Contacts of the helix formed by residues 311 - 325 (chain A) in PDB entry 4N3Z
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 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299A PHE* 5.8 1.1 - - - -
306A LYS* 3.5 8.6 - - - +
309A PRO 5.1 0.9 - - - -
310A ALA* 1.3 75.6 - - - +
312A ALA* 1.3 55.4 + - - +
313A ASP* 2.9 22.0 + - - -
314A ASP* 2.7 56.0 + - - +
315A PHE* 3.3 4.0 + - - +
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Residues in contact with ALA 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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299A PHE* 5.9 1.8 - - - -
310A ALA 4.2 0.6 + - - -
311A SER* 1.3 71.5 - - - +
313A ASP* 1.3 61.6 + - - +
314A ASP 3.4 0.7 + - - -
315A PHE* 3.4 20.0 + - - +
316A LEU* 4.0 2.1 + - - +
354A TYR* 4.4 13.4 + - - +
358A ASN* 5.6 0.7 - - - +
396A SER* 3.9 9.9 + - - -
400A GLU* 3.4 36.1 - - + +
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Residues in contact with ASP 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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311A SER* 2.9 27.8 + - - -
312A ALA* 1.3 74.9 + - - +
314A ASP* 1.3 65.9 + - - +
317A PRO* 3.4 20.0 - - - +
393A ASP* 4.8 11.4 - - - +
396A SER* 3.9 18.6 + - - -
397A GLN* 4.8 3.8 - - - +
400A GLU* 3.7 8.7 + - - +
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Residues in contact with ASP 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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254A CYS 5.5 1.0 - - - +
256A PRO* 3.9 31.2 - - + +
302A ILE* 4.4 7.9 - - + -
306A LYS* 2.7 31.8 + - - +
311A SER* 2.7 36.4 + - - +
313A ASP* 1.3 81.3 - - - +
315A PHE* 1.3 60.0 + - - +
317A PRO* 3.3 11.2 - - - +
318A THR* 2.8 22.8 + - - -
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Residues in contact with PHE 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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295A SER* 3.2 50.3 - - - -
298A ILE* 3.8 17.9 - - + -
299A PHE* 3.5 37.9 - + + -
302A ILE* 4.3 7.6 - - - -
311A SER 3.3 4.8 + - - +
312A ALA* 3.4 12.5 + - - +
314A ASP* 1.3 78.9 - - - +
316A LEU* 1.3 62.6 + - - +
318A THR* 3.3 3.8 + - - -
319A LEU* 3.0 33.8 + - + +
354A TYR* 5.0 6.3 - - - +
355A TYR* 3.8 12.3 - + - -
358A ASN* 3.3 42.6 - - + -
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Residues in contact with LEU 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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312A ALA 4.0 3.2 + - - +
315A PHE* 1.3 83.3 - - - +
317A PRO* 1.4 72.2 - - + +
319A LEU* 3.0 15.4 + - + +
320A ILE* 3.1 15.5 + - + +
358A ASN* 3.1 45.5 - - + +
361A CYS* 4.1 8.1 - - + -
362A ALA* 3.8 15.0 - - + +
392A LEU* 3.7 22.0 - - + +
395A LEU* 3.5 34.1 - - + -
396A SER* 3.4 22.0 - - - +
399A ASN* 5.2 0.4 - - - +
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Residues in contact with PRO 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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253A LEU* 3.7 31.5 - - + +
255A VAL* 4.8 4.3 - - + -
313A ASP 3.4 18.2 - - - +
314A ASP* 3.3 12.8 - - - +
316A LEU* 1.4 95.4 - - + +
318A THR* 1.3 64.6 + - - +
320A ILE* 2.9 28.0 + - + +
321A TYR* 3.0 12.5 + - - +
392A LEU* 3.6 30.3 - - + -
396A SER* 4.4 2.0 - - - +
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Residues in contact with THR 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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255A VAL* 3.4 20.1 - - + +
256A PRO* 4.1 1.7 - - - +
257A VAL* 3.6 29.2 - - + -
268A VAL* 6.5 0.2 - - + -
298A ILE* 3.6 26.2 - - + +
301A ALA* 5.5 0.7 - - + -
302A ILE* 3.6 11.5 - - + +
314A ASP 2.8 15.2 + - - -
315A PHE 3.3 7.6 + - - -
316A LEU 3.3 0.6 - - - -
