Contacts of the helix formed by residues 250 - 265 (chain A) in PDB entry 3LDH
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 LYS 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A HIS* 2.8 38.1 - - + -
163A SER* 5.3 0.8 + - - -
166A ASN* 3.2 23.0 + - - -
167A LEU* 4.2 26.3 - - + +
171A ARG* 5.2 1.8 - - - +
247A VAL* 3.7 18.1 - - + +
249A TRP* 1.3 75.7 - - - +
251A GLY* 1.3 56.3 + - - +
252A CYS* 2.4 22.1 + - - +
253A SER* 2.7 23.8 + - - -
254A VAL* 3.1 27.7 + - - +
332A NAD 3.2 34.6 + - + -
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Residues in contact with GLY 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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35A ALA* 4.1 14.3 - - - +
36A ASP* 4.1 21.8 - - - +
39A SER* 3.6 14.2 + - - -
138A HIS* 5.1 1.3 - - - -
249A TRP* 2.5 8.4 - - - +
250A LYS* 1.3 81.7 - - - +
252A CYS* 1.3 60.1 + - - -
254A VAL* 3.8 9.0 + - - +
255A ALA* 3.2 19.9 + - - +
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Residues in contact with CYS 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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39A SER* 4.3 7.6 - - - -
249A TRP* 3.6 19.1 - - - -
250A LYS* 2.4 16.0 + - - +
251A GLY* 1.3 66.9 - - - -
253A SER* 1.3 52.5 + - - +
255A ALA* 2.7 13.9 + - - +
256A ASP* 2.6 37.1 + - - +
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Residues in contact with SER 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASN* 2.0 42.4 + - - +
167A LEU* 3.4 15.2 - - - +
170A ALA* 5.0 4.7 - - - +
250A LYS* 2.7 21.2 + - - +
252A CYS* 1.3 72.9 - - - +
254A VAL* 1.3 50.7 + - - -
256A ASP* 3.1 7.9 + - - +
257A LEU* 2.5 43.7 + - - +
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Residues in contact with VAL 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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36A ASP* 2.9 27.8 - - - +
95A VAL* 4.2 20.4 - - + -
136A GLU* 3.4 19.0 - - + +
138A HIS* 3.5 15.5 - - + +
163A SER* 4.3 13.5 - - - +
250A LYS* 3.1 37.5 - - - +
251A GLY* 4.0 4.5 - - - +
252A CYS 3.2 0.4 - - - -
253A SER* 1.3 74.2 - - - +
255A ALA* 1.3 63.2 + - - +
257A LEU* 3.2 11.1 + - + +
258A ALA* 3.1 20.8 + - - +
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Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASP* 4.6 1.5 + - - +
39A SER* 3.9 18.2 - - - -
40A VAL* 4.3 23.4 - - + +
43A LYS* 5.0 14.2 - - + +
45A LEU* 5.2 3.3 - - - +
251A GLY 3.2 12.7 + - - +
252A CYS* 2.7 21.9 + - - +
254A VAL* 1.3 76.1 - - - +
256A ASP* 1.3 53.4 + - - +
258A ALA* 3.6 3.1 + - - +
259A GLN* 2.8 29.2 + - - +
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Residues in contact with ASP 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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43A LYS* 5.9 0.2 - - - +
252A CYS 2.6 15.4 + - - +
253A SER* 3.4 10.8 - - - +
255A ALA* 1.3 73.1 - - - +
257A LEU* 1.3 58.9 + - + +
259A GLN* 1.9 72.4 + - - +
260A THR* 3.3 5.1 + - - +
267A ARG* 3.8 12.7 + - - -
269A HIS* 3.5 28.8 + - - -
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Residues in contact with LEU 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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136A GLU* 4.0 9.4 - - + +
161A ILE* 5.9 5.2 - - + -
163A SER* 3.8 29.2 - - - +
166A ASN* 3.1 39.9 - - + +
253A SER* 2.5 33.5 + - - +
254A VAL* 3.3 20.9 - - + +
256A ASP* 1.3 74.2 - - + +
258A ALA* 1.3 58.2 + - - +
260A THR* 2.7 27.6 + - - -
261A ILE* 3.7 3.3 - - - +
269A HIS* 5.2 16.4 - - + +
270A PRO 5.1 9.2 - - - +
271A VAL* 5.7 4.7 - - + -
293A LEU* 3.1 15.7 - - + +
