Contacts of the helix formed by residues 253 - 268 (chain A) in PDB entry 3LMK
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 GLY 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A VAL* 6.0 2.0 - - - +
251A ASN 3.5 3.2 + - - -
252A ALA* 1.3 77.9 - - - +
254A GLU* 1.3 65.2 + - - -
255A GLN* 3.2 4.0 - - - -
256A SER* 3.1 18.4 + - - -
257A PHE* 3.4 12.5 + - - -
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Residues in contact with GLU 254 (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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253A GLY* 1.3 71.7 - - - +
255A GLN* 1.3 62.7 + - - +
257A PHE* 3.5 1.9 + - - +
258A ASP* 2.8 25.9 + - - +
292A ARG* 3.2 43.8 + - - +
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Residues in contact with GLN 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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253A GLY* 3.2 1.7 - - - -
254A GLU* 1.3 79.9 - - - +
256A SER* 1.3 62.8 + - - +
258A ASP* 3.4 13.4 - - - +
259A LYS* 3.3 48.0 + - - +
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Residues in contact with SER 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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248A ILE* 4.0 7.7 - - - +
252A ALA* 3.5 20.9 - - - +
253A GLY* 3.1 21.9 + - - -
255A GLN* 1.3 76.3 - - - +
257A PHE* 1.3 64.2 + - - +
259A LYS* 3.3 13.1 + - - +
260A LEU* 3.2 19.9 + - - +
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Residues in contact with PHE 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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248A ILE* 3.6 31.6 - - + -
249A TYR 3.7 18.8 - - - -
250A SER 3.9 10.1 - - - -
252A ALA 3.5 15.7 - - - -
253A GLY 3.4 15.4 + - - -
254A GLU* 4.1 5.4 - - - +
255A GLN 3.5 0.2 - - - -
256A SER* 1.3 75.5 - - - +
258A ASP* 1.3 59.7 + - - +
260A LEU* 3.4 5.7 + - + +
261A LEU* 2.9 30.3 + - - +
281A MET 4.3 0.2 - - - -
282A THR* 3.3 34.8 - - + -
285A GLY* 3.4 41.1 - - - +
286A LEU* 3.5 13.7 - - + +
289A ALA* 3.9 8.8 - - + +
292A ARG* 4.3 4.0 - - - +
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Residues in contact with ASP 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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254A GLU* 2.8 22.9 + - - +
255A GLN* 3.4 16.3 - - + +
257A PHE* 1.3 76.0 - - - +
259A LYS* 1.3 62.8 + - + +
261A LEU* 3.3 3.4 + - - +
262A LYS* 2.9 32.6 + - + +
289A ALA* 4.2 11.4 - - - +
292A ARG* 3.5 32.2 + - - +
293A LEU* 4.6 10.0 - - + +
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Residues in contact with LYS 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 GLN* 3.3 41.0 + - + +
256A SER* 3.3 10.7 + - - +
258A ASP* 1.3 77.9 - - + +
260A LEU* 1.3 64.5 + - - +
262A LYS* 3.1 10.7 + - - +
263A LYS* 3.0 31.5 + - + +
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Residues in contact with LEU 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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217A VAL* 4.2 13.5 - - + -
246A TYR* 3.6 39.0 - - + -
247A LYS 4.9 3.6 - - - +
248A ILE* 3.7 39.5 - - + -
256A SER 3.2 10.6 + - - +
257A PHE* 3.6 10.1 - - + +
259A LYS* 1.3 77.6 - - - +
261A LEU* 1.3 63.5 + - - +
263A LYS* 3.1 10.3 + - + +
264A LEU* 2.9 29.0 + - + +
286A LEU* 4.1 23.1 - - + -
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Residues in contact with LEU 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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257A PHE 2.9 17.2 + - - +
258A ASP 3.8 3.4 - - - +
260A LEU* 1.3 77.2 - - - +
262A LYS* 1.3 53.7 + - - +
264A LEU* 2.9 18.5 + - + +
265A THR* 2.7 41.0 + - + +
286A LEU* 4.3 10.1 - - + +
289A ALA* 3.4 16.8 - - + +
290A MET* 3.4 48.5 - - + +
293A LEU* 3.8 16.8 - - + -
295A LEU* 4.9 4.3 - - + -
299A PHE* 3.7 28.7 - - + -
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Residues in contact with LYS 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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258A ASP* 2.9 23.2 + - + +
259A LYS* 3.4 10.8 - - - +
261A LEU* 1.3 74.0 - - - +
263A LYS* 1.3 64.2 + - + +
265A THR* 2.5 29.8 + - + +
266A SER* 3.2 9.2 + - - -
293A LEU* 4.0 32.4 - - + +
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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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244A HIS* 5.6 5.6 + - - -
246A TYR* 3.5 47.6 + - + +
259A LYS* 3.0 24.2 + - + +
260A LEU* 3.4 9.6 - - - +
262A LYS* 1.3 75.0 - - + +
264A LEU* 1.3 62.3 + - - +
266A SER* 2.5 26.2 + - - -
267A HIS* 3.3 4.7 + - - +
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Residues in contact with LEU 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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215A SER* 3.9 30.1 - - - +
217A VAL* 4.0 21.1 - - + -
246A TYR* 4.0 19.3 - - + -
260A LEU* 2.9 22.1 + - + +
261A LEU* 3.3 14.4 - - + +
263A LYS* 1.3 77.6 - - - +
265A THR* 1.3 60.0 + - - +
267A HIS* 3.2 15.7 + - - +
268A LEU 3.3 8.0 + - - -
271A ALA 4.8 0.5 - - - +
274A VAL* 4.3 13.2 - - + -
286A LEU* 3.9 28.5 - - + -
290A MET* 6.5 0.4 - - + -
299A PHE* 3.6 24.6 - - + -
301A LEU* 6.2 1.1 - - + -
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Residues in contact with THR 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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261A LEU* 2.7 31.1 + - + +
262A LYS* 2.5 27.9 + - + +
264A LEU* 1.3 72.3 - - - +
266A SER* 1.3 58.1 + - - +
268A LEU* 3.1 26.7 + - - +
293A LEU* 5.4 4.7 - - + -
295A LEU* 4.7 12.6 - - + -
299A PHE* 4.0 20.9 - - + -
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Residues in contact with SER 266 (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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246A TYR* 4.8 1.9 + - - -
262A LYS 3.2 6.4 + - - -
263A LYS* 2.5 25.9 + - - +
265A THR* 1.3 80.9 + - - +
267A HIS* 1.3 60.4 + - - +
268A LEU 3.2 8.6 - - - +
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Residues in contact with HIS 267 (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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215A SER* 3.7 22.2 - - - +
243A ALA* 4.9 10.4 - - + +
244A HIS* 5.8 1.8 - - + -
246A TYR* 4.8 8.3 - - + +
263A LYS 3.3 7.1 + - - +
264A LEU* 3.2 16.0 + - + +
266A SER* 1.3 80.3 + - - +
268A LEU* 1.4 58.9 + - - +
270A LYS* 3.6 7.8 + - - +
271A ALA* 3.2 23.7 + - + +
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Residues in contact with LEU 268 (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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264A LEU 3.3 7.4 + - - +
265A THR* 3.1 23.0 + - - +
266A SER* 3.3 11.1 - - - +
267A HIS* 1.4 81.1 - - - +
269A PRO* 1.4 71.1 - - + +
270A LYS* 3.4 0.7 - - - -
271A ALA 4.2 10.7 + - - +
272A ARG* 5.6 2.0 - - + -
298A GLU* 5.7 4.5 - - + +
299A PHE* 5.0 8.1 - - + -
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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