Contacts of the helix formed by residues 295 - 308 (chain B) in PDB entry 3DL2
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 PRO 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B TYR* 3.5 29.8 - - + +
266B VAL* 4.1 30.3 - - + -
269B ASN* 4.7 0.7 - - + +
293B SER 3.9 0.2 - - - -
294B GLN* 1.4 87.3 - - + +
296B VAL* 1.3 65.7 + - - +
297B GLU* 3.3 9.8 + - - +
298B ILE* 3.3 17.1 + - + -
299B MET* 3.0 26.4 + - + +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B VAL* 3.6 24.2 - - + +
293B SER 3.3 15.3 - - - +
294B GLN* 3.0 26.5 + - - +
295B PRO* 1.3 71.8 - - - +
297B GLU* 1.3 78.4 + - - +
299B MET 4.5 0.2 - - - +
300B THR* 2.7 42.8 + - - +
317B ILE* 3.7 20.0 - - + +
318B GLY* 3.9 12.6 - - - +
349B GLN* 4.2 8.5 - - + -
412B SER* 3.8 14.1 - - - +
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Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B GLN* 5.4 0.2 - - - +
295B PRO* 4.5 5.7 - - - +
296B VAL* 1.3 95.4 + - + +
298B ILE* 1.3 63.6 + - + +
300B THR* 3.8 2.4 - - - -
301B TYR* 3.1 22.5 + - - +
318B GLY* 5.2 1.6 - - - -
347B GLY 4.0 2.6 - - - +
348B GLU* 3.4 17.1 - - - +
349B GLN* 2.8 33.6 + - - +
412B SER* 4.6 6.9 + - - +
426B PHE* 3.0 36.5 + - - +
427B LEU* 4.5 8.5 - - + -
462B ILE* 3.7 26.1 - - + +
466B GLN* 4.3 2.8 + - - -
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B TYR* 4.9 1.6 - - - +
266B VAL* 3.8 13.2 - - + -
270B VAL* 4.5 0.4 - - + -
295B PRO* 3.3 22.6 + - + +
297B GLU* 1.3 79.9 + - + +
299B MET* 1.3 62.8 + - - +
301B TYR* 3.3 2.9 + - - +
302B VAL* 2.9 36.1 + - + +
462B ILE* 4.1 17.3 - - + -
465B LEU* 3.2 39.7 - - + -
466B GLN* 4.0 27.4 - - + +
469B LEU* 3.8 25.1 - - + -
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Residues in contact with MET 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B VAL* 4.6 1.3 - - - -
269B ASN* 3.6 36.6 - - - +
270B VAL* 3.8 19.7 - - + +
273B PHE* 3.5 43.6 - - + -
291B VAL* 3.8 11.2 - - + -
293B SER* 3.8 15.3 - - - +
294B GLN 3.7 19.1 - - - +
295B PRO* 3.0 25.0 + - - +
296B VAL 4.1 0.2 - - - +
298B ILE* 1.3 82.9 - - - +
300B THR* 1.3 53.3 + - - +
302B VAL* 3.6 4.7 + - + +
303B THR* 2.7 37.2 + - - -
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Residues in contact with THR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B VAL* 3.6 12.4 - - + +
296B VAL* 2.7 22.7 + - - +
297B GLU 3.8 3.8 - - - -
299B MET* 1.3 73.5 - - - +
301B TYR* 1.3 59.7 + - - +
303B THR* 3.2 2.9 + - - -
304B TRP* 2.9 28.4 + - - +
314B VAL* 3.7 7.9 - - + +
315B ILE* 3.7 10.1 - - - +
316B GLY* 3.3 37.6 - - - +
412B SER* 3.9 2.4 - - - +
426B PHE* 3.5 31.9 - - + -
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Residues in contact with TYR 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A SER 5.3 1.9 + - - -
297B GLU 3.1 9.8 + - - +
298B ILE 3.6 3.8 - - - +
300B THR* 1.3 76.7 - - - +
302B VAL* 1.3 61.3 + - + +
304B TRP* 3.1 24.3 + + - +
305B LYS* 2.9 35.4 + - + +
424B GLU* 3.4 43.9 + - + +
426B PHE* 3.7 20.3 - + + -
466B GLN* 3.3 43.9 - - + +
471B LEU* 3.6 28.7 - - + +
