Contacts of the helix formed by residues 303 - 315 (chain A) in PDB entry 3N4E
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 GLY 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A MSE 5.6 0.2 - - - +
41A GLU* 4.8 0.6 + - - -
301A GLN* 3.5 2.4 - - - +
302A PRO* 1.3 82.1 - - - +
304A VAL* 1.3 66.2 + - - +
305A GLY 3.3 1.6 - - - -
306A HIS* 3.1 2.9 + - - +
307A PHE* 3.1 24.8 + - - -
336A PHE* 3.8 20.8 - - - -
339A PRO* 4.6 1.3 - - - -
357A ILE* 3.7 19.1 - - - -
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Residues in contact with VAL 304 (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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27A PHE* 4.0 9.2 - - + -
39A TRP* 3.7 35.2 - - + +
40A GLY* 3.7 25.4 - - - -
41A GLU* 3.5 18.7 + - + +
100A ILE* 3.9 10.5 - - + -
303A GLY* 1.3 70.7 - - - +
305A GLY* 1.3 64.0 + - - +
307A PHE* 3.2 6.4 + - - +
308A ALA* 3.0 21.3 + - - +
336A PHE* 3.8 27.3 - - + -
355A LEU* 3.9 5.5 - - + +
357A ILE* 4.0 12.1 - - + +
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Residues in contact with GLY 305 (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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41A GLU* 2.9 13.4 + - - -
272A ILE* 3.7 2.8 - - - +
273A VAL* 3.6 27.8 - - - -
299A GLN* 3.6 16.8 + - - -
301A GLN* 4.7 0.2 - - - -
303A GLY 3.3 0.4 - - - -
304A VAL* 1.3 76.1 - - - +
306A HIS* 1.3 55.3 + - - +
308A ALA* 3.4 3.6 + - - -
309A ASN* 2.9 29.8 + - - +
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Residues in contact with HIS 306 (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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299A GLN* 4.1 10.5 - - + +
301A GLN 3.2 24.7 + - - +
302A PRO* 3.5 7.2 - - + +
303A GLY 3.1 7.9 + - - +
305A GLY* 1.3 73.3 - - - +
307A PHE* 1.3 79.0 + + - +
309A ASN* 3.2 3.9 + - - +
310A ILE* 3.0 58.4 + - + +
323A VAL* 4.6 5.4 - - + +
324A GLU 5.2 3.4 + - - -
325A LEU* 5.9 0.2 - - - +
340A ALA* 3.6 25.2 - - + +
347A PHE* 3.5 47.7 - + - +
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Residues in contact with PHE 307 (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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303A GLY 3.1 22.8 + - - +
304A VAL* 3.6 9.4 - - - +
306A HIS* 1.3 90.1 - + - +
308A ALA* 1.3 66.7 + - - +
310A ILE* 3.4 15.7 + - + +
311A HIS* 3.1 31.2 + - - -
338A ASN* 3.0 41.3 - - - -
339A PRO* 4.1 6.5 - - + -
349A LEU* 5.7 3.1 - - + -
350A GLY 6.3 0.9 - - - -
355A LEU* 3.3 36.1 - - + +
356A GLY* 3.6 18.8 - - - -
357A ILE* 3.5 21.3 - - + -
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Residues in contact with ALA 308 (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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100A ILE* 4.1 20.4 - - + -
272A ILE* 3.6 32.0 - - + +
278A ILE* 4.3 8.0 - - + +
304A VAL 3.0 12.9 + - - +
305A GLY 3.7 7.6 - - - +
307A PHE* 1.3 76.6 - - - +
309A ASN* 1.3 63.3 + - - +
311A HIS* 3.5 4.1 + - - +
312A VAL* 3.3 18.2 + - - +
355A LEU* 3.7 16.9 - - + +
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Residues in contact with ASN 309 (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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272A ILE* 4.1 12.4 - - + +
281A MSE 4.7 3.3 - - - +
297A PRO* 3.4 29.2 + - - +
298A HIS 4.8 0.5 - - - +
299A GLN* 3.7 31.9 + - + +
305A GLY 2.9 17.1 + - - +
306A HIS* 3.3 6.7 + - - +
307A PHE 3.2 0.2 - - - -
308A ALA* 1.3 76.7 - - - +
