Contacts of the helix formed by residues 288 - 296 (chain C) in PDB entry 5H1C
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 GLY 288 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241C ARG* 3.8 15.3 - - - -
242C GLN* 2.9 26.9 - - - +
245C LEU* 4.4 3.5 - - - +
287C ILE* 1.3 78.4 - - - +
289C GLY* 1.3 62.8 + - - +
291C ILE* 3.8 4.2 + - - +
292C ILE* 3.5 21.9 + - - +
8D T 2.4 18.1 + - - -
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Residues in contact with GLY 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C LYS* 6.1 3.8 - - - -
286C PRO* 4.4 4.6 + - - +
287C ILE 3.3 4.1 - - - +
288C GLY* 1.3 81.9 - - - +
290C ASN* 1.3 65.1 + - - +
291C ILE 3.4 0.2 + - - -
292C ILE* 3.7 6.4 + - - +
293C ALA* 3.7 10.1 + - - +
7D T 3.8 27.1 - - - -
8D T 3.1 8.1 + - - -
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Residues in contact with ASN 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLU* 3.3 38.8 + - - +
229B ARG* 4.7 2.5 - - - +
269B VAL* 3.8 15.1 - - - +
270B VAL* 4.5 0.2 - - - -
271B ALA* 3.3 37.4 + - - +
289C GLY* 1.3 73.1 - - - -
291C ILE* 1.3 57.3 + - + +
293C ALA* 2.8 26.7 + - - +
294C HIS* 2.9 36.0 + - + +
6D T 5.9 0.2 - - - +
7D T 4.1 10.2 + - - +
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Residues in contact with ILE 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ARG* 3.2 29.8 - - - +
230B THR* 6.1 0.9 - - + -
242C GLN* 3.3 49.1 - - + +
245C LEU* 4.8 2.9 - - + -
246C ALA* 4.0 32.8 - - + +
249C LEU* 3.8 7.5 - - + +
288C GLY 4.4 0.2 - - - +
289C GLY 3.3 1.4 - - - -
290C ASN* 1.3 77.3 - - + +
292C ILE* 1.3 64.2 + - + +
294C HIS* 3.9 2.9 + - - +
295C ALA* 3.6 17.7 + - - +
6D T 4.3 20.0 - - - +
7D T 3.5 5.6 - - - +
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Residues in contact with ILE 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C GLU* 2.7 31.6 - - - +
225C THR* 3.7 25.4 - - + -
245C LEU* 4.6 12.8 - - + -
249C LEU* 3.8 24.0 - - + -
265C ILE* 5.8 5.2 - - + -
267C ASN* 3.9 4.0 - - - +
286C PRO* 6.0 2.5 - - + -
287C ILE 3.2 26.0 - - - +
288C GLY* 3.5 16.5 + - - +
289C GLY 3.7 6.1 + - - +
290C ASN 3.2 0.2 - - - -
291C ILE* 1.3 77.7 - - - +
293C ALA* 1.3 65.1 + - - +
295C ALA* 3.0 13.0 + - - +
296C SER* 3.4 10.3 + - - -
299C ARG* 3.9 4.1 + - - +
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Residues in contact with ALA 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLU* 4.7 1.1 - - + +
129B PHE* 3.7 34.3 - - + +
602B ANP 4.0 0.2 + - - -
286C PRO* 6.2 0.9 - - + -
289C GLY 3.7 9.1 + - - +
290C ASN* 2.8 15.3 + - - +
292C ILE* 1.3 81.2 - - - +
294C HIS* 1.3 61.8 + - - +
295C ALA 3.3 0.3 + - - -
296C SER* 3.6 7.6 + - - +
299C ARG* 3.1 16.8 + - - +
316C ASP* 3.3 21.7 - - - +
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Residues in contact with HIS 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLY 4.2 2.0 - - - -
128B GLU* 2.4 38.6 + - - -
129B PHE* 4.3 2.2 - - - +
133B LYS* 4.7 4.3 + - - -
163B GLU* 3.7 15.4 - - - +
229B ARG* 4.1 7.4 - - - +
268B GLN* 2.8 49.3 + - + +
269B VAL* 3.6 17.1 + - - +
602B ANP 2.6 27.4 + - - -
290C ASN* 2.9 45.8 + - + +
291C ILE* 4.5 2.9 - - - +
293C ALA* 1.3 77.2 - - - +
295C ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLU* 5.1 8.8 - - - +
122C ILE* 5.0 13.3 - - + +
249C LEU* 4.1 24.0 - - + -
253C LEU* 5.1 15.8 - - + +
291C ILE 3.6 12.7 + - - +
292C ILE 3.0 9.9 + - - +
294C HIS* 1.3 80.3 - - - +
296C SER* 1.3 66.6 + - - +
297C THR* 3.4 5.5 + - - +
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Residues in contact with SER 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B THR* 5.8 0.4 - - - +
602B ANP 3.3 20.1 + - - -
122C ILE* 4.2 22.4 - - - -
124C GLU* 3.0 27.5 + - - -
292C ILE 3.4 3.6 + - - -
293C ALA 3.6 3.1 + - - +
295C ALA* 1.3 78.6 - - - +
297C THR* 1.3 62.9 + - - +
298C THR 2.9 20.8 + - - -
299C ARG* 3.1 15.2 + - - -
316C ASP* 3.9 5.0 + - - +
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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