Contacts of the helix formed by residues 294 - 305 (chain B) in PDB entry 4NH1
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 294 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B ASP* 5.1 2.0 - - - -
134B ARG* 2.8 25.7 + - - -
292B LEU 4.7 1.5 + - - -
293B VAL* 1.3 76.5 - - - +
295B PRO* 1.3 71.4 - - - +
296B GLU* 3.1 18.0 + - - -
297B ALA* 2.9 35.6 + - - +
298B LEU* 3.0 17.5 + - - +
323B TYR* 4.3 0.3 - - - -
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Residues in contact with PRO 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B SER* 1.3 86.6 - - - +
296B GLU* 1.3 72.5 + - + +
298B LEU* 3.8 10.0 + - + +
299B ASP* 3.2 24.1 + - - +
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Residues in contact with GLU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ARG* 3.1 28.2 + - - -
294B SER* 3.1 8.7 + - - +
295B PRO* 1.3 91.2 - - + +
297B ALA* 1.3 59.5 + - - +
299B ASP* 4.4 4.5 - - - -
300B PHE* 3.0 24.3 + - - +
321B HIS* 3.1 13.1 - - - -
322B PRO* 4.1 22.4 - - + +
323B TYR* 4.0 23.2 - - - +
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B LEU* 4.3 4.2 - - + +
226B ILE* 4.5 14.9 - - + +
292B LEU 4.4 7.4 - - - +
294B SER* 2.9 31.2 + - - +
296B GLU* 1.3 77.3 - - - +
298B LEU* 1.3 61.9 + - + +
300B PHE* 3.3 3.0 + - - +
301B LEU* 2.9 29.9 + - - +
323B TYR* 3.4 29.4 - - + -
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ILE* 4.6 5.4 - - + -
227B PHE* 3.5 32.3 - - + -
281B TRP* 3.7 22.1 - - + +
282B GLU* 3.5 43.3 - - + +
285B VAL* 5.2 0.2 - - + -
293B VAL* 3.7 24.0 - - + -
294B SER 3.0 18.8 + - - +
295B PRO* 4.2 8.3 - - + +
297B ALA* 1.3 72.8 - - - +
299B ASP* 1.3 60.4 + - - +
301B LEU* 3.7 5.7 - - + +
302B ASP* 2.8 32.2 + - - +
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Residues in contact with ASP 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B PRO 3.2 17.8 + - - +
296B GLU* 3.8 6.5 - - - +
297B ALA 3.3 0.2 - - - -
298B LEU* 1.3 78.6 - - - +
300B PHE* 1.3 61.5 + - - +
302B ASP* 3.5 7.6 + - - +
303B LYS* 2.7 54.2 + - - +
321B HIS* 3.1 22.3 + - + +
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Residues in contact with PHE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B MET* 4.4 8.3 - - + -
141B LEU* 4.1 4.9 - - + -
218B LEU* 5.0 1.6 - - + -
222B LEU* 3.5 22.9 - - + -
296B GLU 3.0 18.4 + - - +
297B ALA 3.6 3.1 - - - +
299B ASP* 1.3 75.3 - - - +
301B LEU* 1.3 63.7 + - - +
303B LYS* 3.4 4.2 + - - +
304B LEU* 3.2 45.7 + - + +
313B LEU* 3.9 14.6 - - + -
318B ALA* 3.5 35.9 - - + -
321B HIS* 3.3 27.5 + + + +
323B TYR* 3.7 18.8 - + + -
324B PHE* 3.5 26.5 - + - -
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B GLY* 3.2 33.0 - - - +
222B LEU* 3.7 18.6 - - + +
223B ALA* 3.7 12.6 - - + -
226B ILE* 4.0 9.2 - - + -
227B PHE* 3.6 32.1 - - + -
281B TRP* 4.0 19.2 - - + -
297B ALA 2.9 17.3 + - - +
298B LEU* 3.7 5.6 - - + +
300B PHE* 1.3 74.1 - - - +
302B ASP* 1.3 60.8 + - - +
304B LEU* 3.0 2.4 + - - -
305B LEU* 3.0 43.8 + - + +
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Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B ARG* 2.5 36.4 + - - -
281B TRP* 3.2 23.4 + - + +
298B LEU 2.8 19.0 + - - +
299B ASP* 3.7 8.9 - - - +
300B PHE 3.3 0.2 - - - -
301B LEU* 1.3 76.6 - - - +
303B LYS* 1.3 55.6 + - + +
304B LEU 3.6 0.2 + - - -
305B LEU 3.7 4.0 - - - +
306B ARG* 2.6 47.7 + - - -
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Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ASP* 2.7 49.6 + - - +
300B PHE 3.8 1.3 - - - +
301B LEU 3.2 0.6 - - - -
302B ASP* 1.3 80.4 + - + +
304B LEU* 1.3 61.6 + - - +
306B ARG* 4.1 23.1 - - - +
311B SER 4.6 1.2 - - - +
312B ARG* 3.9 5.7 - - - -
313B LEU* 3.3 57.1 + - + -
321B HIS* 4.6 7.4 - - + +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B MET* 3.6 48.7 - - + +
216B TRP* 4.3 1.7 - - - -
218B LEU* 4.3 9.4 - - + +
219B GLY* 3.7 31.0 - - - +
222B LEU* 4.1 10.3 - - + -
300B PHE* 3.2 45.9 + - + +
301B LEU 3.0 8.8 + - - +
303B LYS* 1.3 80.8 - - - +
305B LEU* 1.3 61.6 + - - +
312B ARG* 3.1 27.9 - - - +
313B LEU* 4.3 14.1 - - + +
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B TRP* 3.4 56.3 - - + +
219B GLY* 3.8 13.0 - - - +
220B CYS* 3.8 6.7 - - - +
223B ALA* 4.6 6.1 - - + -
233B PHE* 4.2 18.6 - - + -
249B LEU* 3.8 17.5 - - + +
278B ARG* 4.9 1.0 + - - -
281B TRP* 3.6 33.2 - - + -
301B LEU* 3.0 32.2 + - + +
302B ASP 3.7 4.3 - - - +
304B LEU* 1.3 73.1 - - - +
306B ARG* 1.3 70.0 + - - +
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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