Contacts of the helix formed by residues 23 - 40 (chain 2) in PDB entry 6NRB
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 ALA 23 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222 SER* 1.3 80.0 - - - +
242 GLU* 1.3 57.0 + - - -
252 GLN 3.6 1.1 - - - -
262 VAL* 3.5 11.0 + - + +
272 ILE* 3.0 29.9 + - - +
125 LEU* 4.1 27.6 - - + +
165 GLU* 3.5 18.8 - - - +
1355 MET* 4.1 19.9 - - + +
1365 SER* 6.4 0.4 - - - -
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Residues in contact with GLU 24 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1161 LEU* 3.4 39.0 - - - +
1171 MET* 4.4 22.7 - - - +
222 SER* 3.3 12.1 - - - +
232 ALA* 1.3 77.6 - - - +
252 GLN* 1.3 62.2 + - - +
272 ILE* 3.0 11.7 - - - +
282 ALA* 2.7 28.6 + - - +
1325 MET* 4.0 16.5 - - + +
1355 MET* 5.0 1.3 - - + -
1365 SER* 3.5 21.9 - - - +
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Residues in contact with GLN 25 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222 SER 4.7 3.3 + - - +
242 GLU* 1.3 76.5 - - - +
262 VAL* 1.3 59.1 + - + +
282 ALA* 3.8 6.3 - - + -
292 GLY* 2.5 30.9 + - - -
322 ARG* 3.4 32.8 - - - +
1182 PHE* 5.1 13.9 - - + -
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Residues in contact with VAL 26 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222 SER 3.8 18.4 - - - +
232 ALA* 3.5 10.5 - - - +
242 GLU 3.2 0.4 - - - -
252 GLN* 1.3 81.0 - - + +
272 ILE* 1.3 54.9 + - - +
302 PHE* 3.8 8.8 + - - +
1182 PHE* 4.1 8.8 - - - +
1212 LYS* 3.7 43.1 - - + +
1222 HIS* 2.5 37.5 + - + +
165 GLU* 3.3 20.4 - - - +
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Residues in contact with ILE 27 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232 ALA 3.0 16.2 + - - +
242 GLU* 3.0 20.2 - - - +
262 VAL* 1.3 76.6 - - - +
282 ALA* 1.3 59.8 + - + +
312 ASN* 3.2 25.6 + - - +
1222 HIS* 3.2 14.5 - - + +
165 GLU* 3.0 41.3 - - + +
195 LYS* 3.5 33.3 + - + +
205 ASN* 3.1 23.3 - - - +
1325 MET* 4.3 6.3 - - + -
1355 MET* 3.5 20.6 - - + -
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Residues in contact with ALA 28 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242 GLU 2.7 19.7 + - - +
252 GLN* 3.8 9.0 - - + -
272 ILE* 1.3 78.3 - - + +
292 GLY* 1.3 57.2 + - - +
312 ASN* 2.9 4.9 + - - +
322 ARG* 2.4 54.2 + - + +
195 LYS* 4.7 4.3 - - - +
1325 MET* 6.4 0.4 - - + -
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Residues in contact with GLY 29 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252 GLN 2.5 21.5 + - - -
282 ALA* 1.3 72.0 - - - +
302 PHE* 1.3 57.4 + - - +
322 ARG* 3.4 20.7 - - - +
332 LEU* 2.8 35.9 + - - +
1182 PHE* 3.4 22.0 - - - -
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Residues in contact with PHE 30 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262 VAL 3.8 2.0 + - - -
282 ALA 3.4 0.2 - - - -
292 GLY* 1.3 74.0 - - - +
312 ASN* 1.3 53.4 + - - +
342 ARG* 2.5 83.3 + - - +
1152 LEU* 3.5 17.6 - - + +
1182 PHE* 3.2 21.4 - - - +
1192 ARG* 3.1 59.7 - - + -
1222 HIS* 3.2 22.0 - - + -
205 ASN* 3.3 32.8 - - + -
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Residues in contact with ASN 31 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272 ILE 3.2 19.5 + - - +
282 ALA* 2.9 4.5 + - - +
302 PHE* 1.3 83.7 - - - +
322 ARG* 1.3 63.1 + - - +
342 ARG* 3.8 10.9 + - - +
352 GLN* 3.1 31.1 + - - +
195 LYS* 3.2 27.6 + - - +
205 ASN* 3.8 9.2 + - - +
235 ASP* 3.0 42.7 + - - +
1285 LYS* 4.7 2.4 - - - +
