Contacts of the helix formed by residues 277 - 290 (chain A) in PDB entry 1MDL
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 VAL 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A ASP* 2.7 6.4 + - - +
109A MET* 4.4 4.3 - - - +
112A TRP* 3.3 48.7 - - + +
123A LEU* 4.0 10.5 - - + -
127A LEU* 4.3 11.2 - - + -
276A GLY* 1.3 68.9 - - - -
278A THR* 1.3 65.6 + - - +
280A TRP* 3.1 7.7 + - - +
281A ILE* 3.0 35.1 + - + +
302A ILE* 3.7 28.5 - - + -
306A LEU* 4.1 18.6 - - + -
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Residues in contact with THR 278 (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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80A PRO 4.2 6.2 + - - -
81A VAL* 4.1 15.5 - - + +
84A GLU* 4.1 17.7 - - + -
108A ASP* 2.7 30.1 + - - -
112A TRP* 3.0 14.3 + - - +
275A GLY 4.1 2.2 - - - -
277A VAL* 1.3 79.1 - - - +
279A GLY* 1.3 61.9 + - - +
281A ILE* 3.5 10.7 + - - +
282A ARG* 3.5 54.3 + - - +
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Residues in contact with GLY 279 (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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84A GLU* 5.9 0.2 - - - +
252A PRO* 3.9 13.8 - - - +
274A ILE* 3.4 25.5 - - - +
275A GLY* 3.1 16.6 + - - -
276A GLY 3.9 0.2 - - - -
278A THR* 1.3 74.6 - - - +
280A TRP* 1.3 61.1 + - - +
282A ARG* 3.2 6.2 + - - +
283A ALA* 2.8 28.9 + - - +
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Residues in contact with TRP 280 (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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269A PRO* 3.7 27.8 - - + -
271A ALA* 4.2 21.8 - - + -
274A ILE* 3.9 11.7 - - + +
276A GLY 2.9 19.3 + - - +
277A VAL* 3.4 5.8 - - - +
279A GLY* 1.3 75.2 - - - +
281A ILE* 1.3 70.7 + - + +
283A ALA* 3.0 6.3 + - - +
284A SER* 2.8 29.4 + - - -
294A MET* 3.3 21.0 - - + +
295A SER 3.8 18.8 - - - -
296A SER* 3.9 18.6 - - - -
303A SER* 4.8 2.5 - - - -
306A LEU* 3.7 44.1 + - + -
307A LEU* 3.7 26.5 - - + -
310A THR* 2.9 22.7 + - - -
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Residues in contact with ILE 281 (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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112A TRP* 4.4 13.0 - - + -
127A LEU* 4.4 20.4 - - + -
277A VAL* 3.0 38.0 + - + +
278A THR* 3.9 7.0 - - - +
279A GLY 3.3 0.2 - - - -
280A TRP* 1.3 82.3 - - + +
282A ARG* 1.3 66.4 + - + +
284A SER* 3.4 7.8 + - - -
285A ALA* 3.2 20.3 + - - +
306A LEU* 5.6 1.1 - - + -
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Residues in contact with ARG 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 4.0 21.4 + - - +
84A GLU* 3.2 29.7 + - - -
252A PRO* 3.8 20.0 - - + -
278A THR* 3.5 33.8 + - - +
279A GLY* 3.2 8.9 + - - +
280A TRP 3.0 0.2 - - - -
281A ILE* 1.3 81.3 - - + +
283A ALA* 1.3 62.1 + - - +
285A ALA* 3.1 16.3 + - - +
286A LEU* 3.3 17.6 + - - +
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Residues in contact with ALA 283 (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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252A PRO* 4.3 2.4 - - + +
255A MET* 3.4 35.0 - - - +
269A PRO* 4.6 1.6 - - + -
274A ILE* 3.9 17.3 - - + -
279A GLY 2.8 19.7 + - - +
280A TRP* 3.5 6.3 - - - +
282A ARG* 1.3 73.1 - - - +
284A SER* 1.3 58.6 + - - +
286A LEU* 4.3 6.1 - - - -
287A ALA* 2.9 26.9 + - - +
294A MET* 4.2 11.0 - - + -
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Residues in contact with SER 284 (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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280A TRP* 2.8 18.2 + - - -
281A ILE* 3.5 9.0 + - - -
283A ALA* 1.3 80.4 - - - +
285A ALA* 1.3 63.0 + - - +
287A ALA* 3.9 2.0 - - - +
288A GLN* 2.9 23.0 + - - +
294A MET* 4.0 19.3 - - - +
309A ALA 4.4 3.0 + - - -
310A THR* 4.0 15.0 - - - +
311A PRO* 3.4 26.3 - - - +
312A THR* 5.4 1.0 + - - -
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Residues in contact with ALA 285 (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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281A ILE 3.2 8.5 + - - +
282A ARG* 3.1 12.1 + - - +
284A SER* 1.3 81.4 + - - +
286A LEU* 1.4 63.4 + - + +
288A GLN* 3.3 9.8 + - - +
289A GLN* 3.1 29.9 + - - +
311A PRO* 6.1 0.4 - - - -
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Residues in contact with LEU 286 (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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252A PRO* 3.9 37.0 - - + +
255A MET* 4.3 12.8 - - + -
256A PHE* 4.2 31.2 - - + +
259A LEU* 4.4 10.5 - - + -
282A ARG 3.3 11.4 + - - +
283A ALA* 3.6 6.5 - - - +
284A SER 3.2 0.2 - - - -
285A ALA* 1.4 75.5 - - + +
287A ALA* 1.3 68.0 + - - +
288A GLN 3.0 1.1 - - - -
289A GLN* 2.9 5.9 + - - -
290A PHE* 2.8 35.8 + - + -
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Residues in contact with ALA 287 (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 MET* 3.9 10.7 - - + +
259A LEU* 4.5 3.4 - - - -
283A ALA 2.9 17.8 + - - +
284A SER* 3.9 3.1 - - - +
286A LEU* 1.3 77.4 - - - +
288A GLN* 1.3 64.4 + - - +
290A PHE 3.5 0.3 + - - -
291A GLY 3.1 3.3 + - - -
292A ILE* 3.1 52.4 + - + +
294A MET* 3.7 21.8 - - + -
312A THR* 4.0 6.5 - - - +
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Residues in contact with GLN 288 (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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284A SER 2.9 15.4 + - - +
285A ALA* 3.5 12.9 - - - +
286A LEU 3.0 0.4 - - - -
287A ALA* 1.3 80.8 - - - +
289A GLN* 1.3 80.8 + - - +
291A GLY* 3.4 8.5 + - - -
311A PRO* 3.6 36.7 - - + +
312A THR* 4.0 16.3 - - + +
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Residues in contact with GLN 289 (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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285A ALA 3.4 11.3 + - - +
286A LEU* 2.9 8.3 + - + +
288A GLN* 1.3 105.3 + - - +
290A PHE* 1.3 67.0 + - + +
291A GLY 3.1 1.3 + - - -
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Residues in contact with PHE 290 (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 PHE* 4.0 25.4 - + - -
259A LEU* 3.6 50.9 - - + -
260A SER* 4.0 22.0 - - - -
286A LEU* 2.8 36.8 + - + +
289A GLN* 1.3 76.6 - - + +
291A GLY* 1.3 62.0 + - - +
292A ILE* 3.6 25.0 - - + +
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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