Contacts of the helix formed by residues 316 - 332 (chain B) in PDB entry 3DGR
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 ASN 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B GLY* 1.3 69.6 - - - -
317B PRO* 1.4 64.2 - - - +
318B LEU* 3.2 13.9 - - - +
319B ASP* 3.0 52.4 + - + +
320B THR* 2.7 37.9 + - - -
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Residues in contact with PRO 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B GLY 3.1 9.8 - - - +
316B ASN* 1.4 88.8 - - - +
318B LEU* 1.3 61.3 + - - +
320B THR* 4.1 0.2 - - - -
321B VAL* 3.2 21.7 + - - +
352B GLN* 3.5 25.3 + - - +
354B ASP* 4.1 20.0 - - - +
355B GLY* 4.6 13.9 - - - +
360B THR* 5.2 8.7 - - + -
364B ILE* 3.9 22.7 - - + -
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ASN* 3.2 9.3 - - - +
317B PRO* 1.3 78.4 - - - +
319B ASP* 1.3 70.6 + - - +
321B VAL* 3.2 4.0 + - + +
322B LEU* 3.0 51.4 + - + +
363B GLU* 3.8 27.1 - - + +
364B ILE* 4.0 25.1 - - + +
367B GLY* 3.8 23.8 - - - -
368B MET* 5.2 0.7 - - + -
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Residues in contact with ASP 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B TYR* 5.1 1.3 - - - +
316B ASN* 3.0 35.9 + - + +
318B LEU* 1.3 84.0 - - - +
320B THR* 1.3 63.7 + - - +
322B LEU* 3.4 10.7 + - - +
323B LYS* 3.0 25.8 + - - +
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Residues in contact with THR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ILE* 4.5 6.1 - - + -
284B TYR* 3.4 32.7 + - + +
312B PRO* 3.8 25.6 - - + -
314B SER 3.1 25.1 + - - +
315B GLY* 3.7 6.1 - - - -
316B ASN 2.7 25.5 + - - -
317B PRO 4.1 2.5 - - - -
319B ASP* 1.3 71.9 - - - +
321B VAL* 1.3 56.4 + - - +
323B LYS* 3.2 2.3 + - - +
324B VAL* 2.8 32.5 + - + +
352B GLN* 4.8 4.7 - - - -
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B PRO* 4.7 8.1 - - + -
317B PRO 3.2 20.1 + - - +
318B LEU* 3.2 3.6 + - + +
320B THR* 1.3 79.4 - - - +
322B LEU* 1.3 57.3 + - + +
324B VAL* 3.7 6.1 - - - +
325B LEU* 2.9 49.6 + - + +
350B VAL* 4.9 5.4 - - + -
352B GLN* 3.7 25.6 - - + +
364B ILE* 4.4 8.3 - - + -
368B MET* 4.1 15.0 - - + -
378B ILE* 3.9 31.0 - - + -
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 3.0 47.6 + - + +
319B ASP* 3.9 10.3 - - - +
321B VAL* 1.3 74.3 - - - +
323B LYS* 1.3 59.0 + - - +
325B LEU* 3.3 5.7 + - + +
326B GLU* 2.9 35.1 + - + +
367B GLY* 3.9 17.7 - - - +
368B MET* 4.1 18.2 - - + -
371B LYS* 4.2 32.8 - - + -
373B TRP* 4.4 9.3 + - + +
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Residues in contact with LYS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B TYR* 3.5 52.0 - - + +
319B ASP 3.0 17.4 + - - +
320B THR 3.9 1.8 - - - +
322B LEU* 1.3 74.0 - - - +
324B VAL* 1.3 67.0 + - - +
326B GLU* 3.3 7.3 + - + +
327B ILE* 2.9 39.3 + - + +
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Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ILE* 3.7 31.9 - - + -
284B TYR* 4.6 5.3 - - + -
287B CYS* 4.1 15.4 - - - +
310B ILE* 4.7 4.7 - - + -
312B PRO* 4.5 6.7 - - + -
320B THR* 2.8 32.0 + - + +
321B VAL* 3.7 6.1 - - - +
323B LYS* 1.3 70.2 - - - +
325B LEU* 1.3 57.5 + - - +
327B ILE* 3.1 10.1 + - - +
328B LEU* 3.0 50.7 + - + +
350B VAL* 4.1 22.2 - - + -
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Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B VAL* 2.9 39.5 + - + +
322B LEU* 3.7 4.9 - - - +
324B VAL* 1.3 75.6 - - - +
