Contacts of the helix formed by residues 243 - 253 (chain A) in PDB entry 2H1H
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 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLN* 4.1 13.0 + - - -
242A MET* 1.3 77.6 - - - +
244A LEU* 1.3 59.9 + - - +
245A GLU* 3.5 8.9 + - - +
246A GLY* 3.1 16.6 + - - -
247A VAL* 2.8 28.8 + - - +
400A AFH 3.6 3.4 - - - -
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Residues in contact with LEU 244 (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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11A MET* 3.4 30.1 - - + -
40A GLY 3.6 23.6 - - - +
41A PHE* 4.1 4.9 - - - -
43A GLN* 3.6 12.1 - - + +
44A ILE* 3.6 35.7 - - + +
47A TRP* 4.1 9.2 - - + -
243A SER* 1.3 74.2 - - - +
245A GLU* 1.3 57.8 + - - +
247A VAL* 3.1 8.4 - - + +
248A ALA* 2.8 30.6 + - - +
264A LEU* 4.0 17.9 - - + -
267A LEU* 4.2 6.3 - - + -
400A AFH 3.7 12.4 + - - +
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Residues in contact with GLU 245 (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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43A GLN* 3.1 33.6 - - - +
46A SER* 4.9 1.7 + - - -
47A TRP* 3.3 36.0 + - + +
168A HIS* 3.4 17.4 + - - -
169A PHE* 3.7 14.9 - - + -
243A SER* 3.2 4.0 - - - +
244A LEU* 1.3 81.0 - - - +
246A GLY* 1.3 57.7 + - - +
248A ALA* 3.1 4.0 + - - +
249A ARG* 2.9 25.5 + - - +
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Residues in contact with GLY 246 (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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242A MET* 3.6 17.3 - - - +
243A SER* 3.1 18.0 + - - -
245A GLU* 1.3 78.2 - - - +
247A VAL* 1.3 61.4 + - - +
249A ARG* 3.1 17.4 + - - +
250A VAL* 3.2 15.1 + - - +
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Residues in contact with VAL 247 (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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184A LEU* 5.3 0.2 - - + -
216A PRO* 3.9 33.2 - - + -
239A LEU* 5.1 0.7 - - + -
242A MET* 3.7 15.9 - - + -
243A SER 2.8 18.4 + - - +
244A LEU* 3.1 22.0 - - + +
246A GLY* 1.3 72.6 - - - -
248A ALA* 1.3 57.6 + - - +
250A VAL* 3.3 6.6 + - + +
251A LEU* 3.0 33.9 + - + +
264A LEU* 4.0 30.3 - - + -
267A LEU* 4.4 1.3 - - + -
400A AFH 4.0 16.8 - - - +
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Residues in contact with ALA 248 (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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47A TRP* 3.9 8.1 - - + -
169A PHE* 3.6 24.5 - - + -
244A LEU 2.8 19.2 + - - +
245A GLU 3.3 6.5 - - - +
246A GLY 3.0 0.2 - - - -
247A VAL* 1.3 76.4 - - - +
249A ARG* 1.3 59.5 + - - +
251A LEU* 4.4 0.4 - - - -
252A ALA* 3.1 25.1 + - - +
267A LEU* 3.8 24.0 - - + -
271A LEU* 3.4 12.7 - - + +
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Residues in contact with ARG 249 (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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169A PHE* 3.8 20.9 - - + -
172A ASN* 2.5 44.6 + - - +
173A LEU* 3.5 8.2 + - - -
174A PRO* 3.5 47.1 - - + +
175A THR* 4.7 2.2 + - - +
245A GLU* 2.9 12.7 + - + +
246A GLY* 3.1 10.3 + - - +
248A ALA* 1.3 73.9 - - - +
250A VAL* 1.3 70.2 + - + +
252A ALA* 3.4 4.7 + - - +
253A GLY 3.3 15.9 + - - -
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Residues in contact with VAL 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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174A PRO* 4.5 6.3 - - + -
180A TYR* 2.4 36.0 + - + +
182A VAL* 3.8 22.9 - - + -
214A LYS* 4.4 9.6 - - + +
239A LEU* 4.1 26.9 - - + -
242A MET* 3.8 20.9 - - + -
246A GLY 3.2 13.4 + - - +
247A VAL* 3.5 11.7 - - + +
248A ALA 3.3 0.2 - - - -
249A ARG* 1.3 79.6 - - + +
251A LEU* 1.3 62.4 + - + +
253A GLY 3.3 1.6 + - - -
254A ALA 3.3 3.3 + - - -
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Residues in contact with LEU 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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182A VAL* 3.7 29.8 - - + -
184A LEU* 4.1 8.7 - - + -
247A VAL* 3.0 30.6 + - + +
248A ALA 3.8 0.2 - - - +
249A ARG 3.3 0.2 - - - -
250A VAL* 1.3 78.3 - - + +
252A ALA* 1.3 62.0 + - - +
254A ALA* 3.0 19.4 + - - +
257A VAL* 4.0 12.3 - - + +
264A LEU* 3.9 16.6 - - + +
267A LEU* 3.9 25.6 - - + -
268A THR* 3.6 27.6 - - - +
271A LEU* 3.7 12.6 - - + -
273A ARG* 3.3 16.2 - - + +
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Residues in contact with ALA 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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166A ALA* 5.7 2.0 - - + +
169A PHE* 4.0 18.8 - - + -
170A LEU* 6.4 0.2 - - + -
173A LEU* 3.7 25.0 - - + +
248A ALA 3.1 17.3 + - - +
249A ARG 3.6 6.7 - - - +
250A VAL 3.3 0.2 - - - -
251A LEU* 1.3 76.0 - - - +
253A GLY* 1.3 57.3 + - - +
254A ALA 3.2 0.2 - - - -
271A LEU* 4.0 10.0 - - + +
273A ARG* 3.4 32.4 + - - +
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Residues in contact with GLY 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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173A LEU* 4.1 2.2 - - - +
174A PRO* 4.0 7.9 - - - -
177A ALA* 3.3 22.3 - - - -
178A GLY 2.7 29.6 + - - -
180A TYR* 3.1 19.6 - - - -
249A ARG 3.3 4.8 + - - -
250A VAL 3.3 3.6 + - - -
251A LEU 3.2 0.8 - - - -
252A ALA* 1.3 76.5 - - - +
254A ALA* 1.3 58.7 + - - +
273A ARG* 5.4 0.4 - - - -
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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