Contacts of the helix formed by residues 247 - 261 (chain A) in PDB entry 8LDH
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 TRP 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ALA* 4.6 17.0 - - + -
37A ILE* 5.1 12.8 - - + -
38A SER* 5.2 0.9 + - - -
242A LYS* 3.5 29.8 - - + +
244A TYR* 5.4 6.0 + + - -
246A SER* 1.3 91.3 + - - +
248A ALA* 1.3 57.8 + - - +
250A GLY* 3.9 0.3 - - - -
251A LEU* 3.0 43.7 + - + +
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Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A LEU* 3.7 27.8 - - + +
169A ARG* 4.2 12.1 - - - +
245A THR* 6.3 1.8 - - + -
246A SER 3.4 1.2 - - - +
247A TRP* 1.3 79.5 - - - +
249A ILE* 1.3 59.3 + - + +
251A LEU* 3.7 10.1 - - - +
252A SER* 3.0 27.9 + - - -
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Residues in contact with ILE 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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31A VAL* 4.1 27.1 - - + -
35A CYS* 4.9 0.4 - - - -
136A VAL* 4.1 12.1 - - + -
161A SER* 4.9 5.6 - - - +
165A LEU* 3.4 25.4 - - + -
245A THR* 4.3 20.2 - - + +
246A SER 3.4 7.3 + - - +
247A TRP 3.3 0.4 - - - -
248A ALA* 1.3 78.5 - - + +
250A GLY* 1.3 72.0 + - - +
252A SER* 2.9 20.6 - - - +
253A VAL* 3.0 16.3 + - + +
330A CIT 3.1 46.2 - - + +
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Residues in contact with GLY 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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31A VAL 5.0 0.2 + - - -
34A ALA* 3.8 4.2 - - - +
35A CYS* 3.7 35.5 - - - -
38A SER* 4.3 7.6 - - - -
246A SER 2.8 20.7 + - - -
247A TRP 3.9 0.7 - - - -
249A ILE* 1.3 76.1 - - - +
251A LEU* 1.3 63.5 - - - +
253A VAL* 2.9 13.0 + - - +
254A ALA* 3.1 12.1 + - - +
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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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38A SER* 3.8 23.4 + - - +
247A TRP* 3.0 34.3 + - + +
248A ALA* 3.7 8.3 - - - +
250A GLY* 1.3 72.7 - - - +
252A SER* 1.3 63.9 + - - +
253A VAL 3.1 0.3 + - - -
254A ALA* 3.2 5.0 + - - +
255A ASP* 3.1 21.9 + - - +
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Residues in contact with SER 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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161A SER* 4.7 4.9 + - - -
164A ASN* 2.9 32.1 + - - +
165A LEU* 3.9 21.8 + - - +
168A ALA* 6.0 1.3 - - - -
248A ALA 3.0 16.0 + - - -
249A ILE* 2.9 19.0 + - - +
251A LEU* 1.3 77.3 - - - +
253A VAL* 1.3 62.2 + - - +
255A ASP* 3.3 9.7 - - - +
256A LEU* 3.3 16.3 + - - +
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Residues in contact with VAL 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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35A CYS* 3.8 25.1 - - + -
39A ILE* 5.0 5.6 - - + -
93A VAL* 3.9 24.9 - - + -
134A LEU* 4.5 12.0 - - + +
136A VAL* 3.7 24.2 - - + -
161A SER* 4.4 7.0 - - - +
249A ILE* 3.5 17.9 - - + +
250A GLY 2.9 9.5 + - - +
252A SER* 1.3 77.3 - - - +
254A ALA* 1.3 57.8 + - - +
255A ASP 3.1 1.1 - - - -
256A LEU* 3.1 11.6 + - + +
257A ALA* 2.8 32.4 + - + +
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Residues in contact with ALA 254 (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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38A SER* 3.9 39.5 - - - +
39A ILE* 4.3 8.3 - - + +
42A LYS* 4.5 15.8 + - + +
44A LEU* 3.8 4.6 - - + +
250A GLY 3.1 6.0 + - - +
251A LEU* 3.7 8.1 - - + +
253A VAL* 1.3 73.5 - - - +
255A ASP* 1.3 60.3 + - - +
257A ALA* 3.6 7.4 - - - +
258A GLU* 2.8 32.7 + - - +
