Contacts of the helix formed by residues 318 - 332 (chain B) in PDB entry 3NZG
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 THR 318 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ASN 5.4 0.7 - - - +
31B THR* 3.8 23.6 - - + -
47B GLU* 2.7 27.6 + - - +
315B ASN* 5.0 0.2 - - - +
317B LYS* 1.3 87.7 + - + +
319B GLY* 1.3 66.2 + - - +
320B ILE* 3.0 15.6 + - - +
321B THR* 3.2 3.3 + - - -
322B SER* 3.2 19.9 + - - -
341B VAL* 5.3 0.2 - - - +
350B LEU* 4.0 25.8 - - + -
351B ARG* 3.8 12.7 - - - +
354B LEU* 3.8 16.8 - - + +
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Residues in contact with GLY 319 (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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318B THR* 1.3 76.1 - - - +
320B ILE* 1.3 56.3 + - - +
322B SER* 3.7 6.0 - - - -
323B ALA* 3.0 28.9 + - - +
350B LEU 4.8 0.6 + - - -
351B ARG* 3.8 26.3 + - - +
355B VAL* 3.4 26.5 - - - +
358B GLU* 5.5 1.1 - - - -
376B ILE* 4.5 1.9 - - - +
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Residues in contact with ILE 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 3.8 32.8 - - + -
45B LEU* 4.0 5.4 - - + +
46B GLY* 3.5 42.0 - - - +
47B GLU* 3.6 14.6 - - + +
112B MSE 4.0 5.7 - - - +
318B THR* 3.0 12.0 - - - +
319B GLY* 1.3 76.1 - - - +
321B THR* 1.3 63.8 + - - +
323B ALA* 3.7 3.5 - - - +
324B ALA* 3.2 19.2 + - - +
354B LEU* 4.3 1.6 - - + -
355B VAL* 3.6 26.2 - - + -
374B LEU* 4.2 3.8 - - + +
376B ILE* 3.6 20.2 - - + -
378B LEU* 4.6 2.5 - - + -
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Residues in contact with THR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLU* 2.5 34.5 + - - +
112B MSE 4.2 10.1 - - - -
287B ASP* 4.7 0.4 - - - +
288B TYR* 3.4 31.6 - - + -
289B ASN* 2.9 27.9 + - - +
315B ASN* 3.2 23.8 - - + +
317B LYS* 4.0 3.1 - - - -
318B THR 3.2 2.9 + - - -
320B ILE* 1.3 71.7 - - - +
322B SER* 1.3 56.2 + - - +
324B ALA* 2.9 3.4 + - - +
325B ALA* 2.7 32.6 + - - +
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Residues in contact with SER 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ASN* 3.8 11.3 + - - +
318B THR 3.2 7.5 + - - -
319B GLY* 3.7 8.7 - - - -
320B ILE 3.3 0.2 - - - -
321B THR* 1.3 79.6 - - - +
323B ALA* 1.3 61.4 + - - +
325B ALA* 3.2 3.8 + - - +
326B ILE* 3.1 19.1 + - - +
340B TYR* 3.4 33.2 - - - -
341B VAL* 3.6 12.6 - - - +
351B ARG* 3.2 32.9 + - - -
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Residues in contact with ALA 323 (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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319B GLY 3.0 18.5 + - - +
320B ILE 3.7 4.9 - - - +
321B THR 3.2 0.2 - - - -
322B SER* 1.3 73.2 - - - +
324B ALA* 1.3 66.7 + - - +
325B ALA 3.3 0.2 + - - -
326B ILE* 3.3 9.6 + - - +
327B HIS* 3.0 31.0 + - + -
374B LEU* 3.7 17.9 - - + +
376B ILE* 3.6 26.0 - - + -
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Residues in contact with ALA 324 (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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112B MSE 4.1 26.7 - - + -
288B TYR* 4.3 9.2 - - + -
294B LEU* 3.9 17.9 - - + +
320B ILE 3.2 10.3 + - - +
321B THR* 2.9 9.1 + - - +
323B ALA* 1.3 78.6 - - - +
325B ALA* 1.3 56.5 + - - +
327B HIS* 3.3 3.8 + - - +
328B TYR* 2.9 29.6 + - - +
374B LEU* 3.9 16.7 - - + +
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B TYR* 3.3 30.7 + - + +
315B ASN* 3.7 18.6 - - - +
321B THR 2.7 13.4 + - - +
322B SER 3.3 10.5 - - - +
324B ALA* 1.3 77.3 - - - +
326B ILE* 1.3 63.1 + - - +
328B TYR* 3.2 2.1 + - - +
