Contacts of the helix formed by residues 339 - 351 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E ASP* 6.1 0.4 - - - -
18E LEU* 5.9 2.4 - - + +
20E LYS* 3.9 28.5 - - + +
28E ALA* 5.5 5.2 - - + -
29E PRO* 3.9 26.0 - - + -
32E VAL* 4.2 24.6 - - + +
336E GLU* 3.0 17.2 + - + +
338E LYS* 1.3 125.2 + - + +
340E SER* 1.3 57.5 + - - +
341E VAL* 3.3 2.5 - - - -
342E TRP* 3.2 8.0 + - + +
343E ILE* 2.9 38.3 + - + +
400E ATP 6.1 0.4 - - - -
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Residues in contact with SER 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E SER* 3.5 24.5 + - - -
146E ALA* 3.7 13.8 - - - +
301E MET 5.2 0.2 + - - -
302E SER* 4.1 6.8 - - - -
334E PRO* 4.5 7.6 - - - +
336E GLU* 3.3 15.0 + - - -
337E ARG* 3.4 28.6 + - - +
338E LYS 3.6 0.8 - - - -
339E TYR* 1.3 76.8 - - - +
341E VAL* 1.3 58.3 + - - +
343E ILE* 3.3 7.7 + - - +
344E GLY* 2.8 29.1 + - - -
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Residues in contact with VAL 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ASP* 3.3 33.7 - - - +
108E THR* 4.2 8.9 - - + +
139E GLN* 3.6 34.3 - - + +
142E LEU* 3.6 13.3 - - + +
143E SER* 3.2 18.6 - - - +
156E ASP* 3.9 18.2 - - - +
302E SER* 4.5 2.9 - - - +
303E GLY* 6.1 0.9 - - - +
337E ARG 5.3 0.2 + - - -
338E LYS 5.6 0.2 - - - -
339E TYR 3.3 0.4 - - - -
340E SER* 1.3 77.2 - - - +
342E TRP* 1.3 64.5 + - - +
344E GLY 3.2 0.5 + - - -
345E GLY 3.0 17.3 + - - -
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Residues in contact with TRP 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E VAL* 2.9 41.4 + - + +
13E ASP* 3.8 12.4 + - + +
20E LYS* 3.1 39.0 - - + -
21E ALA 3.6 0.8 - - - -
22E GLY* 3.4 29.7 - - - +
23E PHE 3.6 22.4 - - - -
26E ASP* 3.3 24.9 - - + -
27E ASP 4.1 1.1 - - - -
28E ALA 3.4 24.9 - - - -
29E PRO* 3.5 26.9 - - + -
339E TYR* 3.2 11.2 + - - +
341E VAL* 1.3 78.8 - - - +
343E ILE* 1.3 67.6 + - + +
345E GLY* 2.9 4.9 + - - -
346E SER* 2.8 32.8 + - - -
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Residues in contact with ILE 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D GLN* 3.7 31.2 - - + +
125D PHE* 4.6 9.9 - - + -
27E ASP 3.4 24.9 - - - +
28E ALA* 4.8 1.1 - - + -
146E ALA* 4.4 2.2 - - + -
336E GLU* 3.5 33.4 - - + +
339E TYR* 2.9 28.9 + - + +
340E SER* 3.7 4.5 - - - +
342E TRP* 1.3 89.5 - - + +
344E GLY* 1.3 63.9 + - - +
346E SER* 2.9 14.1 + - - +
347E ILE* 2.9 27.1 + - + +
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Residues in contact with GLY 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ILE* 4.7 3.6 - - - +
142E LEU* 3.4 32.6 - - - +
145E TYR* 5.1 2.6 - - - +
146E ALA* 4.0 10.3 - - - +
340E SER 2.8 17.0 + - - -
341E VAL 3.7 1.8 - - - -
343E ILE* 1.3 72.1 - - - +
345E GLY* 1.3 56.5 + - - +
347E ILE* 3.5 6.6 + - - +
348E LEU* 3.1 28.2 + - - +
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Residues in contact with GLY 345 (chain E).
