Contacts of the helix formed by residues 257 - 274 (chain E) in PDB entry 1NZB
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 257 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E ALA* 5.6 0.7 - - - -
255E GLN* 2.8 12.2 + - - -
256E LEU* 1.3 80.7 - - - +
258E THR* 1.3 59.0 + - - +
259E ARG* 3.2 9.7 + - - +
260E ALA* 2.7 26.0 + - - +
261E LEU* 2.9 23.2 + - - +
107H T 3.2 32.1 + - - +
108H T 4.4 11.9 - - - -
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Residues in contact with THR 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174E ILE* 3.6 24.0 - - + +
175E ALA* 4.6 22.0 - - + -
178E ALA* 5.1 6.3 - - + -
257E SER* 1.3 71.3 - - - +
259E ARG* 1.3 60.2 + - - +
261E LEU* 3.1 9.9 + - - +
262E GLU* 2.7 46.5 + - - +
125G T 4.9 5.8 + - - +
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Residues in contact with ARG 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257E SER* 3.2 9.2 + - - +
258E THR* 1.3 81.3 + - - +
260E ALA* 1.3 56.8 + - - +
262E GLU* 3.2 23.2 + - - +
263E GLY* 3.1 19.5 + - - +
266E GLU* 4.0 18.2 + - - -
127G C 3.6 26.7 - - - +
128G G 2.4 50.2 + - - -
129G A 3.7 6.6 + - - +
107H T 4.1 11.6 - - + +
108H T 3.6 30.3 - - + +
109H C 3.9 4.0 - - - +
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Residues in contact with ALA 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256E LEU* 3.0 31.9 - - + -
257E SER* 2.7 17.3 + - - +
259E ARG* 1.3 72.9 - - - +
261E LEU* 1.3 64.3 + - - +
262E GLU 3.0 1.3 - - - -
263E GLY* 2.8 13.8 + - - -
264E ILE* 3.0 15.9 + - - +
106H C 4.2 13.9 - - - +
107H T 3.4 15.9 - - + +
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Residues in contact with LEU 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E PHE* 3.2 43.9 - - + -
174E ILE* 3.9 18.2 - - + +
177E ILE* 4.3 3.1 - - + -
178E ALA* 3.8 31.0 - - + +
239E PHE* 5.0 3.8 - - + -
256E LEU* 3.5 35.2 - - + +
257E SER 2.9 16.5 + - - +
258E THR* 3.7 8.3 - - - +
260E ALA* 1.3 74.6 - - - +
262E GLU* 1.3 64.8 + - - +
264E ILE* 3.2 34.4 + - + +
265E PHE* 3.6 5.3 + - - -
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Residues in contact with GLU 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174E ILE* 3.9 16.2 - - + +
258E THR* 2.7 32.6 + - - +
259E ARG* 3.2 30.4 + - - +
260E ALA 3.0 0.2 - - - -
261E LEU* 1.3 71.0 - - - +
263E GLY* 1.3 59.0 + - - +
265E PHE* 2.9 35.6 + - - +
266E GLU* 3.1 6.8 + - - +
286E TRP 4.7 0.9 - - - +
287E SER* 5.1 3.6 - - - -
288E GLY* 5.2 5.6 - - - +
125G T 4.8 1.8 - - - +
126G A 3.0 51.4 + - - +
127G C 3.9 17.7 + - - -
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Residues in contact with GLY 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E ARG* 3.1 10.0 + - - +
260E ALA* 2.8 9.4 + - - -
262E GLU* 1.3 73.8 - - - +
264E ILE* 1.3 65.2 + - - -
265E PHE 2.8 2.4 + - - -
266E GLU* 2.8 16.7 + - - -
267E ALA* 2.7 29.3 + - - +
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Residues in contact with ILE 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159E ARG* 4.2 18.8 - - - +
160E ASN* 3.5 58.6 + - + +
163E PHE* 4.0 23.1 - - + -
164E LEU* 4.4 4.3 - - + -
239E PHE* 5.9 0.2 - - + -
256E LEU* 4.4 3.8 - - + -
260E ALA 3.0 12.5 + - - +
261E LEU* 3.2 38.6 + - + +
263E GLY* 1.3 74.1 - - - +
265E PHE* 1.3 55.5 + - - +
267E ALA* 4.2 3.6 - - - +
268E THR* 2.6 33.3 + - - -
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Residues in contact with PHE 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E PHE* 3.1 36.3 - + - -
163E PHE* 3.7 26.7 - + - -
164E LEU* 3.4 19.3 - - + -
167E ALA* 4.2 8.7 - - + -
174E ILE* 4.8 3.1 - - + -
261E LEU 3.6 8.5 + - - -
262E GLU* 2.9 9.0 + - - +
263E GLY 2.8 0.6 + - - -
264E ILE* 1.3 77.4 - - - +