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Residues in contact with ALA 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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40A VAL* 5.8 5.6 - - + -
45A LEU* 5.8 3.6 - - + -
93A LEU* 3.2 26.2 - - + -
136A GLU* 2.9 31.3 + - - +
254A VAL 3.1 8.4 + - - +
255A ALA* 4.0 4.0 - - - +
257A LEU* 1.3 77.6 - - - +
259A GLN* 1.3 70.7 + - - +
261A ILE* 2.7 15.4 + - - -
262A MET* 2.9 14.9 + - + +
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Residues in contact with GLN 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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43A LYS* 2.4 41.9 - - + +
45A LEU* 5.5 8.1 - - + -
255A ALA 2.8 11.3 + - - +
256A ASP* 1.9 72.4 + - - +
258A ALA* 1.3 75.3 - - - +
260A THR* 1.3 52.4 + - - +
262A MET* 4.2 2.8 - - - +
263A LYS* 2.5 59.3 + - + +
267A ARG* 3.8 10.2 + - - +
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Residues in contact with THR 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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256A ASP* 3.3 4.0 + - - +
257A LEU* 2.7 1.6 + - - -
259A GLN* 1.3 77.7 - - - +
261A ILE* 1.3 52.1 + - - +
263A LYS* 3.3 0.2 - - - +
264A ASP* 2.5 39.5 + - - -
265A LEU* 3.3 15.7 + - + -
267A ARG* 3.0 50.5 - - + +
269A HIS* 4.7 5.4 - - + -
293A LEU* 1.4 83.3 - - + +
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Residues in contact with ILE 261 (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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92A LYS* 5.4 1.3 - - + +
93A LEU* 3.4 11.9 - - + -
134A LEU* 2.7 51.8 - - + -
136A GLU* 3.1 25.1 - - + +
161A ILE* 4.0 24.9 - - + -
257A LEU 3.7 9.4 - - - +
258A ALA 2.7 13.8 + - - +
260A THR* 1.3 75.7 + - - +
262A MET* 1.3 62.0 + - - +
264A ASP* 2.5 29.3 + - - -
293A LEU* 3.8 14.3 - - + +
294A ASN* 3.8 13.5 - - - +
295A ASN* 3.4 7.7 + - - -
296A GLY 3.9 2.7 - - - +
297A ILE 5.1 2.5 - - - +
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Residues in contact with MET 262 (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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22A ASN* 3.6 34.1 - - + +
23A LYS 5.2 6.5 - - - +
24A ILE* 5.3 1.8 - - + -
45A LEU* 4.5 45.1 - - + +
46A ALA* 4.6 4.3 - - - -
92A LYS* 3.3 36.1 + - + +
93A LEU* 3.8 28.0 - - + +
258A ALA 2.9 11.4 + - - +
259A GLN 4.2 2.0 - - - +
261A ILE* 1.3 83.5 - - - +
263A LYS* 1.3 61.3 + - - +
295A ASN* 3.4 1.9 + - - -
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Residues in contact with LYS 263 (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 LYS* 6.3 0.4 - - - +
45A LEU* 5.0 14.0 - - + +
259A GLN* 2.5 58.3 - - + +
260A THR 3.3 1.3 - - - +
261A ILE 2.8 0.6 + - - -
262A MET* 1.3 74.9 - - - +
264A ASP* 1.3 69.6 + - - +
265A LEU* 3.0 42.2 - - + +
295A ASN* 3.7 3.5 - - - +
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Residues in contact with ASP 264 (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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260A THR 2.5 20.5 + - - -
261A ILE 2.5 3.8 + - - -
263A LYS* 1.3 73.0 - - - +
265A LEU* 1.3 59.0 + - - +
266A CYS* 3.7 5.5 + - - -
294A ASN* 2.3 26.4 - - - +
295A ASN* 1.7 72.6 + - - +
299A HIS* 5.2 2.2 - - - -
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Residues in contact with LEU 265 (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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260A THR* 3.3 21.2 + - + -
263A LYS* 3.0 51.1 - - + +
264A ASP* 1.3 74.9 - - - +
266A CYS* 1.3 73.7 + - - +
267A ARG* 4.2 21.5 - - + +
293A LEU 4.4 0.2 + - - -
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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