Contacts of the helix formed by residues 260 - 272 (chain A) in PDB entry 1MD9
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 SER 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A SER* 3.2 14.9 + - - -
259A PRO* 1.3 81.4 - - - +
261A PRO* 1.3 75.4 - - - +
262A ASP* 2.7 36.5 + - - +
263A ASP* 2.9 13.0 + - - -
264A ALA* 3.0 10.7 + - - +
282A LEU* 5.3 1.1 - - - -
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Residues in contact with PRO 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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259A PRO 4.2 2.0 - - - +
260A SER* 1.3 90.1 - - - +
262A ASP* 1.3 62.5 + - - +
263A ASP 3.3 0.2 - - - -
264A ALA* 4.5 0.4 - - + -
265A PHE* 3.1 66.8 + - + +
266A PRO* 3.5 0.9 - - - +
282A LEU* 5.4 1.3 - - + -
285A VAL* 4.2 13.7 - - + +
286A TRP* 3.8 28.0 - - + +
289A ALA* 3.5 22.0 - - + -
293A ARG* 4.1 5.6 - - - -
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Residues in contact with ASP 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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260A SER* 2.7 18.9 + - - +
261A PRO* 1.3 82.8 - - - +
263A ASP* 1.3 62.6 + - - +
266A PRO* 3.3 21.0 - - - +
293A ARG* 3.5 26.5 + - - +
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Residues in contact with ASP 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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256A SER* 3.7 14.6 - - - +
257A PRO* 3.4 24.1 - - + +
258A SER* 2.4 37.6 + - - +
260A SER* 2.9 3.5 + - - -
262A ASP* 1.3 85.9 - - - +
264A ALA* 1.3 62.6 - - - +
265A PHE 3.7 0.2 - - - -
266A PRO* 3.7 2.3 - - - +
267A LEU* 3.1 32.8 + - - +
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Residues in contact with ALA 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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227A LEU* 3.6 19.3 - - + -
229A ALA* 5.1 1.6 - - + -
256A SER* 4.0 8.2 + - - +
258A SER 4.9 0.4 - - - +
259A PRO 4.4 1.6 - - - +
260A SER 3.0 12.5 + - - +
261A PRO* 4.5 0.7 - - + -
263A ASP* 1.3 76.7 - - - +
265A PHE* 1.3 53.6 + - - +
267A LEU* 3.1 4.6 + - - +
268A ILE* 2.5 40.7 + - - +
286A TRP* 3.3 35.4 - - + -
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Residues in contact with PHE 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 PRO* 3.1 41.1 + - + +
264A ALA* 1.3 72.7 - - + +
266A PRO* 1.3 70.6 - - + +
268A ILE* 2.9 8.0 + - + +
269A GLU* 2.8 24.8 + - - +
286A TRP* 3.6 46.4 - + - -
289A ALA* 3.5 16.8 - - + -
290A ALA* 3.8 11.7 - - - -
293A ARG* 3.9 22.2 - - + +
295A ASP* 3.3 17.3 - - - +
297A LEU* 3.5 36.9 - - + +
322A PHE* 4.3 3.1 - + - -
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Residues in contact with PRO 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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261A PRO 3.5 1.8 - - - +
262A ASP 3.3 26.5 - - - +
263A ASP 3.7 3.8 - - - +
264A ALA 3.6 1.3 - - - -
265A PHE* 1.3 94.6 - - + +
267A LEU* 1.3 54.1 + - + +
269A GLU* 3.2 4.0 + - + +
270A ARG* 2.7 39.4 + - - +
293A ARG* 3.9 17.3 - - - +
295A ASP* 4.0 10.5 - - - +
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Residues in contact with LEU 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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47A GLY* 5.9 9.2 - - - +
227A LEU* 4.3 6.1 - - + -
254A VAL* 4.2 15.7 - - + -
255A LEU 4.1 4.7 - - - +
256A SER* 3.7 17.3 - - - -
257A PRO* 3.6 29.6 - - + -
263A ASP 3.1 21.7 + - - +
264A ALA* 3.1 8.0 + - - +
266A PRO* 1.3 82.6 - - + +
268A ILE* 1.3 54.8 + - - +
270A ARG* 4.4 16.6 - - - +
271A GLU* 3.0 44.9 + - + +
273A VAL* 4.0 2.8 - - - +
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Residues in contact with ILE 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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227A LEU* 3.5 10.3 - - + -
264A ALA 2.5 25.9 + - - +
265A PHE* 2.9 18.4 + - + +
267A LEU* 1.3 73.9 - - - +
269A GLU* 1.3 57.4 + - - +
272A LYS* 2.8 30.5 + - - -
273A VAL* 3.2 33.0 + - + -
276A THR* 5.2 0.2 - - + -
286A TRP* 3.7 36.3 - - + -
297A LEU* 3.6 24.2 - - + -
299A SER* 3.2 15.0 + - - +
300A LEU* 4.0 18.4 - - + -
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Residues in contact with GLU 269 (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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265A PHE 2.8 11.7 + - - +
266A PRO* 3.6 7.9 - - - +
268A ILE* 1.3 80.0 - - - +
270A ARG* 1.3 68.4 + - + +
272A LYS* 3.4 22.3 + - - +
295A ASP* 2.9 25.7 - - - +
296A ASP* 3.2 42.9 + - + +
299A SER* 4.5 1.6 - - - -
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Residues in contact with ARG 270 (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 GLY* 4.2 15.1 + - - -
48A ASN* 3.2 32.9 + - - +
266A PRO 2.7 22.6 + - - +
267A LEU* 4.0 15.6 - - - +
269A GLU* 1.3 81.6 - - + +
271A GLU* 1.3 76.1 + - + +
272A LYS* 3.0 12.1 + - - +
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Residues in contact with GLU 271 (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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45A THR* 4.1 19.2 - - + +
47A GLY 4.4 7.1 - - - +
50A HIS* 4.7 7.4 + - - -
225A VAL* 3.8 4.3 - - - +
252A ARG* 2.8 40.7 + - - +
254A VAL* 3.8 33.4 - - + -
267A LEU* 3.0 23.4 + - + +
270A ARG* 1.3 97.5 + - + +
272A LYS* 1.3 69.8 - - - +
273A VAL* 4.4 2.9 - - + -
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Residues in contact with LYS 272 (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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225A VAL* 3.6 13.5 - - - +
268A ILE 2.8 14.9 + - - -
269A GLU* 3.4 18.0 + - - +
270A ARG 3.0 9.0 + - - +
271A GLU* 1.3 82.2 - - - +
273A VAL* 1.3 65.2 + - - +
274A THR* 3.9 5.2 - - - +
296A ASP* 5.8 2.8 + - - -
299A SER* 3.4 18.4 - - - -
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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