Contacts of the helix formed by residues 240 - 251 (chain A) in PDB entry 1Q2L
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 PRO 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A SER* 3.8 4.5 - - - +
238A ASN 4.4 2.0 - - - +
239A LYS* 1.3 91.5 - - + +
241A LEU* 1.3 65.9 + - - +
242A PRO* 3.8 13.0 - - + -
243A GLU* 2.9 31.2 + - + +
244A LEU* 3.0 11.1 + - - +
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Residues in contact with LEU 241 (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* 3.7 33.9 - - + +
44A TYR 4.3 5.4 - - - +
45A GLN* 3.5 35.4 + - + +
57A LEU* 3.5 44.7 - - + +
58A VAL 4.7 0.2 - - - -
59A SER* 3.9 20.3 - - - -
239A LYS 3.7 1.4 + - - -
240A PRO* 1.3 70.8 - - - +
242A PRO* 1.3 71.1 - - + +
244A LEU* 4.5 4.5 - - + +
245A ALA* 3.0 25.8 + - - +
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Residues in contact with PRO 242 (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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27A TRP* 4.5 10.4 - - + -
45A GLN* 5.6 1.6 - - - +
240A PRO* 3.3 14.1 - - + -
241A LEU* 1.3 96.1 - - + +
243A GLU* 1.3 56.6 + - - +
245A ALA* 3.8 6.8 + - + +
246A LYS* 3.1 27.6 + - - +
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Residues in contact with GLU 243 (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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239A LYS* 3.0 47.3 + - + +
240A PRO* 2.9 23.9 + - + +
242A PRO* 1.3 77.3 - - - +
244A LEU* 1.3 62.0 + - + +
245A ALA 3.1 1.6 - - - -
246A LYS* 2.8 27.1 + - + +
247A MET* 2.9 18.1 + - + +
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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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57A LEU* 3.5 20.1 - - + +
58A VAL 3.7 30.7 - - - +
59A SER* 4.3 2.7 - - - +
235A ILE* 3.8 28.5 - - + +
237A SER* 3.7 26.2 - - - +
239A LYS* 3.5 35.7 - - + +
240A PRO 3.0 9.2 + - - +
241A LEU* 4.0 4.0 - - - +
243A GLU* 1.3 77.4 - - + +
245A ALA* 1.3 58.3 + - - +
247A MET* 3.4 19.4 + - + +
248A ALA* 2.9 28.6 + - - +
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Residues in contact with ALA 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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27A TRP* 3.4 41.6 - - + -
45A GLN* 5.5 0.2 - - - +
47A ILE* 3.7 11.1 - - + +
57A LEU* 3.5 18.8 - - + +
241A LEU 3.0 18.8 + - - +
242A PRO 3.8 2.0 - - - +
243A GLU 3.1 0.2 - - - -
244A LEU* 1.3 77.1 - - - +
246A LYS* 1.3 57.4 + - - +
248A ALA* 3.3 2.8 + - - +
249A ALA* 3.0 28.1 + - - +
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Residues in contact with LYS 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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24A GLU* 3.7 25.5 + - - +
25A THR* 3.8 13.9 + - - +
27A TRP* 4.1 15.7 - - + +
242A PRO 3.1 19.5 - - - +
243A GLU* 2.8 11.1 + - + +
245A ALA* 1.3 74.2 - - - +
247A MET* 1.3 59.3 + - - +
248A ALA 3.0 1.8 - - - -
249A ALA* 3.1 6.4 + - - +
250A ASP* 2.9 45.2 + - - +
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Residues in contact with MET 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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138A LEU* 3.2 33.7 - - + -
139A PRO* 3.3 41.3 - - + -
142A VAL* 3.9 12.6 - - - -
235A ILE* 4.4 11.2 - - - -
237A SER* 5.7 0.2 - - - +
239A LYS* 5.0 11.4 - - + +
243A GLU* 2.9 16.7 + - + +
244A LEU* 3.7 20.2 - - + +
246A LYS* 1.3 76.3 - - - +
248A ALA* 1.3 52.0 + - - +
250A ASP* 3.7 5.7 + - - -
251A THR* 2.6 44.2 + - + +
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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 ILE* 4.2 6.5 - - + -
49A LEU* 3.8 15.7 - - + +
55A VAL* 4.4 10.1 - - + -
57A LEU* 4.3 3.8 - - + -
235A ILE* 3.8 17.0 - - + +
244A LEU 2.9 17.1 + - - +
245A ALA* 3.4 9.0 - - - +
247A MET* 1.3 76.8 - - - +
249A ALA* 1.3 62.0 + - - +
251A THR* 3.8 4.0 - - - -
252A PHE* 3.1 14.2 + - + +
253A GLY 3.0 22.3 + - - -
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Residues in contact with ALA 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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25A THR 4.2 10.3 - - - +
26A GLY* 4.0 13.2 - - - +
27A TRP* 3.8 21.1 - - + -
49A LEU* 3.8 9.3 - - - +
245A ALA 3.0 14.3 + - - +
246A LYS* 3.1 9.8 + - - +
248A ALA* 1.3 76.0 - - - +
250A ASP* 1.3 63.0 + - - +
253A GLY* 3.2 24.1 - - - -
254A ARG* 5.0 0.9 - - - +
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Residues in contact with ASP 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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100A LYS* 5.8 0.2 + - - -
143A ASP* 4.3 3.1 - - - +
246A LYS* 2.9 30.7 + - - +
247A MET* 4.1 7.0 - - - +
249A ALA* 1.3 82.4 - - - +
251A THR* 1.3 61.8 + - + +
254A ARG* 3.3 23.3 - - - +
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Residues in contact with THR 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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139A PRO 4.4 3.6 - - - +
142A VAL* 3.2 25.2 - - + +
143A ASP* 3.5 39.5 - - + +
146A ALA* 3.4 20.5 - - - +
247A MET* 2.6 28.5 + - + +
248A ALA* 3.5 4.2 + - - -
250A ASP* 1.3 80.4 - - + +
252A PHE* 1.3 72.3 + - - +
253A GLY 3.0 2.7 - - - -
254A ARG* 3.0 24.3 + - - +
255A VAL 4.2 0.5 + - - -
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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