Contacts of the helix formed by residues 242 - 251 (chain A) in PDB entry 1L6N
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 THR 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A PRO* 5.7 1.1 - - - -
238A GLY 5.2 0.4 - - - -
241A SER* 1.3 76.8 + - - +
243A LEU* 1.3 57.6 + - + +
244A GLN* 3.2 25.8 - - + +
245A GLU* 3.2 13.8 + - + +
246A GLN* 2.7 36.0 + - - +
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Residues in contact with LEU 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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144A HIS 5.5 6.1 - - - +
180A THR* 3.2 21.1 - - - +
181A PRO* 3.6 17.0 - - + +
182A GLN* 3.7 30.1 - - + +
242A THR* 1.3 79.2 + - + +
244A GLN* 1.3 68.7 + - + +
246A GLN* 2.8 14.1 + - - +
247A ILE* 2.8 57.6 + - + +
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Residues in contact with GLN 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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138A LEU* 5.0 6.5 + - - +
139A GLN* 5.5 0.2 - - - +
140A GLY* 3.9 30.0 - - - +
141A GLN 5.4 3.7 + - - +
142A MET 5.5 7.0 - - - +
242A THR* 3.2 12.3 - - + +
243A LEU* 1.3 86.7 - - - +
245A GLU* 1.3 95.6 + - - +
247A ILE* 3.5 4.1 + - - +
248A GLY* 2.9 27.5 + - - -
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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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138A LEU* 6.0 2.1 - - - +
228A MET* 3.7 26.9 - - + +
241A SER* 3.3 18.4 - - - +
242A THR* 3.2 16.7 + - - +
243A LEU 3.2 0.4 - - - -
244A GLN* 1.3 105.2 + - - +
246A GLN* 1.3 54.2 + - - +
248A GLY* 4.9 0.7 - - - -
249A TRP* 2.8 49.8 + - + +
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Residues in contact with GLN 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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181A PRO* 3.6 31.3 - - + +
231A PRO* 5.8 0.2 - - - +
235A ASP 3.3 6.4 + - - +
236A ILE* 2.6 41.3 + - - +
238A GLY* 3.9 4.3 - - - +
241A SER* 2.9 28.6 + - - -
242A THR 2.7 15.0 + - - +
243A LEU* 2.8 15.4 + - + +
245A GLU* 1.3 70.4 - - - +
247A ILE* 1.3 67.6 + - - +
248A GLY 3.0 1.1 - - - -
249A TRP* 2.8 11.0 + - - +
250A MET* 2.7 28.1 + - + +
258A VAL* 3.1 27.0 - - + +
259A GLY* 5.0 0.6 - - - +
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Residues in contact with ILE 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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141A GLN 5.7 0.7 - - - +
142A MET* 5.4 8.3 - - + +
144A HIS* 3.4 44.0 - - + +
180A THR* 3.3 27.1 - - + -
243A LEU* 2.8 69.1 + - + +
244A GLN* 4.1 3.6 - - - +
246A GLN* 1.3 73.1 - - - +
248A GLY* 1.3 53.2 + - - +
250A MET* 3.1 13.3 + - + +
251A THR* 2.7 41.7 + - + +
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Residues in contact with GLY 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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141A GLN 4.9 9.2 - - - -
228A MET* 5.4 0.7 - - - -
244A GLN* 2.9 18.4 + - - -
245A GLU* 3.8 1.8 - - - -
247A ILE* 1.3 76.3 - - - +
249A TRP* 1.3 54.4 + - - +
251A THR* 2.9 12.6 + - - -
252A HIS* 2.6 49.9 + - - +
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Residues in contact with TRP 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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228A MET* 3.0 43.3 + - + +
229A ARG* 3.0 38.5 + - + -
231A PRO* 3.4 33.8 - - + +
235A ASP* 4.4 5.8 - - - -
240A THR 5.1 2.5 - - - -
241A SER* 3.5 31.6 - - - -
245A GLU* 2.8 37.7 + - + +
246A GLN* 2.8 8.2 + - - +
248A GLY* 1.3 71.4 - - - -
250A MET* 1.3 61.5 + - - +
252A HIS* 3.3 16.5 - + - +
256A ILE* 3.2 48.6 + - + +
258A VAL* 3.9 12.8 - - + -
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Residues in contact with MET 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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178A GLY* 5.0 7.0 - - - +
179A ALA 4.3 5.2 - - - +
180A THR* 3.8 36.8 - - + -
246A GLN* 2.7 13.1 + - + +
247A ILE* 3.1 36.1 - - + +
249A TRP* 1.3 79.2 - - - +
251A THR* 1.3 55.5 + - - +
252A HIS 3.2 0.4 - - - -
255A PRO* 3.2 23.7 - - - +
256A ILE 3.3 16.0 - - - +
257A PRO* 4.9 1.1 - - + -
258A VAL* 3.8 2.7 - - + +
259A GLY* 3.3 38.1 - - - +
260A GLU* 4.5 3.4 - - - -
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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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141A GLN 5.1 0.2 - - - +
142A MET* 4.0 37.5 - - + -
247A ILE* 2.7 28.1 + - + +
248A GLY* 3.5 11.4 - - - +
250A MET* 1.3 71.9 - - - +
252A HIS* 1.3 64.8 + - - +
253A ASN* 4.4 7.4 + - - -
255A PRO* 4.6 2.2 - - - -
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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