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Residues in contact with ASP 255 (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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42A LYS* 5.0 5.6 + - - +
164A ASN* 5.1 3.5 + - - +
251A LEU 3.1 11.9 + - - +
252A SER* 3.3 14.4 - - - +
253A VAL 3.1 0.2 - - - -
254A ALA* 1.3 79.4 - - - +
256A LEU* 1.3 58.9 + - - +
258A GLU* 3.5 8.1 + - - +
259A THR* 3.4 17.5 + - - -
266A ARG* 3.5 23.1 + - - -
268A HIS* 2.8 30.0 + - + -
331A CIT 5.7 0.3 + - - -
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Residues in contact with LEU 256 (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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134A LEU* 4.0 31.0 - - + -
159A ILE* 5.3 2.2 - - + -
160A GLY 5.3 0.2 - - - +
161A SER* 4.7 8.7 - - - +
164A ASN* 3.7 19.1 - - - +
252A SER* 3.3 10.3 + - - +
253A VAL* 3.1 15.1 + - + +
255A ASP* 1.3 78.2 - - - +
257A ALA* 1.3 59.4 + - - +
259A THR* 3.7 3.3 + - - -
260A ILE* 2.9 36.6 + - + +
268A HIS* 3.3 44.9 - - + +
270A VAL* 3.8 20.2 - - + -
292A LEU* 4.2 10.2 - - + +
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Residues in contact with ALA 257 (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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23A ILE* 4.6 3.4 - - + -
39A ILE* 4.7 6.5 - - + -
44A LEU* 3.3 23.3 - - + -
91A LEU* 3.9 28.5 - - + -
134A LEU* 4.9 0.4 - - - +
253A VAL* 2.8 17.0 + - + +
254A ALA* 3.7 2.0 - - - +
256A LEU* 1.3 75.0 - - - +
258A GLU* 1.3 61.6 + - - +
260A ILE* 4.4 2.2 - - - -
261A MET* 2.8 40.1 + - + +
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Residues in contact with GLU 258 (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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42A LYS* 3.3 30.6 + - - -
44A LEU* 3.8 16.4 - - + +
254A ALA 2.8 16.0 + - - +
255A ASP* 3.5 7.1 + - - +
257A ALA* 1.3 74.7 - - - +
259A THR* 1.3 66.5 + - - +
261A MET* 4.6 0.7 - - - -
262A LYS* 2.8 68.8 + - + +
264A LEU* 4.6 4.7 - - + -
266A ARG* 3.6 21.9 + - - +
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Residues in contact with THR 259 (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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255A ASP 3.4 3.6 + - - -
256A LEU 3.8 7.6 - - - -
257A ALA 3.4 0.4 - - - -
258A GLU* 1.3 78.5 - - - +
260A ILE* 1.3 61.8 + - - +
263A ASN* 3.0 3.6 + - - -
264A LEU* 2.9 36.9 + - + -
265A CYS 3.9 2.5 - - - +
266A ARG* 2.8 42.7 + - + +
268A HIS* 3.0 23.0 + - + -
292A LEU* 3.2 38.5 - - + +
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Residues in contact with ILE 260 (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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91A LEU* 4.7 16.8 - - + -
132A ILE* 4.5 20.0 - - + -
134A LEU* 4.4 17.0 - - + -
159A ILE* 4.2 17.3 - - + -
256A LEU* 2.9 26.8 + - + +
257A ALA* 3.9 4.9 - - - +
259A THR* 1.3 73.9 - - - +
261A MET* 1.3 68.5 + - - +
263A ASN 3.3 7.1 + - - -
292A LEU* 3.9 25.1 - - + -
293A ASN 3.6 22.2 - - - +
294A ASP* 3.2 36.2 + - - +
296A GLY* 5.0 1.1 - - - +
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Residues in contact with MET 261 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ASN* 3.6 38.3 + - + +
23A ILE* 4.2 19.7 - - + -
44A LEU* 3.6 34.1 - - + +
90A LYS* 4.0 31.4 - - + -
91A LEU* 4.6 9.0 - - + -
257A ALA* 2.8 33.7 + - + +
258A GLU 4.1 1.6 - - - +
260A ILE* 1.3 79.8 - - + +
262A LYS* 1.3 63.5 + - + +
263A ASN* 3.3 1.3 + - - +
294A ASP* 4.9 7.3 - - - +
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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