.3 73.6 - - - +
306B ILE* 1.3 52.7 + - - +
308B ARG* 3.3 4.0 + - - +
309B ALA* 2.7 32.2 + - - +
325B ILE* 3.9 17.9 - - + -
440B THR* 3.8 23.8 - - + -
441B MET 3.7 4.5 - - - +
442B GLU* 3.7 40.4 - - + +
470B ILE* 3.8 23.6 - - + +
471B THR 3.6 1.8 - - - -
472B GLU* 3.3 25.8 - - - +
515B MET* 4.5 6.9 - - - +
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B ARG* 3.0 24.6 + - + +
303B GLU* 3.5 12.1 - - - +
305B ILE* 1.3 72.4 - - - +
307B LYS* 1.3 61.5 + - - +
309B ALA* 3.1 8.1 + - - +
310B ALA* 2.9 29.8 + - - +
325B ILE* 3.9 24.7 - - + +
328B LEU* 3.4 40.2 - - + -
329B ALA* 3.7 11.1 - - - +
332B PHE* 3.5 36.1 - - + -
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Residues in contact with LYS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B GLU* 2.8 44.8 + - + +
306B ILE* 1.3 73.9 - - - +
308B ARG* 1.3 58.6 + - - +
310B ALA* 4.0 2.0 - - - +
311B LEU* 3.9 4.3 - - - +
332B PHE* 4.3 26.2 - - + -
517B GLN* 3.4 35.2 - - + +
518B ILE* 2.9 56.2 + - + +
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Residues in contact with ARG 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B ARG 3.1 5.5 + - - -
305B ILE 3.6 6.1 - - - +
307B LYS* 1.3 75.2 - - - +
309B ALA* 1.3 64.8 + - - +
310B ALA 3.2 1.8 - - - -
311B LEU* 3.1 17.0 + - - +
312B GLU* 2.8 21.6 + - - +
468B ARG* 3.5 22.0 - - - +
470B ILE* 3.4 24.9 - - + +
475B VAL* 3.8 16.6 - - + +
487B ILE* 4.9 1.4 - - - +
488B GLU* 3.0 36.8 + - - -
515B MET* 3.4 28.7 - - + -
516B GLN* 3.3 36.9 + - - +
517B GLN* 3.3 3.7 - - - +
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B ILE 2.7 20.7 + - - +
306B ILE* 3.1 8.7 + - - +
308B ARG* 1.3 72.0 - - - +
310B ALA* 1.3 53.6 + - - +
312B GLU* 2.8 35.5 + - - +
313B PHE* 3.9 5.9 - - - -
325B ILE* 4.6 3.1 - - + -
329B ALA* 3.6 17.7 - - + -
398B MET* 3.8 18.0 - - - +
440B THR* 4.1 14.4 - - + -
470B ILE* 4.0 12.3 - - - +
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B ILE 2.9 15.8 + - - +
307B LYS 4.0 0.9 - - - +
309B ALA* 1.3 77.3 - - - +
311B LEU* 1.3 57.6 + - - +
312B GLU 3.2 0.4 - - - -
313B PHE* 3.2 32.3 + - - +
329B ALA* 3.6 8.2 - - - +
332B PHE* 3.6 33.2 - - + +
333B ILE* 5.4 1.9 - - - +
518B ILE* 3.7 25.9 - - + +
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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