Contacts of the helix formed by residues 318 - 332 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASN 5.5 0.2 - - - +
31A THR* 3.7 14.1 - - + -
47A GLU* 2.8 28.3 + - - +
315A ASN* 4.9 0.2 - - - +
317A LYS* 1.3 86.7 + - + +
319A GLY* 1.3 65.5 + - - +
320A ILE* 3.0 15.6 + - - +
321A THR* 3.3 2.9 + - - -
322A SER* 3.3 19.6 + - - -
350A LEU* 4.0 26.7 - - + +
351A ARG* 3.7 11.2 - - - +
354A LEU* 3.7 26.2 - - + +
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Residues in contact with GLY 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A THR* 1.3 76.2 - - - +
320A ILE* 1.3 61.4 + - - +
322A SER* 3.8 3.9 - - - -
323A ALA* 3.0 24.3 + - - +
350A LEU 5.1 0.2 + - - -
351A ARG* 3.6 31.3 + - - +
354A LEU* 5.5 0.4 - - - +
355A VAL* 3.6 23.0 - - - +
358A GLU* 5.4 0.9 - - - -
376A ILE* 4.3 2.1 - - - +
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Residues in contact with ILE 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 4.0 32.1 - - + -
45A LEU* 4.3 8.1 - - + +
46A GLY* 3.5 39.9 - - - +
47A GLU* 3.7 9.0 - - + +
112A MSE 3.8 8.9 - - + +
318A THR* 3.0 14.0 - - - +
319A GLY* 1.3 80.0 - - - +
321A THR* 1.3 62.7 + - - +
323A ALA* 3.4 3.6 + - - +
324A ALA* 3.2 19.2 + - - +
354A LEU* 4.5 1.6 - - + -
355A VAL* 3.6 22.2 - - + -
374A LEU* 4.5 2.0 - - + +
376A ILE* 3.5 26.7 - - + +
378A LEU* 4.8 0.7 - - + -
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Residues in contact with THR 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 2.6 31.9 + - - +
112A MSE 4.2 5.3 - - - -
287A ASP* 4.6 0.7 - - - +
288A TYR* 3.5 31.9 - - + -
289A ASN* 3.0 28.5 + - - +
315A ASN* 3.1 23.3 - - + +
317A LYS* 4.2 2.2 - - - -
318A THR 3.3 2.6 + - - -
320A ILE* 1.3 71.2 - - - +
322A SER* 1.3 62.7 + - - +
324A ALA* 3.0 7.7 + - - +
325A ALA* 2.8 26.9 + - - +
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Residues in contact with SER 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASN* 3.6 21.7 + - - +
318A THR 3.3 10.2 + - - -
319A GLY* 3.9 5.2 - - - -
321A THR* 1.3 78.3 - - - +
323A ALA* 1.3 61.7 + - - +
325A ALA* 3.3 3.3 + - - +
326A ILE* 3.2 18.2 + - - +
340A TYR* 3.4 30.6 - - - -
341A VAL* 3.7 6.9 + - - +
351A ARG* 3.3 34.5 + - - -
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Residues in contact with ALA 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLY 3.0 18.6 + - - +
320A ILE 3.5 4.9 - - - +
322A SER* 1.3 74.8 - - - +
324A ALA* 1.3 67.0 + - - +
325A ALA 3.2 0.5 + - - -
326A ILE* 3.2 17.4 + - - +
327A HIS* 3.2 22.1 + - + -
374A LEU* 3.7 28.0 - - + +
376A ILE* 3.8 15.0 - - + -
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A MSE 4.0 28.3 - - + -
288A TYR* 4.3 13.0 - - + -
294A LEU* 3.9 16.2 - - + +
320A ILE 3.2 10.0 + - - +
321A THR* 3.0 9.0 + - - +
323A ALA* 1.3 79.1 - - - +
325A ALA* 1.3 57.4 + - - +
327A HIS* 3.4 2.8 + - - +
328A TYR* 2.9 29.3 + - - +
374A LEU* 3.9 14.3 - - + +
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Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A TYR* 3.3 34.1 + - + +
315A ASN* 3.9 13.9 - - - +
321A THR 2.8 11.7 + - - +
322A SER 3.4 10.5 - - - +
323A ALA 3.1 0.2 - - - -
324A ALA* 1.3 74.1 - - - +
326A ILE* 1.3 65.8 + - - +
328A TYR* 3.3 1.9 + - - +
329A GLN* 2.9 26.2 + - - +
338A PHE* 3.7 18.6 - - + -
339A GLU 4.3 0.2 - - - +
340A TYR* 4.7 0.2 - - + -
