Contacts of the helix formed by residues 250 - 259 (chain A) in PDB entry 2HV9
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 PHE 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ASN* 3.2 26.9 - - - -
53A ILE* 3.2 38.8 - - + +
54A LYS* 5.8 0.2 - - + -
141A PHE* 3.8 20.2 - + - -
173A THR* 3.8 19.3 - - + -
249A GLY* 1.3 71.6 - - - -
251A ILE* 1.3 57.6 + - - +
253A PHE* 4.5 0.9 - - - -
254A TYR* 2.8 31.8 + - - +
281A VAL* 3.0 35.0 - - + +
282A GLY* 4.9 1.2 + - - -
284A TYR* 3.1 46.0 + + + +
285A GLU* 3.6 18.8 - - - -
286A VAL* 4.1 9.0 - - + -
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Residues in contact with ILE 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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249A GLY 3.4 0.6 - - - -
250A PHE* 1.3 72.5 - - - +
252A ASP* 1.3 71.8 + - - +
254A TYR* 3.2 6.5 - - + +
255A GLU* 2.9 51.9 + - + +
273A LEU* 4.8 8.3 - - + -
278A SER* 3.8 33.9 - - - +
281A VAL* 4.2 16.6 - - + -
282A GLY* 4.0 17.0 - - - -
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Residues in contact with ASP 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 LYS* 4.4 11.2 - - + +
249A GLY* 3.5 9.8 + - - +
250A PHE 3.5 0.2 - - - -
251A ILE* 1.3 80.1 - - - +
253A PHE* 1.3 65.9 + - - +
255A GLU* 2.9 19.5 + - - +
256A ASP* 2.7 38.7 + - - +
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Residues in contact with PHE 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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52A PHE* 6.5 0.2 - + - -
53A ILE* 3.8 40.2 - - + -
56A CYS* 4.0 9.9 - - + -
57A LEU* 4.2 13.5 - - + -
60A LEU* 4.1 26.7 - - + -
246A GLU* 5.5 7.6 - - + -
248A LYS* 3.3 32.6 - - + +
249A GLY 2.9 21.6 + - - +
250A PHE* 4.0 2.7 - - - +
252A ASP* 1.3 75.8 - - - +
254A TYR* 1.3 58.3 + - - +
256A ASP* 3.4 3.3 + - - +
257A GLU* 2.9 61.8 + - + +
286A VAL* 4.2 25.4 - - + -
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Residues in contact with TYR 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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49A ALA* 4.1 20.0 - - + +
52A PHE* 3.8 21.6 - + - -
53A ILE* 4.0 17.0 - - + -
250A PHE 2.8 23.2 + - - +
251A ILE* 3.2 9.6 - - + +
253A PHE* 1.3 79.4 - - - +
255A GLU* 1.3 65.6 + - + +
257A GLU* 3.7 2.9 - - - +
258A GLY* 2.7 33.8 + - - -
270A LEU* 3.2 40.0 - - + +
271A GLY 3.3 17.9 + - - -
272A CYS* 5.7 1.6 - - - -
273A LEU* 4.1 31.6 - - + +
281A VAL* 5.7 1.8 - - + -
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Residues in contact with GLU 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 ILE* 2.9 36.5 + - + +
252A ASP* 2.9 24.7 + - - +
254A TYR* 1.3 83.0 - - + +
256A ASP* 1.3 59.0 + - - +
258A GLY* 3.5 1.3 - - - +
259A ARG* 2.9 53.5 + - - +
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Residues in contact with ASP 256 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A LYS* 2.7 33.2 + - - +
252A ASP* 2.7 37.4 + - - +
253A PHE 3.4 3.1 + - - +
255A GLU* 1.3 75.2 - - - +
257A GLU* 1.3 68.5 + - - +
258A GLY 3.1 1.2 + - - -
259A ARG* 3.2 24.7 + - - +
260A ARG* 3.2 20.3 + - - +
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Residues in contact with GLU 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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52A PHE* 4.4 3.8 - - + -
56A CYS* 4.0 18.8 - - + -
59A ARG* 3.4 21.3 + - - -
60A LEU* 4.3 10.1 - - - +
248A LYS* 5.6 2.1 + - - -
253A PHE* 2.9 53.3 + - + +
254A TYR* 3.9 2.5 - - - +
256A ASP* 1.3 81.4 - - + +
258A GLY* 1.3 55.2 + - - +
260A ARG* 3.2 42.8 + - - +
261A ASN* 2.5 32.6 + - - +
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Residues in contact with GLY 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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52A PHE* 4.4 10.9 - - - -
254A TYR* 2.7 18.7 + - - -
255A GLU* 3.5 2.5 - - - -
256A ASP 3.0 0.4 - - - -
257A GLU* 1.3 73.7 - - - +
259A ARG* 1.3 57.1 + - - +
260A ARG 2.8 10.0 + - - -
261A ASN* 3.4 12.1 + - - -
262A PRO* 3.6 17.3 - - - +
265A SER* 5.2 5.5 - - - -
270A LEU* 5.9 2.7 - - - -
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Residues in contact with ARG 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 GLU* 2.9 52.2 + - - +
256A ASP* 3.6 23.0 + - - +
258A GLY* 1.3 68.2 - - - +
260A ARG* 1.3 58.4 + - - +
262A PRO* 4.5 9.1 - - - +
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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