Contacts of the helix formed by residues 308 - 326 (chain A) in PDB entry 2NTZ
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 SER 308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ARG* 5.6 2.4 - - - +
307A LEU* 1.3 69.4 - - - +
309A LYS* 1.3 53.9 + - - +
310A GLU* 2.6 28.3 + - - +
311A LEU* 2.5 58.0 + - - +
312A GLN* 3.4 1.7 + - - +
5U T 3.6 21.3 + - - -
6U G 5.9 3.1 - - - -
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Residues in contact with LYS 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU 3.2 7.3 + - - +
308A SER* 1.3 69.3 + - - +
310A GLU* 1.3 62.3 + - - +
312A GLN* 3.9 25.1 - - + +
313A GLU* 3.3 35.1 + - - +
316A ASP* 5.1 1.0 + - - -
293B LYS* 6.1 0.9 - - - +
298B ARG* 5.8 1.3 - - - +
4U G 5.0 12.6 - - - +
5U T 3.5 15.9 + - - +
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Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A SER* 2.6 19.8 + - - +
309A LYS* 1.3 76.3 - - - +
311A LEU* 1.3 74.3 + - - +
313A GLU* 3.8 6.8 - - - +
314A GLU* 3.0 36.0 + - + +
326B SER* 5.7 0.9 + - - -
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 3.1 38.8 - - + -
308A SER* 2.5 48.7 + - - +
310A GLU* 1.3 80.8 - - - +
312A GLN* 1.3 67.4 + - - +
314A GLU* 2.9 14.3 - - - +
315A LEU* 2.9 24.6 - - + +
300B PHE* 5.0 0.9 - - + -
322B ILE* 4.9 17.0 - - + +
323B LEU* 5.7 10.1 - - + -
326B SER* 4.6 14.8 - - - +
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Residues in contact with GLN 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU 5.4 2.7 - - - +
308A SER 3.4 2.7 + - - +
309A LYS* 3.9 28.9 - - + +
310A GLU 3.3 0.2 - - - -
311A LEU* 1.3 76.5 - - - +
313A GLU* 1.3 56.2 + - - +
315A LEU* 2.5 30.8 + - - +
316A ASP* 2.7 26.3 + - - +
293B LYS* 2.7 34.0 + - - +
295B VAL* 4.4 10.1 - - - +
299B ALA 5.5 0.6 - - - -
300B PHE* 3.2 59.8 - - + +
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LYS* 3.3 29.0 + - - +
310A GLU* 3.8 6.7 - - - +
312A GLN* 1.3 77.7 - - - +
314A GLU* 1.3 66.0 + - - +
316A ASP* 3.4 10.2 + - - -
317A ARG* 2.6 57.9 + - + +
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Residues in contact with GLU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A GLU* 3.0 26.2 + - + +
311A LEU* 2.9 14.4 - - - +
312A GLN 2.8 2.4 + - - -
313A GLU* 1.3 83.4 - - - +
315A LEU* 1.3 51.6 + - - +
317A ARG* 3.8 1.2 - - - +
318A MSE 2.6 58.4 + - - +
322B ILE* 4.1 30.8 - - + +
325B LYS* 4.9 13.0 + - - +
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE* 4.8 9.2 - - + -
311A LEU* 2.9 18.6 - - + +
312A GLN 2.5 7.7 + - - +
314A GLU* 1.3 68.7 - - - +
316A ASP* 1.3 59.8 + - - +
318A MSE 2.6 8.2 + - - -
319A ILE* 2.4 53.3 + - + +
300B PHE* 3.6 33.0 - - + -
302B TYR* 4.1 9.0 - - + +
318B MSE 4.6 2.9 - - + -
319B ILE* 4.2 24.2 - - + -
322B ILE* 3.5 39.7 - - + -
323B LEU* 5.8 4.3 - - + -
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Residues in contact with ASP 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LYS* 5.1 1.7 + - - -
312A GLN* 2.7 43.8 + - - +
313A GLU* 3.3 14.0 + - - +
315A LEU* 1.3 75.9 - - - +
317A ARG* 1.3 61.9 + - - +
319A ILE* 3.8 5.9 - - - +
320A GLY* 3.1 15.8 + - - -
281B LEU* 5.5 4.3 - - - +
293B LYS* 3.1 28.6 + - - +
302B TYR* 2.6 28.3 + - - -
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Residues in contact with ARG 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A GLU* 2.6 37.7 + - + +
314A GLU 4.0 1.3 - - - +
316A ASP* 1.3 73.4 - - - +
318A MSE 1.3 59.1 + - - +