329B GLN* 3.0 25.3 + - - +
338B PHE* 3.9 17.9 - - + -
339B GLU 4.2 0.2 - - - +
340B TYR* 4.6 0.2 - - + -
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Residues in contact with ILE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 4.5 3.4 - - + -
322B SER 3.1 9.5 + - - +
323B ALA* 3.3 10.9 + - - +
325B ALA* 1.3 77.7 - - - +
327B HIS* 1.3 64.3 + - + +
329B GLN* 3.4 2.4 + - - +
330B PHE* 3.2 46.3 + - + -
338B PHE* 4.1 10.3 - - + -
340B TYR* 4.0 13.2 - - + +
359B ALA* 3.5 32.3 - - + -
366B PHE* 3.7 33.2 - - + -
367B ALA 4.8 1.1 - - - +
369B PRO* 4.0 16.2 - - + -
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Residues in contact with HIS 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PRO* 3.9 5.2 - - + -
126B ALA* 3.5 16.4 - - + +
127B TYR* 2.9 43.1 + + + +
130B LEU* 4.8 6.0 - - + +
294B LEU* 5.6 1.6 - - + -
323B ALA* 3.0 24.2 + - - -
324B ALA* 3.7 7.9 - - - +
326B ILE* 1.3 75.1 - - + +
328B TYR* 1.3 66.6 + - - +
330B PHE* 3.3 2.3 + - - -
331B ALA* 3.2 20.6 + - - +
369B PRO* 3.3 36.3 - - + +
371B ALA 5.2 0.2 - - - -
373B GLY 3.4 24.0 + - - -
374B LEU* 3.8 24.7 + - + -
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Residues in contact with TYR 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 4.8 2.2 - - - -
288B TYR* 3.5 27.8 - + + -
294B LEU* 4.0 12.9 - - + +
297B LEU* 4.1 22.9 - - + -
301B THR* 2.9 33.4 + - - +
311B VAL* 3.3 24.8 + - - +
313B PRO* 3.5 23.3 - - + -
324B ALA 2.9 17.6 + - - +
325B ALA 3.4 3.8 - - - +
327B HIS* 1.3 76.0 - - - +
329B GLN* 1.3 78.3 + - + +
330B PHE 3.2 0.3 + - - -
332B VAL* 2.7 59.1 + - + +
333B GLY* 3.0 15.7 + - - -
338B PHE* 5.2 0.9 - - + -
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Residues in contact with GLN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LYS* 2.8 31.4 + - - +
138B VAL* 3.6 19.7 - - + +
139B HIS 4.9 0.8 + - - +
311B VAL 5.0 1.4 - - - +
325B ALA 3.0 16.9 + - - +
326B ILE 3.8 5.2 - - - +
327B HIS 3.3 0.2 - - - -
328B TYR* 1.3 88.0 - - - +
330B PHE* 1.3 59.1 + - - +
333B GLY* 3.4 19.9 + - - +
335B ALA 2.9 29.1 + - - +
336B PRO 4.1 2.6 + - - -
337B TYR* 3.3 21.7 + - - +
338B PHE* 3.3 35.9 - - + +
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Residues in contact with PHE 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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127B TYR* 4.3 12.3 - + + -
133B THR* 2.6 46.5 + - + +
135B LYS* 3.8 20.5 + - + +
137B LYS* 3.9 9.0 - - - -
138B VAL* 3.6 32.3 - - + -
326B ILE* 3.2 35.6 + - + -
327B HIS* 3.8 6.7 - - - +
328B TYR 3.2 0.2 - - - -
329B GLN* 1.3 79.1 - - - +
331B ALA* 1.3 57.3 + - - +
366B PHE 3.5 15.9 - - - -
367B ALA 3.6 14.6 - - - -
368B LYS* 3.4 35.9 - - + -
369B PRO* 3.7 12.1 - - + -
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Residues in contact with ALA 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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84A ASN* 4.7 9.2 - - - +
127B TYR* 3.3 23.8 - - + +
130B LEU* 3.7 26.3 - - + +
131B GLY* 5.3 0.2 - - - -
132B GLY 3.1 23.4 - - - +
135B LYS* 5.7 0.7 - - - -
327B HIS 3.2 9.8 + - - +
330B PHE* 1.3 78.9 - - - +
332B VAL* 1.3 62.3 + - - +
333B GLY 4.0 0.2 - - - -
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 4.1 38.8 - - + +
294B LEU 5.6 0.9 - - - +
298B ARG* 3.8 28.0 - - + +
301B THR* 3.2 29.7 - - + +
302B GLU* 5.6 2.5 - - + -
328B TYR* 2.7 41.9 + - + +
331B ALA* 1.3 78.9 - - - +
333B GLY* 1.3 69.2 + - - +
334B ASN* 4.3 1.0 - - - +
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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