Contacts of the helix formed by residues 27 - 46 (chain A) in PDB entry 1MU5
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 ASN 27 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE 3.3 1.6 - - - -
26A PRO* 1.3 96.1 - - - +
28A PRO* 1.3 71.7 - - + +
29A ALA* 3.2 15.4 - - - +
30A ARG* 3.1 36.3 + - - +
31A ALA* 2.9 27.5 + - - +
118A TYR* 3.9 6.5 - - - -
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Residues in contact with PRO 28 (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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27A ASN* 1.3 90.4 - - + +
29A ALA* 1.3 56.0 + - - +
31A ALA* 3.4 2.6 - - + +
32A LEU* 2.9 25.1 + - - +
118A TYR* 3.6 17.5 - - - +
177A PRO* 3.9 10.5 - - + +
178A GLY* 3.4 40.6 - - - +
179A ASP* 4.6 3.6 - - + -
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Residues in contact with ALA 29 (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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27A ASN* 3.2 12.3 - - - +
28A PRO* 1.3 78.9 - - - +
30A ARG* 1.3 64.7 + - + +
32A LEU* 3.4 0.5 + - - +
33A TYR* 3.1 19.1 + - - +
179A ASP* 3.9 21.4 - - + +
182A LYS* 3.8 35.0 - - + -
183A ALA* 3.4 17.3 - - + +
381A TYR* 5.9 0.9 - - - -
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Residues in contact with ARG 30 (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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24A GLY* 3.8 18.5 + - - +
26A PRO* 3.5 38.5 - - + +
27A ASN* 3.1 16.1 - - - +
29A ALA* 1.3 75.5 - - + +
31A ALA* 1.3 56.8 + - - +
33A TYR* 3.2 14.6 + - - +
34A GLN* 2.7 39.1 + - - +
108A TYR* 4.7 1.4 + - - -
381A TYR* 3.6 62.9 - - + +
382A ASP* 4.7 2.8 + - - -
426A GLY 3.6 22.8 + - - -
428A GLU* 4.3 16.6 + - - +
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Residues in contact with ALA 31 (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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24A GLY 4.3 0.8 + - - -
25A PHE* 3.6 22.1 - - + +
27A ASN 2.9 17.9 + - - +
28A PRO* 3.4 6.1 - - + +
30A ARG* 1.3 76.9 - - - +
32A LEU* 1.3 54.4 + - - +
35A THR* 2.8 37.2 + - - -
118A TYR* 3.3 38.6 - - + +
176A ILE* 3.9 2.2 - - + -
177A PRO 4.0 2.7 - - - +
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Residues in contact with LEU 32 (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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28A PRO 2.9 16.8 + - - +
29A ALA 3.7 4.5 - - - +
30A ARG 3.2 0.2 - - - -
31A ALA* 1.3 77.6 - - - +
33A TYR* 1.3 62.7 + - - +
35A THR* 3.4 1.2 + - - -
36A VAL* 3.2 28.6 + - - +
60A ILE* 4.0 10.1 - - + -
70A TYR* 4.0 26.0 - - + -
72A VAL* 3.7 29.8 - - + -
176A ILE* 3.7 10.5 - - + +
178A GLY* 4.0 6.3 - - - -
179A ASP 4.1 5.6 - - - +
180A TRP* 4.0 48.7 - - + +
183A ALA* 4.3 2.0 - - + -
187A ILE* 4.0 10.1 - - + -
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Residues in contact with TYR 33 (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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29A ALA 3.1 16.4 + - - +
30A ARG* 3.2 23.3 + - - +
32A LEU* 1.3 78.1 - - - +
34A GLN* 1.3 68.9 + - - +
36A VAL* 3.5 3.8 + - - +
37A ARG* 2.7 62.5 + - + +
183A ALA* 4.6 4.0 - - + +
186A ARG* 4.2 23.1 - - + -
187A ILE* 3.8 25.7 - - + +
190A TYR* 4.4 6.5 - - + -
380A ILE* 3.4 16.6 - - + +
381A TYR* 3.6 27.1 - + - +
428A GLU* 2.6 35.4 + - - -
