Contacts of the helix formed by residues 339 - 351 (chain B) in PDB entry 1MDU
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 TYR 339 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 6.0 2.6 - - + +
20B LYS* 3.9 15.3 - - + +
28B ALA* 5.4 4.3 - - + -
29B PRO* 3.8 32.8 - - + -
32B VAL* 4.0 35.2 - - + +
336B GLU* 2.7 19.3 + - + +
338B LYS* 1.3 115.6 + - + +
340B SER* 1.3 62.3 + - - -
341B VAL* 3.2 3.4 - - - -
342B TRP* 3.0 6.0 + - - +
343B ILE* 2.9 33.6 + - + +
400B ATP 6.0 0.9 - - - -
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Residues in contact with SER 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 5.7 0.4 - - - +
142B LEU 4.0 1.0 - - - +
143B SER* 3.2 26.2 - - - -
146B ALA* 3.6 17.3 - - - +
301B MET 4.8 0.9 + - - -
302B SER* 4.1 5.2 - - - -
334B PRO* 4.7 8.3 - - - +
336B GLU 3.3 4.0 + - - -
337B ARG* 2.8 37.8 + - - +
338B LYS 3.7 0.2 - - - -
339B TYR* 1.3 75.6 - - - +
341B VAL* 1.3 57.8 + - - +
343B ILE* 3.3 6.4 + - - +
344B GLY* 2.8 27.7 + - - -
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ASP* 3.4 34.3 - - - +
108B THR* 4.0 9.8 - - + +
139B GLN* 3.8 35.4 - - + +
142B LEU* 3.4 16.1 - - + +
143B SER* 3.4 17.2 + - - +
156B ASP* 3.9 17.5 - - - +
302B SER* 4.1 3.8 - - - +
303B GLY* 6.4 0.7 - - - -
339B TYR 3.2 1.7 + - - -
340B SER* 1.3 78.9 - - - +
342B TRP* 1.3 56.9 + - - +
345B GLY* 3.1 20.8 + - - -
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Residues in contact with TRP 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 2.9 45.9 + - + +
13B ASP* 4.3 9.3 + - + +
20B LYS* 3.4 33.7 - - + -
21B ALA 3.7 0.6 - - - -
22B GLY* 3.5 33.9 - - - +
23B PHE 3.3 20.6 - - - -
26B ASP* 3.3 22.4 - - + -
27B ASP 4.1 0.7 - - - -
28B ALA* 3.3 29.8 - - - -
29B PRO* 3.6 30.3 - - + -
339B TYR* 3.0 10.3 + - + +
341B VAL* 1.3 76.2 - - - +
343B ILE* 1.3 62.0 + - + +
345B GLY* 3.1 2.6 + - - -
346B SER* 2.8 40.1 + - - -
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Residues in contact with ILE 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 3.6 40.2 - - + +
125A PHE* 4.5 9.6 - - + -
26B ASP 5.6 0.2 - - - -
27B ASP 3.6 24.7 - - - +
28B ALA* 4.9 1.3 - - + -
146B ALA* 4.5 0.7 - - + -
336B GLU* 4.4 21.3 - - + +
339B TYR* 2.9 35.8 + - + +
340B SER* 3.7 7.4 - - - +
342B TRP* 1.3 86.2 - - + +
344B GLY* 1.3 62.9 + - - +
346B SER* 3.0 5.0 + - - -
347B ILE* 2.9 41.0 + - + +
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Residues in contact with GLY 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ILE* 4.7 3.5 - - - +
142B LEU* 3.4 30.3 - - - +
145B TYR* 5.1 3.0 - - - +
146B ALA* 4.1 8.5 - - - +
340B SER 2.8 12.4 + - - -
341B VAL 3.9 1.1 - - - -
343B ILE* 1.3 76.7 - - - +
345B GLY* 1.3 56.5 + - - +
347B ILE* 3.7 8.7 - - - +
348B LEU* 3.0 28.6 + - - +
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Residues in contact with GLY 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 4.1 14.4 - - - -