266E GLU* 1.3 69.9 + - - +
268E THR* 3.0 16.0 + - - -
269E HIS* 3.2 10.9 + - - +
286E TRP* 3.6 27.9 - + + +
287E SER* 3.1 30.1 - - - +
288E GLY* 3.8 13.7 - - - -
290E SER* 4.5 2.2 - - - -
291E ALA* 4.1 22.7 - - + -
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Residues in contact with GLU 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E ARG* 4.0 21.1 + - - -
262E GLU* 3.1 3.9 + - - +
263E GLY* 2.8 23.1 + - - +
265E PHE* 1.3 77.0 - - - +
267E ALA* 1.3 63.5 + - - +
269E HIS* 3.2 6.8 + - - +
270E ARG* 3.2 32.9 + - + +
276E LYS* 3.3 33.9 + - + +
285E ALA* 4.7 9.0 - - + +
286E TRP 3.7 11.7 + - - +
127G C 5.2 5.8 - - - +
128G G 4.0 6.8 + - - -
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Residues in contact with ALA 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E ASN* 5.7 5.2 - - - +
263E GLY 2.7 19.1 + - - +
264E ILE* 4.2 4.7 - - - +
266E GLU* 1.3 74.1 - - - +
268E THR* 1.3 63.9 + - - +
270E ARG* 2.9 46.5 + - - +
271E LEU* 2.9 15.2 + - - +
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Residues in contact with THR 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E VAL* 3.4 33.9 - - + -
149E MET* 4.7 15.2 - - + +
160E ASN* 5.2 4.0 + - - +
164E LEU* 3.1 28.8 - - + +
264E ILE* 2.6 24.6 + - - +
265E PHE* 3.0 6.7 + - - -
267E ALA* 1.3 77.9 - - - +
269E HIS* 1.3 60.3 + - - +
271E LEU* 3.7 17.8 + - + +
272E ILE* 3.8 12.3 + - - +
286E TRP* 4.0 8.1 - - + -
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Residues in contact with HIS 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E LEU* 4.2 9.6 - - + +
265E PHE 3.2 6.6 + - - +
266E GLU 3.6 9.0 - - - +
267E ALA 3.1 0.6 - - - -
268E THR* 1.3 74.1 - - - +
270E ARG* 1.3 63.2 + - - +
272E ILE 3.1 2.3 + - - -
273E TYR* 3.0 74.6 + + + -
274E GLY 5.2 1.8 + - - -
276E LYS* 6.0 0.6 - - + +
284E LEU 3.7 20.2 - - - -
285E ALA* 3.3 20.1 - - + +
286E TRP* 3.3 44.3 - + + +
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Residues in contact with ARG 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E GLU* 3.2 20.2 + - + +
267E ALA* 3.1 41.8 + - - +
269E HIS* 1.3 75.0 + - - +
271E LEU* 1.3 59.1 + - - +
272E ILE 2.9 6.6 + - - -
274E GLY* 2.7 55.2 + - - +
275E ALA* 4.8 7.0 - - + +
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Residues in contact with LEU 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E VAL* 6.0 1.1 - - + -
148E LEU* 5.1 16.6 - - + +
149E MET* 4.1 28.3 - - + -
157E ASP* 5.9 1.8 - - - +
267E ALA 2.9 14.1 + - - +
268E THR* 3.8 9.6 - - + +
269E HIS 3.3 0.2 - - - -
270E ARG* 1.3 76.0 - - - +
272E ILE* 1.3 72.3 + - + +
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Residues in contact with ILE 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E GLN* 2.9 44.6 - - + +
145E VAL* 3.5 32.3 - - + +
148E LEU* 4.3 9.4 - - + -
268E THR 3.8 7.0 - - - +
269E HIS 3.1 2.9 + - - +
270E ARG 2.9 2.4 + - - -
271E LEU* 1.3 98.0 - - + +
273E TYR* 1.3 91.3 + - + +
274E GLY 3.5 0.7 - - - -
286E TRP* 5.1 0.9 - - + -
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Residues in contact with TYR 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E ASP* 3.8 13.2 + - - -
144E GLN* 3.5 20.9 + - - -
269E HIS* 3.0 55.4 + + + +
272E ILE* 1.3 98.4 - - + +
274E GLY* 1.3 60.5 + - - +
275E ALA 4.1 3.5 + - - +
286E TRP* 3.9 14.1 - + - -
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Residues in contact with GLY 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E HIS* 5.2 2.4 + - - -
270E ARG* 2.7 49.5 + - - +
272E ILE 3.5 1.2 - - - -
273E TYR* 1.3 81.4 - - - +
275E ALA* 1.3 61.5 + - - -
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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