Contacts of the helix formed by residues 305 - 323 (chain A) in PDB entry 4NTX
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 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A ASP 4.5 3.8 + - - -
255A GLU* 3.5 36.2 - - - +
256A PRO* 3.8 2.4 - - - +
303A THR 3.8 1.2 + - - -
304A TYR* 1.3 87.7 - - - +
306A ILE* 1.3 65.1 + - - +
307A THR 3.6 3.3 + - - -
308A ALA* 3.1 23.4 + - - +
309A CYS* 3.0 22.0 + - - +
365A PRO* 4.3 6.7 - - - -
367A ASN 5.9 0.7 - - - -
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Residues in contact with ILE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A TYR* 4.8 0.9 - - - -
305A SER* 1.3 71.9 - - - +
307A THR* 1.3 60.3 + - - +
309A CYS* 3.2 10.0 + - - +
310A ARG* 2.8 44.4 + - + +
362A CYS* 4.5 17.3 - - + +
363A GLU 4.4 8.5 - - - +
364A MET* 4.6 12.6 - - + -
365A PRO* 3.7 31.7 - - + +
368A VAL* 5.6 1.8 - - + -
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Residues in contact with THR 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLU* 3.9 14.4 + - - -
256A PRO* 3.2 32.6 + - + +
257A PRO 3.7 14.4 - - - +
258A LEU* 3.9 23.3 + - + +
262A LEU* 4.0 12.5 - - - +
305A SER* 3.2 7.4 + - - -
306A ILE* 1.3 77.0 - - - +
308A ALA* 1.3 60.1 + - - +
310A ARG* 3.1 8.1 + - - +
311A ILE* 2.8 35.8 + - + +
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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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256A PRO* 4.1 8.5 - - + +
295A THR* 6.0 2.0 - - + -
301A TYR* 3.8 38.2 - - + -
303A THR 4.0 5.6 - - - +
304A TYR* 4.8 3.6 - - + -
305A SER* 3.1 29.7 + - - +
307A THR* 1.3 76.1 - - - +
309A CYS* 1.3 63.8 + - - +
311A ILE* 3.3 1.7 + - - +
312A ASP* 3.0 31.1 + - - +
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Residues in contact with CYS 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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304A TYR* 3.4 27.9 - - + +
305A SER 3.0 7.5 + - - +
306A ILE 3.2 5.6 - - - +
308A ALA* 1.3 79.1 - - - +
310A ARG* 1.3 62.7 + - - +
312A ASP* 3.3 9.9 + - - +
313A CYS* 3.0 24.2 + - - -
360A CYS* 4.0 6.5 - - - -
361A VAL 4.9 0.4 - - - -
362A CYS* 2.1 52.9 - - + -
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Residues in contact with ARG 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LEU* 3.8 28.9 - - + +
261A GLN* 4.0 23.4 + - - +
262A LEU* 4.9 9.3 - - - +
306A ILE* 2.8 36.1 + - + +
307A THR* 3.1 6.0 + - - +
309A CYS* 1.3 73.3 - - - +
311A ILE* 1.3 59.0 + - - +
313A CYS* 3.3 1.9 + - - +
314A GLU* 2.9 39.2 + - - +
353A VAL* 4.1 17.6 + - - +
360A CYS* 4.2 9.6 - - - -
362A CYS* 3.9 14.1 - - - -
503A CL 3.3 29.7 - - + +
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Residues in contact with ILE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PRO* 4.1 8.7 - - + -
257A PRO 3.9 21.3 - - - +
258A LEU* 3.9 18.2 - - + -
301A TYR* 3.8 26.0 - - + +
307A THR* 2.8 25.2 + - + +
308A ALA 3.9 2.9 - - - +
310A ARG* 1.3 74.6 - - - +
312A ASP* 1.3 63.4 + - - +
314A GLU* 3.8 10.9 - - + +
315A THR* 2.8 31.4 + - - +
328A HIS* 5.8 9.0 - - + +
329A MET* 5.1 4.7 - - + -
330A PRO* 3.8 27.6 - - + -
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Residues in contact with ASP 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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295A THR* 5.2 3.1 - - - +
299A GLU 3.4 22.7 + - - -
300A PHE* 2.9 43.1 + - + +
301A TYR* 4.1 5.4 + - - -
304A TYR* 6.0 1.2 - - - -
308A ALA* 3.0 23.9 + - - +
309A CYS* 3.4 10.6 - - - +
311A ILE* 1.3 75.7 - - - +
313A CYS* 1.3 64.5 + - - +
315A THR* 3.1 3.6 + - - -
316A ARG* 2.9 33.9 + - - +
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Residues in contact with CYS 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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309A CYS* 3.0 15.8 + - - -
310A ARG 3.6 3.8 - - - +
312A ASP* 1.3 79.8 - - - +
314A GLU* 1.3 55.4 + - + +
316A ARG* 3.2 7.8 + - - +
317A TYR* 2.8 37.7 + - - +
352A LEU* 4.5 2.0 - - + -
359A TYR* 3.7 13.0 - - + -
360A CYS* 2.1 54.5 - - + -
30B ARG* 4.0 16.8 - - - -
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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
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258A LEU* 4.4 16.8 - - - +
261A GLN* 5.6 1.0 - - - +
310A ARG* 2.9 33.7 + - - +
311A ILE* 3.8 11.9 - - + +