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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11E VAL* 3.8 10.7 - - - +
106E LEU* 3.3 19.5 - - - +
142E LEU* 3.9 20.7 - - - +
341E VAL 3.0 7.0 + - - -
342E TRP 2.9 8.4 + - - -
344E GLY* 1.3 76.9 - - - +
346E SER* 1.3 64.1 + - - +
348E LEU* 4.5 0.4 - - - -
349E ALA* 3.1 21.0 + - - +
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Residues in contact with SER 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D PHE* 5.5 0.2 - - - -
125D PHE* 4.5 4.8 - - - -
11E VAL* 3.9 10.9 - - - +
24E ALA* 3.7 3.2 - - - +
25E GLY* 3.0 20.1 + - - -
26E ASP 2.8 28.8 + - - -
342E TRP* 2.8 27.9 + - - -
343E ILE* 2.9 8.5 + - - -
345E GLY* 1.3 76.1 - - - +
347E ILE* 1.3 57.5 + - - +
349E ALA* 3.6 1.2 + - - -
350E SER* 2.7 33.5 + - - -
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Residues in contact with ILE 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D PHE* 4.1 12.1 - - + -
71D GLN* 3.6 27.8 - - + +
72D ASP* 3.8 18.2 - - - +
75D GLY* 4.1 10.8 - - - -
76D ALA* 3.8 26.0 - - - +
79D ILE* 4.1 9.6 - - + -
125D PHE* 4.2 12.8 - - + -
145E TYR 5.2 0.2 - - - +
146E ALA* 4.7 4.7 - - - -
343E ILE* 2.9 30.2 + - + +
344E GLY* 3.7 8.1 - - - +
346E SER* 1.3 76.9 - - - +
348E LEU* 1.3 63.0 + - - +
350E SER* 3.0 13.3 + - - -
351E LEU* 3.3 15.3 + - + +
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Residues in contact with LEU 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ILE* 3.9 37.9 - - + -
83D GLN* 4.9 0.2 - - - +
106E LEU* 4.2 9.0 - - + -
135E TYR* 4.2 16.2 - - + +
137E ALA* 4.5 2.7 - - + -
142E LEU* 3.9 20.9 - - + -
145E TYR* 5.5 6.5 - - + -
344E GLY 3.1 15.6 + - - +
345E GLY 3.9 3.4 - - - +
347E ILE* 1.3 80.2 - - - +
349E ALA* 1.3 61.3 + - - +
350E SER 3.2 1.0 + - - -
351E LEU* 3.4 11.5 + - + +
354E PHE* 3.3 53.2 - - + +
357E MET* 4.5 7.6 - - + -
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Residues in contact with ALA 349 (chain E).
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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9E ALA* 4.6 4.0 - - + +
11E VAL* 4.3 4.5 - - + -
24E ALA* 3.8 24.6 - - + +
106E LEU* 3.8 14.1 - - + -
345E GLY 3.1 18.5 + - - +
348E LEU* 1.3 76.6 - - - +
350E SER* 1.3 59.1 + - - +
351E LEU 3.5 1.1 - - - +
354E PHE* 3.9 19.5 - - - +
358E TRP* 4.3 22.7 + - + -
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Residues in contact with SER 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D PHE* 3.4 39.5 - - - +
24E ALA* 3.8 3.9 - - - -
25E GLY* 3.2 24.5 + - - -
346E SER 2.7 21.1 + - - -
347E ILE 3.0 6.9 + - - -
349E ALA* 1.3 77.6 - - - +
351E LEU* 1.3 65.5 + - - +
352E SER* 3.6 1.0 + - - -
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Residues in contact with LEU 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D PHE* 3.5 20.9 - - + +
76D ALA* 3.7 28.7 - - + -
79D ILE* 3.5 43.1 - - + -
80D PHE* 4.0 17.3 - - + -
83D GLN* 4.4 1.8 - - - +
347E ILE* 3.3 17.7 + - + +
348E LEU* 3.4 15.5 + - + +
349E ALA 4.6 0.9 - - - +
350E SER* 1.3 79.1 - - - +
352E SER* 1.3 66.2 + - - +
353E THR* 4.0 14.6 - - - +
354E PHE* 2.9 19.3 + - + +
355E GLN* 4.0 2.1 + - - +
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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