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Residues in contact with ARG 32 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252 GLN* 3.4 33.1 - - - +
282 ALA* 2.4 38.7 + - + +
292 GLY* 3.4 28.7 + - - +
312 ASN* 1.3 70.3 - - - +
332 LEU* 1.3 65.8 + - + +
352 GLN* 3.3 8.0 + - - +
362 GLU* 3.2 29.3 + - - +
1182 PHE* 4.2 10.3 - - - -
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Residues in contact with LEU 33 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292 GLY* 2.8 16.6 + - - +
322 ARG* 1.3 80.2 - - + +
342 ARG* 1.3 59.6 + - - +
352 GLN 3.4 0.2 - - - -
362 GLU* 4.7 5.2 - - + +
372 GLN* 3.1 30.7 - - - +
1112 LYS* 4.2 31.6 - - + +
1142 GLU* 3.5 42.2 - - + +
1152 LEU* 3.4 23.2 - - + +
1182 PHE* 3.6 23.8 - - + -
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Residues in contact with ARG 34 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302 PHE* 2.5 50.0 + - + +
312 ASN* 3.8 10.6 + - - +
332 LEU* 1.3 76.0 - - - +
352 GLN* 1.3 58.3 + - - +
382 ARG* 2.9 62.2 + - - +
1152 LEU* 3.4 13.9 - - + +
1192 ARG* 4.6 7.2 - - - +
205 ASN* 2.6 55.4 + - - +
215 GLN* 5.0 0.2 - - - +
235 ASP* 3.5 24.9 + - - +
245 GLN* 4.5 19.9 - - - +
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Residues in contact with GLN 35 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312 ASN* 3.1 28.0 + - - +
322 ARG* 3.3 7.2 + - - +
342 ARG* 1.3 80.1 - - + +
362 GLU* 1.3 59.5 + - + +
382 ARG* 3.4 12.3 - - - +
392 GLY* 2.9 22.9 + - - -
235 ASP* 2.5 37.1 + - - +
275 GLU* 2.8 27.6 + - - +
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Residues in contact with GLU 36 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322 ARG 3.2 13.4 + - - +
332 LEU* 5.2 4.8 - - + +
352 GLN* 1.3 77.9 - - + +
372 GLN* 1.3 56.1 + - - +
392 GLY* 3.0 3.2 + - - +
402 LEU* 2.5 60.1 + - + +
1112 LYS* 3.6 20.4 + - + -
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Residues in contact with GLN 37 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332 LEU 3.1 16.0 + - - +
362 GLU* 1.3 77.9 - - - +
382 ARG* 1.3 56.7 + - - +
402 LEU* 3.5 3.5 - - - +
412 ALA* 2.8 32.3 + - + +
1082 LEU* 3.6 32.1 + - + +
1112 LYS* 3.1 26.0 - - + +
1122 GLY* 3.1 38.8 + - - +
1152 LEU* 3.2 25.3 - - + +
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Residues in contact with ARG 38 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342 ARG* 2.9 74.8 + - - +
352 GLN* 3.4 9.8 - - - +
362 GLU 3.2 0.2 - - - -
372 GLN* 1.3 79.2 - - - +
392 GLY* 1.3 62.1 + - - +
412 ALA* 3.2 19.7 + - + +
422 SER* 4.1 5.5 + - - -
245 GLN* 4.5 15.6 - - - +
275 GLU* 4.3 15.3 + - - -
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Residues in contact with GLY 39 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352 GLN 2.9 16.3 + - - -
362 GLU* 3.0 5.3 + - - -
382 ARG* 1.3 76.2 - - - +
402 LEU* 1.3 63.6 + - - +
412 ALA 3.6 0.3 + - - -
422 SER* 4.2 5.4 + - - -
432 LYS* 4.2 14.0 + - - +
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Residues in contact with LEU 40 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362 GLU* 2.5 35.5 + - + +
372 GLN* 3.5 5.4 - - - +
392 GLY* 1.3 73.5 - - - +
412 ALA* 1.3 61.8 + - - +
422 SER 3.4 1.3 - - - -
432 LYS* 3.4 49.6 + - + +
442 ALA* 4.1 7.1 + - - +
1042 LEU* 5.2 18.4 - - + +
1072 GLN* 5.2 9.2 - - + +
1082 LEU* 3.4 19.7 - - + +
1112 LYS* 3.3 39.5 - - + +
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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