313A CYS* 1.3 75.7 - - - +
315A THR* 1.3 58.2 - - - +
317A TYR* 3.2 2.1 + - - +
318A LEU* 2.9 34.1 + - - +
328A HIS* 5.1 6.8 + - - -
329A MET* 4.4 9.0 - - - +
349A LEU* 3.7 33.1 - - + +
352A LEU* 3.7 13.2 - - + -
353A VAL* 4.1 8.7 - - - +
503A CL 3.2 28.5 - - + +
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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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300A PHE* 4.2 19.7 - - + -
311A ILE* 2.8 21.3 + - - +
312A ASP 3.6 3.4 - - - -
314A GLU* 1.3 74.9 - - - +
316A ARG* 1.3 65.9 + - - +
318A LEU* 3.2 2.4 + - - +
319A VAL* 3.0 37.6 + - + +
325A ARG* 4.5 2.2 - - + -
329A MET* 3.3 36.4 - - + +
330A PRO* 3.5 32.6 - - - +
331A GLY* 5.4 0.4 - - - -
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Residues in contact with ARG 316 (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 GLU* 5.4 6.1 + - - -
300A PHE* 5.0 11.7 - - + -
312A ASP* 2.9 26.8 + - - +
313A CYS* 3.7 7.6 - - - +
315A THR* 1.3 76.0 - - - +
317A TYR* 1.3 56.8 + - - +
319A VAL* 3.9 4.7 - - - +
320A GLU* 2.9 33.3 + - - +
359A TYR* 3.7 14.4 + - - +
30B ARG* 4.9 16.0 - - - +
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Residues in contact with TYR 317 (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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313A CYS 2.8 18.0 + - - +
314A GLU 3.5 4.5 - - - +
316A ARG* 1.3 79.5 - - - +
318A LEU* 1.3 60.4 + - + +
320A GLU* 4.5 0.4 - - - -
321A ASN* 3.0 55.5 + - - +
348A ALA* 3.4 39.5 - - + -
351A PHE* 3.3 28.7 - + - -
352A LEU* 3.7 25.8 - - + -
356A ASP* 4.9 1.5 + - - -
359A TYR* 3.3 46.7 - + + -
29B SER* 5.0 3.8 - - - -
65C PHE* 3.4 13.2 - + - -
67C SER* 5.4 0.2 - - - -
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Residues in contact with LEU 318 (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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314A GLU 2.9 19.9 + - - +
315A THR 3.2 0.2 + - - -
317A TYR* 1.3 80.6 - - + +
319A VAL* 1.3 57.5 + - - +
322A CYS* 2.7 40.7 + - + +
324A CYS 3.3 12.9 - - - +
326A MET* 3.6 33.4 - - + +
329A MET* 3.6 27.1 - - + -
345A ALA* 4.0 22.0 - - + +
348A ALA* 3.7 29.4 - - + -
349A LEU* 4.1 14.4 - - + +
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Residues in contact with VAL 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 THR* 3.0 28.9 + - + +
316A ARG* 3.9 4.7 - - - +
318A LEU* 1.3 76.3 - - - +
320A GLU* 1.3 60.6 + - - +
323A ASN* 2.9 34.9 + - - +
324A CYS 3.8 13.7 - - - +
325A ARG* 4.6 1.6 - - + -
333A ALA* 3.6 32.3 - - + -
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Residues in contact with GLU 320 (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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316A ARG 2.9 21.0 + - - +
317A TYR* 4.0 2.9 - - - +
319A VAL* 1.3 79.8 - - - +
321A ASN* 1.3 72.0 + - - +
323A ASN* 4.7 0.3 + - - -
359A TYR* 4.9 9.6 - - + +
30B ARG* 4.9 2.8 - - - +
3C ASN* 3.2 25.5 - - - +
7C LEU* 3.1 40.6 - - + +
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Residues in contact with ASN 321 (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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317A TYR* 3.0 53.6 + - + +
320A GLU* 1.3 90.4 - - - +
322A CYS* 1.3 63.8 + - - +
344A CYS* 3.2 3.3 - - - -
348A ALA* 4.9 0.7 - - + -
359A TYR* 5.3 0.6 - - - -
1C ASN* 3.1 27.0 + - - +
3C ASN* 3.7 6.0 - - - +
4C GLN* 2.7 33.6 + - - +
7C LEU* 4.2 14.5 - - - +
65C PHE* 4.2 21.6 - - + -
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Residues in contact with CYS 322 (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 LEU* 2.7 19.8 + - + +
321A ASN* 1.3 76.3 - - - +
323A ASN* 1.3 75.2 + - - +
324A CYS* 3.1 20.6 + - - +
340A GLN* 3.6 17.7 + - - +
344A CYS* 2.1 62.3 - - + +
345A ALA* 3.7 7.2 - - - +
348A ALA* 4.1 11.4 - - - -
1C ASN* 4.8 0.7 - - - +
3C ASN* 4.4 1.3 - - - +
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Residues in contact with ASN 323 (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 LEU 3.3 0.2 + - - -
319A VAL* 2.9 27.5 + - - +
320A GLU* 4.7 0.4 + - - +
322A CYS* 1.3 78.1 - - - +
324A CYS* 1.3 59.6 + - - +
333A ALA* 5.3 0.7 - - - -
334A PRO* 3.4 21.4 - - - +
340A GLN* 5.0 4.2 + - - +
3C ASN* 2.9 38.3 + - - +
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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