Contacts of the helix formed by residues 249 - 259 (chain A) in PDB entry 6NIL
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 HIS 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A ASN 4.8 13.5 - - - -
216A SER* 5.5 4.3 - - - -
240A ASN* 3.3 11.1 + - - -
248A ARG* 1.3 80.5 - - - +
250A ALA* 1.3 64.6 + - - +
251A GLU* 3.5 0.9 - - - +
252A ARG* 3.7 14.1 + - + +
253A CYS* 3.2 20.8 + - - +
280A CYS* 3.8 11.9 - - - -
283A CYS* 3.8 13.5 - - - -
286A GLU* 5.3 1.8 - - - +
501A ZN 2.7 31.1 - - - -
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Residues in contact with ALA 250 (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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216A SER* 3.9 25.5 - - - +
217A TRP* 4.8 0.9 - - - +
218A LEU* 3.6 17.7 - - + +
238A PHE* 4.5 3.2 - - - +
239A ARG* 4.0 21.1 - - - +
240A ASN* 2.9 15.0 + - - +
249A HIS* 1.3 76.6 + - - +
251A GLU* 1.3 66.1 + - - +
252A ARG 3.2 0.4 - - - -
253A CYS* 2.9 19.3 + - - +
254A PHE 3.1 10.0 + - - -
501A ZN 4.5 0.4 - - - -
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Residues in contact with GLU 251 (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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216A SER* 3.2 23.2 + - - -
217A TRP 4.8 0.2 - - - +
218A LEU* 3.7 20.2 - - + -
250A ALA* 1.3 76.7 + - - +
252A ARG* 1.3 57.2 + - - +
254A PHE* 3.9 3.3 - - - +
255A LEU* 3.3 23.6 - - - +
273A TRP* 3.6 33.4 - - + -
275A THR* 3.5 19.2 - - + +
278A SER 4.3 6.6 - - - +
279A PRO* 4.5 15.0 - - + -
283A CYS* 4.0 7.9 - - + -
287A VAL* 4.6 6.0 - - + +
501A ZN 2.7 31.6 - - - -
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Residues in contact with ARG 252 (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 ARG* 3.1 57.5 + - - +
249A HIS* 3.7 14.7 + - + +
250A ALA 3.2 0.6 - - - -
251A GLU* 1.3 75.5 + - - +
253A CYS* 1.3 60.0 + - - +
254A PHE 3.1 2.0 - - - -
255A LEU* 2.9 23.8 + - + +
256A SER 3.0 11.3 + - - -
283A CYS* 5.6 2.2 - - + +
286A GLU* 3.4 46.6 + - + +
43C HIS* 5.7 0.6 - - - +
44C TYR* 5.1 6.5 - - - +
49C PRO* 4.4 13.7 + - - +
51C ILE 5.6 2.2 + - - -
70C TRP* 4.0 32.6 - - + +
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Residues in contact with CYS 253 (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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190A ASN* 5.1 14.1 - - - -
238A PHE* 3.9 20.3 - - + -
239A ARG 4.5 11.7 - - - +
240A ASN* 5.6 4.5 - - - +
248A ARG* 3.4 26.9 - - + +
249A HIS 3.2 14.5 + - - +
250A ALA* 2.9 15.5 + - - +
252A ARG* 1.3 73.5 - - - +
254A PHE* 1.3 64.1 + - - +
256A SER* 4.3 0.9 - - - -
257A TRP* 3.4 18.7 + - - +
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Residues in contact with PHE 254 (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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218A LEU* 4.4 8.7 - - + -
220A PHE* 3.6 34.5 - + + -
222A MET* 4.9 2.2 - - + -
238A PHE* 3.7 26.4 - + + -
250A ALA 3.1 9.8 + - - +
251A GLU 3.9 10.3 - - - +
253A CYS* 1.3 78.1 - - - +
255A LEU* 1.3 60.0 + - + +
257A TRP* 3.1 15.2 + + - +
258A PHE* 2.7 66.9 + + - +
271A VAL* 3.6 18.8 - - + -
273A TRP* 3.4 39.3 - + + -
290A PHE* 6.3 0.9 - + - -
299A LEU* 4.8 3.1 - - + -
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Residues in contact with LEU 255 (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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251A GLU 3.3 20.0 - - - +
252A ARG* 2.9 12.1 + - + +
254A PHE* 1.3 95.1 - - + +
256A SER* 1.3 61.6 + - - +
258A PHE* 3.6 6.2 - - + +
259A CYS* 2.8 33.4 + - - +
273A TRP* 4.0 2.9 - - + -
286A GLU 3.9 17.3 - - - +
287A VAL* 3.7 20.2 - - + -
290A PHE* 3.7 48.2 - - + -
299A LEU* 5.6 1.6 - - + -
70C TRP* 4.2 19.9 - - + -
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Residues in contact with SER 256 (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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190A ASN* 6.2 0.4 - - - -
248A ARG* 3.3 29.6 + - - -
252A ARG 3.0 6.6 + - - -
253A CYS* 4.4 1.6 - - - -
254A PHE 3.3 0.2 - - - -
255A LEU* 1.3 76.3 - - - +
257A TRP* 1.3 58.5 + - - +
259A CYS 4.4 0.2 - - - -
260A ASP* 2.9 36.4 + - - +
43C HIS* 3.6 21.5 + - - -
70C TRP* 4.6 19.4 + - - -
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Residues in contact with TRP 257 (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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190A ASN* 4.5 15.2 - - + +
191A PRO* 3.6 31.9 - - + +
220A PHE* 3.5 38.8 - + - -
222A MET* 4.9 4.3 - - + -
234A LYS* 4.7 14.4 - - + -
238A PHE* 3.5 24.9 - + + -
253A CYS 3.4 12.4 + - - +
254A PHE* 3.1 18.5 + + - +
256A SER* 1.3 79.7 - - - +
258A PHE* 1.3 67.9 + + - +
259A CYS 3.5 0.2 - - - -
261A ASP* 3.2 54.2 + - - +
262A ILE* 3.7 31.2 + - + -
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Residues in contact with PHE 258 (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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222A MET* 4.0 10.1 - - + -
254A PHE* 2.7 46.0 + + + +
255A LEU* 3.2 11.6 + - + +
257A TRP* 1.3 77.9 - + - +
259A CYS* 1.3 61.5 + - + +
260A ASP 3.2 1.4 + - - -
262A ILE* 3.3 44.8 + - + +
263A LEU* 3.5 29.4 + - + +
269A TYR* 3.5 27.6 - + - -
271A VAL* 3.9 22.2 - - + -
290A PHE* 3.6 32.1 - + - -
297A VAL* 4.0 12.1 - - + -
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Residues in contact with CYS 259 (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 LEU 2.8 19.7 + - - +
258A PHE* 1.3 72.6 - - - +
260A ASP* 1.3 66.9 + - - +
263A LEU* 4.1 24.3 - - - +
290A PHE* 4.4 17.9 - - + -
294A HIS* 4.9 2.7 - - - -
15C ARG* 4.6 3.5 - - - +
70C TRP* 4.3 13.9 - - + -
71C GLY* 4.1 24.7 - - - -
81C LEU 3.9 21.0 - - - +
82C GLY 5.5 0.4 - - - -
83C GLN* 3.4 12.2 - - - +
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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