310A ILE* 1.3 57.1 + - - +
312A VAL* 3.4 5.0 + - - +
313A LEU* 3.1 47.2 + - - +
323A VAL* 3.9 18.4 - - - +
324A GLU 5.2 1.0 - - - +
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Residues in contact with ILE 310 (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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126A LEU* 3.9 13.5 - - + +
306A HIS* 3.0 55.6 + - + +
307A PHE* 3.5 22.2 - - + +
309A ASN* 1.3 73.7 - - + +
311A HIS* 1.3 64.5 + - - +
313A LEU* 3.8 5.1 - - - -
314A SER* 2.9 31.0 + - - -
323A VAL* 4.1 24.7 - - + -
347A PHE* 4.6 12.8 - - + -
348A ALA 5.0 2.5 - - - +
349A LEU* 3.9 35.6 - - + +
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Residues in contact with HIS 311 (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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113A PRO* 4.1 5.8 - - + -
114A ILE* 3.6 37.9 - - + -
115A TYR* 3.1 39.3 + + - +
118A LEU* 4.8 2.9 - - + -
278A ILE* 5.5 0.9 - - + -
307A PHE* 3.1 29.7 + - + +
308A ALA* 3.8 6.3 - - - +
309A ASN 3.4 0.2 - - - -
310A ILE* 1.3 76.1 - - - +
312A VAL* 1.3 60.4 + - + +
314A SER* 2.7 22.9 + - - -
315A THR* 3.5 10.6 - - - +
349A LEU* 3.7 20.1 - - + +
350A GLY 4.6 2.4 + - - -
352A ALA 5.3 0.2 - - - -
354A GLY 3.6 5.6 + - - -
355A LEU* 3.0 36.4 + - + -
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Residues in contact with VAL 312 (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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118A LEU* 4.7 1.8 - - + -
272A ILE* 3.6 29.2 - - + -
278A ILE* 4.4 17.7 - - + +
281A MSE 4.3 22.7 - - + +
282A MSE 3.9 24.2 - - - -
285A ALA* 5.2 2.5 - - + -
295A PHE* 4.5 19.5 - - + -
297A PRO* 5.8 0.7 - - + -
308A ALA 3.3 5.1 + - - +
309A ASN* 3.8 8.7 - - - +
311A HIS* 1.3 75.3 - - - +
313A LEU* 1.3 60.8 + - + +
315A THR* 2.6 30.8 + - - -
316A LEU* 3.6 5.5 + - + +
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Residues in contact with LEU 313 (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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123A ARG* 2.7 33.6 + - - -
126A LEU* 3.9 17.9 - - + -
295A PHE* 4.5 7.0 - - + +
297A PRO* 3.6 35.9 - - + +
309A ASN* 3.1 46.7 + - - +
310A ILE* 4.1 0.4 - - - +
312A VAL* 1.3 74.2 - - + +
314A SER* 1.3 55.4 + - - +
315A THR 3.1 2.3 + - - -
316A LEU* 3.3 30.2 + - + +
319A MSE 4.1 12.0 - - + +
322A PRO 5.6 1.8 - - - +
323A VAL* 4.2 20.2 - - + -
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Residues in contact with SER 314 (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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115A TYR* 3.3 19.4 - - - +
121A ALA* 3.7 6.6 - - - +
122A TRP* 2.8 37.2 + - - +
123A ARG* 3.6 20.9 + - - +
126A LEU* 4.0 6.2 - - - +
310A ILE 2.9 15.9 + - - -
311A HIS 2.7 18.9 + - - -
313A LEU* 1.3 76.4 - - - +
315A THR* 1.3 54.4 + - - +
316A LEU 3.4 0.2 - - - -
349A LEU* 3.5 17.5 - - - -
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Residues in contact with THR 315 (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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115A TYR* 4.4 3.6 - - + +
118A LEU* 3.9 30.7 - - + +
120A GLY 3.5 23.3 - - - +
122A TRP* 3.3 16.3 + - - -
282A MSE 3.5 25.9 - - - +
311A HIS 3.5 16.6 - - - +
312A VAL 2.6 17.9 + - - -
314A SER* 1.3 79.1 - - - +
316A LEU* 1.3 61.0 + - - +
317A MSE 3.4 1.6 + - - -
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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