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Residues in contact with ILE 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 4.6 0.9 - - + -
322A SER 3.2 9.6 + - - +
323A ALA* 3.2 11.2 + - - +
325A ALA* 1.3 76.4 - - - +
327A HIS* 1.3 66.0 + - + +
329A GLN* 3.4 2.8 + - - +
330A PHE* 3.1 37.7 + - + -
338A PHE* 4.2 8.5 - - + -
340A TYR* 3.9 18.6 - - + +
359A ALA* 3.5 31.9 - - + -
366A PHE* 3.7 34.5 - - + -
367A ALA 4.8 1.1 - - - +
369A PRO* 3.8 25.6 - - + -
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Residues in contact with HIS 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PRO* 3.9 5.6 - - + -
126A ALA* 3.4 15.2 - - + +
127A TYR* 2.9 42.7 + + - +
130A LEU* 4.7 5.7 - - + +
294A LEU* 5.6 1.6 - - + -
323A ALA* 3.2 22.1 + - - -
324A ALA 3.6 7.2 - - - +
326A ILE* 1.3 75.5 - - + +
328A TYR* 1.3 68.8 + - - +
330A PHE* 3.2 3.1 + - - -
331A ALA* 3.2 17.8 + - - +
369A PRO* 3.4 35.0 - - + +
371A ALA 5.0 0.2 - - - -
373A GLY 3.2 26.5 + - - -
374A LEU* 3.7 26.8 + - + -
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Residues in contact with TYR 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 4.8 1.3 - - - -
288A TYR* 3.6 28.5 - + + -
294A LEU* 3.7 15.2 - - + +
297A LEU* 3.9 25.1 - - + -
301A THR* 2.7 27.5 + - - +
311A VAL* 3.3 21.6 + - + +
313A PRO* 3.7 19.5 - - + -
324A ALA 2.9 18.0 + - - +
325A ALA 3.4 4.3 - - - +
327A HIS* 1.3 76.1 - - - +
329A GLN* 1.3 89.8 + - + +
332A VAL* 2.6 65.0 + - + +
333A GLY* 3.0 14.6 + - - -
338A PHE* 5.3 0.9 - - + -
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Residues in contact with GLN 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LYS* 2.9 32.2 + - - +
138A VAL* 3.8 16.2 - - + -
139A HIS 5.0 0.8 + - - +
311A VAL 4.9 2.1 - - - +
325A ALA 2.9 15.9 + - - +
326A ILE 3.8 4.0 - - - +
328A TYR* 1.3 88.2 - - - +
330A PHE* 1.3 59.7 + - - +
333A GLY* 3.4 20.5 + - - +
334A ASN 4.7 0.2 + - - -
335A ALA 2.8 28.8 + - - -
336A PRO 4.1 2.8 + - - -
337A TYR* 3.2 23.2 + - - +
338A PHE* 3.4 37.9 - - + +
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Residues in contact with PHE 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TYR* 4.3 11.9 - + + -
133A THR* 2.7 47.4 + - + +
134A ASN 4.9 0.2 + - - -
135A LYS* 3.3 25.2 - - + +
136A ASP 3.8 8.7 - - - -
138A VAL* 3.5 36.8 - - + -
326A ILE* 3.1 25.7 + - + +
327A HIS 3.6 7.4 - - - +
328A TYR 3.2 0.4 - - - -
329A GLN* 1.3 79.5 - - - +
331A ALA* 1.3 60.0 + - - +
366A PHE 3.8 10.3 - - - -
367A ALA 3.8 16.4 - - - -
368A LYS* 3.3 37.2 - - + -
369A PRO* 3.9 15.0 - - + -
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TYR* 3.3 23.3 - - + +
130A LEU* 3.8 25.0 - - + +
132A GLY 3.0 24.8 - - - +
135A LYS* 5.9 0.2 - - - -
327A HIS 3.2 7.5 + - - +
328A TYR 3.2 2.2 + - - -
329A GLN 4.8 0.2 - - - -
330A PHE* 1.3 78.7 - - - +
332A VAL* 1.3 63.3 + - + +
333A GLY 5.3 0.2 - - - -
84B ASN* 4.5 11.1 - - - +
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU* 4.0 40.6 - - + +
294A LEU* 5.6 0.9 - - + +
298A ARG* 3.7 33.9 - - + +
301A THR* 3.3 22.5 - - - +
302A GLU* 5.6 2.7 - - + -
328A TYR* 2.6 42.9 + - + +
331A ALA* 1.3 78.8 - - - +
333A GLY* 1.3 68.1 + - - +
334A ASN* 4.4 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
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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