Contacts of the helix formed by residues 250 - 257 (chain Q) in PDB entry 1HI0
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 250 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248Q ASP* 2.7 28.0 + - - -
249Q ALA* 1.3 72.4 - - - +
251Q ARG* 1.3 67.0 + - - +
253Q LYS* 2.9 24.1 + - - +
254Q GLU* 3.8 2.6 + - - +
260Q VAL* 4.7 7.8 - - - +
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Residues in contact with ARG 251 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Q GLU* 2.6 45.0 + - - -
93Q PHE* 4.3 2.2 - - - +
94Q PRO 3.1 22.8 + - - -
96Q ILE* 3.8 24.1 - - - +
246Q SER 5.8 0.6 + - - -
248Q ASP* 3.6 23.2 + - - +
249Q ALA 4.4 0.9 - - - -
250Q SER* 1.3 79.8 - - - +
252Q LEU* 1.3 77.1 + - + +
253Q LYS 2.9 1.2 + - - -
254Q GLU* 3.1 12.8 + - - +
255Q GLN* 2.7 73.5 + - + +
266Q CYS* 3.8 10.3 - - - -
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Residues in contact with LEU 252 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90Q MET* 3.8 29.8 - - + -
93Q PHE* 3.2 63.3 - - + -
249Q ALA* 3.0 22.8 + - + +
250Q SER 3.0 0.2 + - - -
251Q ARG* 1.3 92.5 - - - +
253Q LYS* 1.3 57.7 + - - +
256Q TYR* 2.9 40.3 + - + +
257Q GLY 3.1 4.9 + - - -
258Q ILE* 3.2 16.0 + - + -
260Q VAL* 3.6 8.1 - - + -
266Q CYS* 4.9 0.2 - - - -
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Residues in contact with LYS 253 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P LEU* 4.3 1.4 - - - +
250Q SER* 2.9 13.7 + - - +
252Q LEU* 1.3 77.7 - - - +
254Q GLU* 1.3 62.2 + - + +
257Q GLY* 2.6 46.1 + - - -
258Q ILE 3.1 23.2 + - - +
259Q ASP* 4.6 11.4 + - - +
260Q VAL* 4.2 7.5 - - + +
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Residues in contact with GLU 254 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P LEU* 3.3 18.4 - - - +
250Q SER 3.8 2.8 + - - +
251Q ARG* 3.1 14.3 + - - +
253Q LYS* 1.3 83.4 - - + +
255Q GLN* 1.3 65.3 + - + +
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Residues in contact with GLN 255 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P LEU* 3.9 15.2 + - - +
47P ASP* 4.6 11.3 - - - +
34Q GLU* 4.0 1.0 - - - +
251Q ARG* 2.7 76.2 + - + +
252Q LEU 4.1 0.6 - - - +
254Q GLU* 1.3 81.5 - - + +
256Q TYR* 1.3 90.6 + - + +
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Residues in contact with TYR 256 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38P GLU* 3.9 0.9 - - - +
42P GLY* 2.9 46.6 + - - +
43P LEU* 3.4 2.4 + - - +
44P LEU* 3.9 5.4 - - - +
47P ASP* 5.3 1.3 - - - -
49P ARG* 4.2 27.2 + - - -
32Q PHE* 5.4 0.3 - - - -
34Q GLU* 2.6 45.9 + - + +
93Q PHE* 3.6 19.7 - + - -
252Q LEU* 2.9 32.0 + - + +
255Q GLN* 1.3 100.1 + - + +
257Q GLY* 1.3 62.3 + - - +
258Q ILE* 3.6 16.2 - - + -
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Residues in contact with GLY 257 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38P GLU* 3.2 23.8 - - - +
44P LEU* 3.4 21.1 - - - +
534P SER* 4.9 0.7 + - - -
253Q LYS* 2.6 42.7 + - - -
255Q GLN 3.5 1.4 - - - -
256Q TYR* 1.3 74.6 - - - +
258Q ILE* 1.3 60.1 + - - +
259Q ASP 3.8 1.6 + - - -
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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