Contacts of the strand formed by residues 30 - 39 (chain M) in PDB entry 4EMG
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 ARG 30 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25L LYS* 3.0 41.7 - - - +
28L GLY 5.7 1.4 - - - +
29L ASP 5.6 0.2 - - - +
86L ILE* 5.0 11.3 - - - +
87L LEU* 4.4 8.5 - - - -
25M LYS* 3.5 5.7 - - - +
26M LEU* 3.0 55.2 + - + +
27M ARG 4.5 4.6 + - - +
28M GLY 3.2 12.1 + - - +
29M ASP* 1.3 81.4 - - - +
31M GLU* 1.3 72.1 + - - +
32M LEU* 5.0 0.7 - - + -
52M GLU* 2.6 49.4 + - + +
53M ILE 3.7 0.9 - - - -
54M VAL* 3.4 23.5 - - + +
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Residues in contact with GLU 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H LYS* 4.0 12.5 - - - +
23M TYR* 2.6 42.2 + - + +
24M VAL 3.3 6.5 - - - +
25M LYS* 4.0 11.3 - - + +
26M LEU 4.6 0.2 - - - +
30M ARG* 1.3 80.3 - - - +
32M LEU* 1.3 74.5 + - - +
33M ASN* 5.4 0.7 - - - +
52M GLU* 3.4 0.7 - - - +
53M ILE* 2.9 50.7 + - + +
55M THR* 4.0 22.0 - - + +
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Residues in contact with LEU 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87L LEU* 4.3 6.1 - - + -
22M VAL 4.5 0.2 - - - -
23M TYR* 3.5 2.9 - - - -
24M VAL* 2.8 38.7 + - + +
26M LEU* 4.0 28.7 - - + -
30M ARG* 5.0 1.1 - - + -
31M GLU* 1.3 83.9 - - - +
33M ASN* 1.3 73.2 + - - +
47M LEU* 3.9 18.6 - - + -
50M ALA* 5.7 0.4 - - + -
51M GLU 3.2 6.5 - - - +
52M GLU* 3.7 29.2 - - + -
78M LEU* 3.9 17.3 - - + -
80M VAL* 3.5 34.3 - - + -
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Residues in contact with ASN 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M ILE* 4.9 8.7 - - + +
22M VAL 3.3 7.3 - - - +
23M TYR* 3.8 26.4 - - - +
31M GLU* 5.4 0.6 - - - +
32M LEU* 1.3 80.6 + - - +
34M GLY* 1.3 58.1 + - - +
47M LEU* 4.6 2.5 - - - -
49M ASP 4.0 1.2 - - - +
50M ALA* 3.1 5.0 - - - +
51M GLU* 2.8 54.8 + - + +
53M ILE* 4.0 17.0 - - - +
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Residues in contact with GLY 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M ILE* 3.2 12.0 - - - +
22M VAL* 2.8 34.2 + - - +
33M ASN* 1.3 75.9 - - - +
35M ARG* 1.3 63.0 + - - -
36M LEU 3.6 0.5 + - - -
47M LEU* 4.0 15.4 - - - +
48M GLY 3.5 9.9 - - - -
49M ASP 4.0 4.9 - - - -
50M ALA* 4.1 1.6 - - - -
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Residues in contact with ARG 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M ASP* 3.0 49.2 + - - +
20M GLU* 3.4 6.1 + - - +
21M ILE* 3.7 32.6 - - + +
34M GLY* 1.3 71.9 - - - -
36M LEU* 1.3 59.8 + - - +
37M HIS* 3.1 33.6 + - + +
47M LEU* 3.4 2.6 - - - -
48M GLY 2.7 41.1 + - - +
49M ASP* 5.6 4.7 - - + +
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Residues in contact with LEU 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M VAL* 3.3 40.2 - - + +
17M SER* 3.6 26.7 - - - +
18M LEU* 3.7 14.5 - - + +
19M ASP* 2.7 30.7 + - - -
20M GLU 2.9 11.1 + - - +
22M VAL* 4.3 13.2 - - + -
34M GLY 3.6 2.6 + - - -
35M ARG* 1.3 67.2 - - - +
37M HIS* 1.3 60.4 + - - +
38M ALA 3.6 24.7 - - - +
39M TYR* 4.4 1.8 - - + -
45M MSE 3.8 27.8 - - + -
46M VAL 3.9 2.2 - - - +
47M LEU* 4.0 11.0 - - + -
88M ILE* 6.0 1.1 - - + -
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Residues in contact with HIS 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L GLU* 4.7 4.7 - - - +
18M LEU* 3.9 10.1 - - - +
19M ASP* 4.2 20.8 + - - +
35M ARG* 3.1 27.2 + - + -
36M LEU* 1.3 74.1 - - - +
38M ALA* 1.3 64.1 + - + +
46M VAL* 2.9 21.5 + - + +
47M LEU 4.4 0.2 - - - -
48M GLY* 3.6 35.9 + - - -
77M MSE 3.7 22.2 - - + -
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Residues in contact with ALA 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L GLU* 3.3 32.1 - - + +
10L PRO* 3.8 17.9 - - + -
18M LEU* 4.1 7.7 - - - +
36M LEU* 3.5 6.9 - - - +
37M HIS* 1.3 83.8 - - + +
39M TYR* 1.3 64.4 + - - +
45M MSE 3.1 4.2 - - - -
46M VAL* 2.9 32.2 + - + -
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Residues in contact with TYR 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L GLU* 5.1 2.4 - - - +
10L PRO* 3.4 10.6 - - - +
11M LEU* 4.7 13.4 + - + +
14M VAL* 3.7 26.0 - - + -
15M ARG* 3.1 43.4 - - - +
18M LEU* 3.5 34.5 - - + -
36M LEU* 4.4 3.4 - - + -
38M ALA* 1.3 78.5 - - - +
40M ASP* 1.3 76.9 + - - +
43M LEU* 5.0 6.3 - - + -
44M ASN 3.0 13.5 - - - +
45M MSE 4.0 12.6 - - + -
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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