317A PRO* 1.3 76.5 - - - +
319A LEU* 1.3 62.0 + - - +
321A TYR* 3.2 13.7 - - + +
322A ILE* 3.1 29.9 + - + +
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Residues in contact with LEU 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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275A ILE* 5.0 0.9 - - + -
291A ILE* 5.4 4.3 - - + -
294A CYS* 4.1 15.9 - - - -
295A SER* 4.8 6.5 - - - +
298A ILE* 3.6 26.4 - - + +
315A PHE* 3.0 22.6 + - + +
316A LEU* 3.0 9.2 + - + +
318A THR* 1.3 74.7 - - - +
320A ILE* 1.3 66.1 + - - +
322A ILE* 2.9 13.5 + - - +
323A VAL* 3.0 29.6 + - + +
355A TYR 4.3 3.8 - - - +
358A ASN* 3.6 20.6 - - + +
359A LEU* 3.6 38.1 - - + +
362A ALA* 4.3 2.9 - - + -
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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
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253A LEU* 3.9 32.3 - - + -
316A LEU* 3.1 20.4 - - + +
317A PRO* 2.9 13.4 + - + +
319A LEU* 1.3 74.6 - - - +
321A TYR* 1.3 57.5 + - - +
323A VAL* 2.7 14.4 + - - +
324A LEU* 2.3 47.9 + - + +
362A ALA* 3.5 29.8 - - + +
365A PHE* 3.9 25.6 - - + -
366A ILE* 4.1 17.7 - - + -
392A LEU* 5.0 1.3 - - + -
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Residues in contact with TYR 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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248A VAL 5.0 9.4 - - - -
250A PRO* 3.3 36.5 - - + +
253A LEU* 4.5 18.8 - - + -
255A VAL* 4.6 16.2 - - + -
257A VAL* 4.4 11.0 - - + -
259A GLU* 2.6 36.7 + - - -
268A VAL* 5.6 0.7 - - + -
317A PRO 3.0 7.2 + - - +
318A THR* 3.2 15.7 - - + +
320A ILE* 1.3 82.1 - - - +
322A ILE* 1.3 64.0 + - + +
324A LEU* 3.9 10.5 - - + -
325A LYS* 3.0 56.0 + - + +
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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
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268A VAL* 3.9 32.8 - - + -
271A ALA* 3.8 12.3 - - + -
272A ILE* 3.6 34.2 - - + +
275A ILE* 4.2 9.6 - - + +
294A CYS* 3.8 14.8 - - - -
298A ILE* 3.6 24.7 - - + -
318A THR* 3.1 21.1 - - + +
319A LEU* 2.9 8.2 + - + +
321A TYR* 1.3 90.2 - - + +
323A VAL* 1.3 55.4 + - - +
325A LYS* 2.7 22.7 - - - +
326A GLY* 4.1 2.1 - - - +
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Residues in contact with VAL 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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242A ILE* 3.9 10.3 - - + +
275A ILE* 3.5 28.7 - - + -
319A LEU* 3.1 22.0 - - + +
320A ILE* 2.7 17.0 + - - +
322A ILE* 1.3 74.9 - - - +
324A LEU* 1.3 59.3 + - - +
325A LYS 3.3 0.4 - - - -
326A GLY 3.1 16.8 - - - +
327A ASN* 3.8 7.4 + - - -
328A PRO* 4.6 5.4 - - + +
331A LEU* 5.0 14.4 - - + -
359A LEU* 3.7 20.4 - - + -
362A ALA* 4.9 6.3 - - + -
363A VAL* 5.2 5.4 - - + -
366A ILE* 3.7 22.7 - - + -
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Residues in contact with LEU 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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242A ILE* 3.1 35.3 - - + +
245A LEU* 3.5 38.6 - - + +
246A ARG* 5.4 3.1 + - - -
248A VAL* 4.2 32.5 - - + +
253A LEU* 4.6 5.2 - - + -
320A ILE* 2.3 50.1 + - + +
321A TYR* 3.8 10.5 - - + +
323A VAL* 1.3 71.5 - - - +
325A LYS* 1.3 57.4 + - - +
366A ILE* 3.8 19.7 - - + -
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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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259A GLU* 4.2 8.4 + - - +
268A VAL* 3.0 35.0 - - - +
272A ILE* 3.2 23.0 - - + +
321A TYR* 3.0 60.1 + - + +
322A ILE* 2.7 25.2 - - - +
324A LEU* 1.3 77.8 - - - +
326A GLY* 1.3 59.4 + - - +
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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