326B GLU* 1.3 58.1 + - - +
328B LEU* 3.4 4.3 + - + +
329B GLY 2.9 23.2 + - - -
344B LEU* 4.1 18.6 - - + +
350B VAL* 3.9 26.9 - - + -
368B MET* 3.8 19.5 - - + -
373B TRP* 3.3 53.9 - - + +
377B ASN* 4.1 12.3 - - + -
378B ILE* 5.8 0.7 - - + -
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Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LEU* 2.9 24.9 + - + +
323B LYS* 3.8 8.5 - - + +
325B LEU* 1.3 70.0 - - - +
327B ILE* 1.3 68.7 + - + +
329B GLY* 3.4 1.4 + - - -
330B LYS* 3.3 46.2 + - + +
342B LYS* 3.2 15.6 + - - -
371B LYS* 5.5 2.1 - - - +
373B TRP* 3.0 29.8 + - - +
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Residues in contact with ILE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B TYR* 3.8 45.8 - - + +
287B CYS* 3.7 12.8 - - + +
288B GLU* 3.5 53.1 - - + +
323B LYS* 2.9 30.0 + - + +
324B VAL* 3.5 8.7 - - - +
326B GLU* 1.3 77.3 - - + +
328B LEU* 1.3 64.6 + - - +
330B LYS* 3.2 14.8 + - - +
331B LYS* 3.3 14.8 + - + +
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B CYS* 4.0 22.2 - - + +
291B TRP* 5.2 0.4 - - + -
310B ILE* 3.5 33.2 - - + -
324B VAL* 3.0 39.2 + - + +
325B LEU* 4.0 2.7 - - - +
327B ILE* 1.3 75.0 - - - +
329B GLY* 1.3 58.5 + - - +
331B LYS* 3.1 0.8 + - - -
332B PHE* 2.8 56.1 + - + +
344B LEU* 4.0 25.5 - - + +
348B LEU* 4.3 10.1 - - + -
350B VAL* 4.0 16.8 - - + -
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Residues in contact with GLY 329 (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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325B LEU 2.9 17.1 + - - -
326B GLU 3.8 2.5 - - - -
327B ILE 3.2 0.6 - - - -
328B LEU* 1.3 79.1 - - - +
330B LYS* 1.3 60.9 + - - +
332B PHE 3.1 15.1 - - - +
334B VAL* 3.7 27.7 - - - +
344B LEU* 4.5 0.4 - - - +
373B TRP* 4.3 5.8 - - - -
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Residues in contact with LYS 330 (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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288B GLU* 6.0 2.0 - - - +
326B GLU* 3.3 30.6 + - - +
327B ILE* 3.2 9.2 + - - +
329B GLY* 1.3 80.1 - - - +
331B LYS* 1.3 66.7 + - + +
332B PHE 4.6 0.4 - - - -
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Residues in contact with LYS 331 (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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287B CYS 4.7 1.1 - - - +
288B GLU* 3.5 34.8 - - + +
292B GLY* 3.9 17.4 + - - +
293B GLU* 2.7 40.3 + - - +
296B ARG* 2.8 32.1 + - - -
327B ILE 3.3 13.9 + - - +
328B LEU* 3.1 2.9 + - - -
330B LYS* 1.3 85.7 - - + +
332B PHE* 1.3 79.8 + - + +
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Residues in contact with PHE 332 (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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291B TRP* 3.6 24.7 - - + -
292B GLY* 4.0 7.0 - - - -
296B ARG* 3.7 22.0 - - + -
299B ILE* 3.6 30.1 - - + -
300B VAL* 3.8 16.8 - - + -
328B LEU* 2.8 31.2 + - + +
329B GLY 3.1 17.5 - - - +
330B LYS 4.6 0.7 - - - -
331B LYS* 1.3 93.2 - - + +
333B PRO* 1.3 66.4 - - + +
334B VAL* 3.1 9.2 + - - +
344B LEU* 5.4 1.1 - - + -
345B PRO* 4.0 13.9 - - + -
347B TYR* 4.0 11.7 - + - -
348B LEU* 3.4 23.1 - - + -
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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
------------------------------------------------------------
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