106B LEU* 4.5 8.3 - - - +
142B LEU* 3.9 22.3 - - - +
341B VAL 3.1 12.1 + - - -
342B TRP 3.1 4.2 + - - -
344B GLY* 1.3 72.6 - - - +
346B SER* 1.3 65.1 + - - +
348B LEU* 3.7 2.9 - - - +
349B ALA* 2.9 28.2 + - - +
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Residues in contact with SER 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE* 5.5 0.2 - - - -
125A PHE* 4.3 2.9 - - - -
11B VAL* 3.9 12.4 - - - +
24B ALA* 3.9 2.6 - - - +
25B GLY* 3.0 18.6 + - - -
26B ASP 2.6 29.3 + - - -
342B TRP* 2.8 33.4 + - - -
343B ILE* 3.0 9.2 + - - -
345B GLY* 1.3 73.5 - - - +
347B ILE* 1.3 60.7 + - - +
350B SER* 2.8 29.6 + - - -
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Residues in contact with ILE 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE* 4.2 13.4 - - + -
71A GLN* 3.9 24.7 - - + +
72A ASP* 3.9 13.9 - - - +
75A GLY* 4.1 7.4 - - - -
76A ALA* 3.9 25.6 - - - +
79A ILE* 4.0 12.8 - - + -
125A PHE* 4.1 17.9 - - + -
145B TYR* 5.2 0.9 - - + +
146B ALA* 4.6 4.9 - - - -
343B ILE* 2.9 37.7 + - + +
344B GLY* 3.7 9.2 - - - +
346B SER* 1.3 75.5 - - - +
348B LEU* 1.3 64.7 + - - +
350B SER* 3.0 12.8 + - - -
351B LEU* 3.3 14.7 + - + +
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ILE* 3.8 37.9 - - + +
83A GLN* 5.1 3.1 - - - +
106B LEU* 4.0 13.9 - - + -
135B TYR* 4.3 11.2 - - + +
137B ALA* 4.7 2.2 - - + -
142B LEU* 4.0 21.3 - - + -
145B TYR* 5.0 8.3 - - + -
344B GLY 3.0 18.1 + - - +
345B GLY 3.3 4.7 + - - +
347B ILE* 1.3 78.3 - - - +
349B ALA* 1.3 60.9 + - - +
350B SER 2.9 5.4 + - - -
351B LEU* 3.2 13.8 + - + +
354B PHE* 3.5 43.9 - - + +
357B MET* 5.3 3.1 - - + -
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Residues in contact with ALA 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA* 4.5 2.7 - - + +
11B VAL* 4.5 5.8 - - + -
24B ALA* 3.7 23.2 - - + +
106B LEU* 4.6 7.9 - - + -
345B GLY 2.9 19.9 + - - +
348B LEU* 1.3 73.1 - - - +
350B SER* 1.3 59.6 + - - +
351B LEU 3.6 0.6 - - - +
354B PHE* 3.6 22.6 - - + +
358B TRP* 4.1 29.3 + - + -
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Residues in contact with SER 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 3.6 34.8 - - - +
24B ALA* 3.5 4.0 - - - -
25B GLY* 3.0 26.2 + - - -
346B SER 2.8 21.1 + - - -
347B ILE 3.0 5.8 + - - -
348B LEU 2.9 0.8 + - - -
349B ALA* 1.3 77.5 - - - +
351B LEU* 1.3 67.6 + - - +
352B SER* 3.4 2.1 + - - -
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE* 3.5 23.3 - - + +
76A ALA* 3.6 28.7 - - + +
79A ILE* 3.3 43.3 - - + -
80A PHE* 4.0 20.9 - - + -
83A GLN* 4.5 1.6 - - - +
347B ILE* 3.3 17.4 + - + +
348B LEU* 3.2 11.7 + - + +
349B ALA 4.6 0.7 - - - +
350B SER* 1.3 78.8 - - - +
352B SER* 1.3 60.5 + - - +
353B THR* 3.8 13.2 - - - +
354B PHE* 2.9 26.2 + - + +
355B GLN 4.1 1.7 + - - -
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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