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Residues in contact with GLN 34 (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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24A GLY* 3.7 16.0 - - - +
25A PHE* 3.5 28.7 - - + -
30A ARG* 2.7 21.8 + - - +
31A ALA 3.8 2.9 - - - +
33A TYR* 1.3 89.7 - - + +
35A THR* 1.3 61.6 + - - +
37A ARG* 3.2 20.6 + - - +
38A GLU* 2.8 65.7 + - + +
41A GLU* 5.5 1.0 + - - -
107A MET* 6.1 0.4 - - - +
108A TYR* 3.6 26.9 + - + -
428A GLU* 4.2 4.0 - - - +
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Residues in contact with THR 35 (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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25A PHE* 3.9 5.3 - - - -
31A ALA 2.8 20.9 + - - -
32A LEU 3.7 2.7 - - - -
33A TYR 3.4 0.2 - - - -
34A GLN* 1.3 76.0 - - - +
36A VAL* 1.3 64.5 + - - +
38A GLU* 3.4 3.1 + - - +
39A LEU* 3.1 46.4 + - + +
72A VAL* 4.2 12.3 - - + -
115A ALA* 3.6 32.6 - - + +
174A ILE* 4.4 11.9 - - + -
176A ILE* 3.1 24.9 - - + +
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Residues in contact with VAL 36 (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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32A LEU 3.2 14.0 + - - +
33A TYR* 3.7 9.9 - - - +
35A THR* 1.3 81.3 - - - +
37A ARG* 1.3 64.3 + - - +
39A LEU* 3.3 2.1 + - - +
40A ILE* 3.0 44.2 + - + +
58A ILE* 4.6 9.9 - - + -
60A ILE* 3.7 29.2 - - + -
72A VAL* 3.8 23.8 - - + -
74A VAL* 4.9 0.8 - - - +
187A ILE* 4.4 20.9 - - + -
190A TYR* 4.8 6.5 - - + -
191A ILE* 5.0 1.6 - - + -
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Residues in contact with ARG 37 (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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33A TYR* 2.7 69.2 + - + +
34A GLN* 3.6 26.4 - - - +
36A VAL* 1.3 77.9 - - - +
38A GLU* 1.3 55.1 + - - +
40A ILE 3.7 0.2 - - - -
41A GLU* 2.8 47.3 + - - +
107A MET* 5.2 8.5 - - - +
190A TYR* 3.4 42.2 - - + +
377A ILE* 2.4 43.6 - - - +
378A PRO 2.9 14.8 + - - -
379A LEU* 4.9 2.6 - - - +
380A ILE* 4.0 2.6 - - - +
428A GLU* 3.7 11.5 + - - -
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Residues in contact with GLU 38 (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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25A PHE* 5.2 5.4 - - + -
34A GLN* 2.8 53.4 + - + +
35A THR* 3.9 6.1 - - - +
36A VAL 3.4 0.2 - - - -
37A ARG* 1.3 72.2 - - - +
39A LEU* 1.3 58.2 + - - +
41A GLU* 3.5 13.1 + - - +
42A ASN* 3.0 37.1 + - - +
106A GLY* 5.3 4.2 - - - -
107A MET 5.5 1.4 + - - -
108A TYR* 3.7 20.5 + - - +
111A GLY* 3.4 35.7 - - - +
112A VAL* 3.9 18.1 + - + -
114A ALA* 6.0 0.3 - - - +
115A ALA* 5.4 2.2 - - + -
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Residues in contact with LEU 39 (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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35A THR* 3.1 27.3 + - + +
36A VAL 3.9 1.1 - - - +
38A GLU* 1.3 74.2 - - + +
40A ILE* 1.3 65.5 + - - +
42A ASN* 3.4 7.2 + - + +
43A SER* 3.0 27.0 + - - -
72A VAL* 3.8 34.5 - - + +
74A VAL* 3.4 26.7 - - + -
90A PHE* 5.4 0.2 - - + -
112A VAL* 3.6 24.7 - - + -
172A VAL* 3.6 37.0 - - + +
174A ILE* 4.2 6.5 - - + -
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Residues in contact with ILE 40 (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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36A VAL* 3.0 38.1 + - + +