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Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B VAL* 3.8 37.7 - - + -
273B PHE* 4.2 13.2 - - + -
298B ILE* 2.9 25.8 + - + +
299B MET* 3.7 8.7 - - + +
301B TYR* 1.3 80.1 - - + +
303B THR* 1.3 58.3 + - - +
305B LYS* 3.3 1.6 + - - +
306B LEU* 2.9 56.2 + - + +
469B LEU* 5.0 2.7 - - + -
471B LEU* 3.7 26.7 - - + -
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Residues in contact with THR 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PHE* 4.3 4.0 - - + -
273B PHE* 3.4 19.2 - - - -
277B VAL* 3.6 21.8 - - + +
289B LEU* 3.8 28.0 - - + -
291B VAL* 3.4 21.4 - - + +
299B MET 2.7 22.8 + - - -
300B THR 3.5 4.9 - - - -
302B VAL* 1.3 75.3 - - - +
304B TRP* 1.3 54.9 + - - +
307B SER* 2.7 37.0 + - - -
314B VAL* 3.9 9.2 - - + -
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Residues in contact with TRP 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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171A SER* 3.1 34.2 + - - -
172A LYS* 3.7 19.3 - - - +
173A SER 3.7 23.1 + - - -
300B THR 2.9 13.9 + - - +
301B TYR* 3.3 24.7 - + - +
303B THR* 1.3 76.5 - - - +
305B LYS* 1.3 61.4 + - - +
307B SER* 3.3 14.6 + - - -
308B THR* 3.4 10.4 + - - -
309B PHE 3.2 20.6 + - - -
311B ALA* 3.5 18.2 - - + +
314B VAL* 3.7 15.8 - - + +
414B LEU* 4.0 25.1 - - + -
424B GLU* 3.7 35.0 - - - -
426B PHE* 3.6 26.2 - + + -
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Residues in contact with LYS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A SER* 3.8 26.7 - - - +
301B TYR* 2.9 27.3 + - + +
302B VAL 3.7 3.8 - - - +
304B TRP* 1.3 75.3 - - - +
306B LEU* 1.3 67.9 + - + +
307B SER 3.5 0.3 + - - -
308B THR* 3.9 9.4 + - - -
471B LEU* 3.1 62.3 + - + +
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Residues in contact with LEU 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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273B PHE* 3.5 32.5 - - + +
274B ARG* 3.6 27.1 - - + +
277B VAL* 3.8 17.3 - - + -
278B PRO* 3.8 29.4 - - + +
302B VAL* 2.9 41.7 + - + +
304B TRP 3.3 0.2 - - - -
305B LYS* 1.3 84.1 - - + +
307B SER* 1.3 61.1 + - - +
308B THR* 3.6 3.1 + - - -
471B LEU* 4.0 14.8 - - + +
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Residues in contact with SER 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B VAL* 3.7 13.2 - - - -
278B PRO* 5.0 1.3 - - - -
281B GLY* 4.9 4.4 - - - -
289B LEU* 3.6 24.2 - - - +
303B THR 2.7 23.0 + - - -
304B TRP* 3.3 7.1 + - - -
306B LEU* 1.3 76.8 - - - +
308B THR* 1.3 72.9 + - - +
309B PHE* 3.4 34.2 + - - +
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Residues in contact with THR 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LYS* 3.3 31.9 - - + +
173A SER* 4.7 14.3 - - - +
304B TRP 3.4 9.6 + - - -
305B LYS 3.9 8.3 + - - -
306B LEU 3.6 3.6 + - - -
307B SER* 1.3 80.3 + - - +
309B PHE* 1.3 63.1 + - - +
310B PRO* 4.5 0.2 - - - +
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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