320A GLY* 3.1 4.3 + - - -
321A HIS* 2.6 34.9 + - + +
324A ARG* 5.3 11.6 + - - +
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Residues in contact with MSE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLU* 2.6 45.3 + - - +
315A LEU* 2.6 8.2 + - - +
317A ARG* 1.3 75.9 - - - +
319A ILE* 1.3 64.7 + - - +
321A HIS* 3.0 34.5 + - + +
322A ILE* 2.9 31.1 + - + +
318B MSE 3.1 48.0 - - + +
322B ILE* 5.1 1.1 - - + -
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Residues in contact with ILE 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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315A LEU* 2.4 51.2 + - + +
316A ASP* 3.8 5.4 - - - +
318A MSE 1.3 66.3 - - - -
320A GLY* 1.3 51.9 + - - +
322A ILE* 3.2 7.7 + - - +
323A LEU* 2.7 56.8 + - + +
281B LEU* 4.9 4.9 - - + -
302B TYR* 4.2 24.5 - - + -
304B PHE* 3.8 22.4 - - + -
315B LEU* 3.7 24.7 - - + -
318B MSE 5.4 3.6 - - + -
319B ILE* 3.9 20.6 - - + -
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Residues in contact with GLY 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ASP 3.1 7.9 + - - -
317A ARG* 3.1 7.4 + - - -
319A ILE* 1.3 77.0 - - - +
321A HIS* 1.3 70.3 + - - +
323A LEU* 4.1 10.8 - - - -
324A ARG* 3.0 42.4 + - - +
281B LEU* 5.9 1.8 - - - +
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Residues in contact with HIS 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ARG* 2.6 20.9 + - + +
318A MSE 3.0 35.6 + - + +
320A GLY* 1.3 79.0 - - - +
322A ILE* 1.3 71.3 + - + +
324A ARG* 2.9 22.2 + - + +
325A LYS* 3.2 5.8 + - + +
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Residues in contact with ILE 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A MSE 3.0 18.4 - - + +
319A ILE* 3.5 7.0 - - - +
321A HIS* 1.3 84.8 - - + +
323A LEU* 1.3 68.2 + - - +
325A LYS* 3.1 22.4 + - + +
326A SER 3.8 1.0 + - - -
311B LEU* 4.1 18.8 - - + +
314B GLU* 3.5 46.2 - - + +
315B LEU* 4.5 11.2 - - + +
318B MSE 4.1 28.5 - - + -
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ILE* 2.7 45.3 + - + +
320A GLY* 3.8 9.0 - - - +
322A ILE* 1.3 73.3 - - - +
324A ARG* 1.3 53.6 + - - +
326A SER* 2.7 42.9 + - - +
281B LEU* 4.1 26.7 - - + +
282B TRP* 4.2 20.6 - - + +
284B PHE* 5.6 4.5 - - + -
291B ALA* 4.7 15.9 - - + -
304B PHE* 4.4 14.8 - - + -
307B LEU* 5.2 1.8 - - + -
311B LEU* 4.5 22.6 - - + +
315B LEU* 4.9 5.4 - - + -
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Residues in contact with ARG 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ARG* 5.3 11.5 + - - +
320A GLY* 3.0 34.6 + - - +
321A HIS* 2.9 19.5 + - + +
323A LEU* 1.3 77.7 - - - +
325A LYS* 1.3 61.5 + - - +
326A SER* 2.9 2.5 + - - -
327A LEU 3.2 14.0 + - - +
282B TRP* 4.6 20.2 - - - +
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Residues in contact with LYS 325 (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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321A HIS* 3.2 5.1 + - + +
322A ILE* 3.1 19.9 + - - +
323A LEU 3.0 0.6 + - - -
324A ARG* 1.3 76.8 - - - +
326A SER* 1.3 66.0 + - - +
327A LEU* 2.9 2.6 + - - -
314B GLU* 4.1 24.7 + - - +
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE 3.8 0.8 + - - -
323A LEU* 2.7 28.7 + - - +
324A ARG 2.9 1.0 + - - -
325A LYS* 1.3 73.5 - - - +
327A LEU* 1.3 71.8 + - - +
282B TRP* 4.0 22.2 - - - -
311B LEU* 5.8 8.5 - - - -
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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