37A ARG 3.9 2.0 - - - +
39A LEU* 1.3 74.8 - - - +
41A GLU* 1.3 59.1 + - - +
43A SER* 3.2 6.6 + - - -
44A LEU* 2.9 48.5 + - + +
56A ILE* 4.9 3.8 - - + -
58A ILE* 3.6 37.2 - - + -
74A VAL* 4.5 6.5 - - + -
190A TYR* 3.9 28.7 - - + +
191A ILE* 4.2 10.1 - - + -
194A THR* 4.6 4.5 - - + -
203A PHE* 4.5 14.4 - - + -
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Residues in contact with GLU 41 (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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34A GLN* 5.5 0.5 + - - -
37A ARG* 2.8 49.0 + - - +
38A GLU* 3.9 13.8 - - - +
40A ILE* 1.3 78.5 - - + +
42A ASN* 1.3 63.8 + - - +
44A LEU* 3.3 5.5 + - + +
45A ASP* 3.0 28.3 + - - +
105A ARG* 3.9 20.8 - - + +
106A GLY* 3.5 11.4 - - - -
107A MET 4.9 0.2 + - - -
190A TYR* 2.6 27.4 + - - +
377A ILE* 2.8 34.8 - - + +
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Residues in contact with ASN 42 (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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1A CA 3.8 17.7 - - - -
38A GLU* 3.0 20.1 + - - +
39A LEU* 3.9 7.2 - - + +
41A GLU* 1.3 75.1 - - - +
43A SER* 1.3 58.8 + - - +
45A ASP* 3.3 7.3 + - - +
46A ALA* 2.8 30.9 + - - +
90A PHE* 5.4 4.6 - - - -
112A VAL* 3.8 36.5 + - - +
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Residues in contact with SER 43 (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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39A LEU 3.0 17.7 + - - -
40A ILE 3.2 4.7 + - - -
42A ASN* 1.3 78.1 - - - +
44A LEU* 1.3 51.9 + - - +
46A ALA* 3.3 3.1 + - - +
47A THR* 2.7 38.5 + - - +
56A ILE* 3.7 13.5 - - - -
74A VAL* 3.3 18.4 - - - +
76A ASP* 2.6 38.7 + - - -
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Residues in contact with LEU 44 (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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40A ILE* 2.9 28.8 + - + +
41A GLU* 3.8 4.9 - - + +
43A SER* 1.3 75.7 - - - +
45A ASP* 1.3 58.7 + - - +
47A THR* 3.0 13.0 + - - -
48A ASP* 3.0 24.9 + - - +
54A PRO* 3.8 21.5 - - + -
56A ILE* 3.4 23.6 - - + -
105A ARG* 3.4 36.1 - - - +
190A TYR* 5.8 0.2 - - - +
194A THR* 3.8 28.0 - - + -
198A THR* 4.4 12.1 - - + +
203A PHE* 4.3 9.4 - - + -
376A LYS 5.7 1.1 - - - +
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Residues in contact with ASP 45 (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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41A GLU 3.0 18.7 + - - +
42A ASN* 3.6 8.2 - - - +
44A LEU* 1.3 75.7 - - - +
46A ALA* 1.3 60.0 + - - +
49A VAL* 3.4 34.1 - - + +
50A HIS* 3.6 9.4 + - - -
103A GLN 5.4 0.4 - - - +
104A THR* 3.7 12.7 - - - -
105A ARG* 2.8 57.5 + - - +
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Residues in contact with ALA 46 (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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42A ASN 2.8 16.5 + - - +
43A SER* 3.7 8.7 - - - +
44A LEU 3.1 0.6 - - - -
45A ASP* 1.3 79.5 - - - +
47A THR* 1.3 58.3 + - - +
50A HIS* 3.7 14.9 - - - -
76A ASP* 4.8 6.3 - - - +
78A GLY* 3.2 9.8 - - - -
79A ILE* 3.0 34.1 + - + +
80A GLY 5.3 2.9 - - - +
170A THR* 6.1 1.3 - - - +
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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