Contacts of the strand formed by residues 37 - 44 (chain A) in PDB entry 5M61
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 PHE 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A MET* 3.6 9.9 - - - +
33A GLU 4.5 1.7 + - - -
34A SER* 3.4 18.0 + - - +
35A ASP 3.6 0.8 - - - -
36A LYS* 1.3 100.4 - - + +
38A ILE* 1.3 70.7 + - - +
39A CYS* 5.5 0.2 - - - -
52A ILE* 4.2 14.6 - - + -
53A ILE 3.2 14.6 - - - +
54A ASP* 3.8 25.1 - - + -
55A MET* 4.2 2.0 - - - -
73A MET* 3.6 37.4 - - + +
74A ASN 4.3 5.8 - - - -
76A ALA 4.8 3.1 - - - -
77A SER* 4.2 22.7 - - - -
78A LYS* 3.6 34.8 - - + -
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Residues in contact with ILE 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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13A LEU* 5.1 0.2 - - + -
15A LEU* 4.6 8.1 - - + -
30A LEU* 3.8 26.7 - - + -
31A THR 3.4 9.2 - - - +
32A MET* 3.9 26.7 - - + -
37A PHE* 1.3 79.5 - - - +
39A CYS* 1.3 64.7 + - - +
40A ILE* 4.0 15.0 - - + -
51A VAL 3.6 2.1 - - - +
52A ILE* 3.7 1.6 - - - +
53A ILE* 2.8 42.3 + - + +
55A MET* 3.9 19.9 - - + +
318A VAL* 4.1 5.4 - - + -
324A VAL* 3.7 30.5 - - + -
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Residues in contact with CYS 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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29A THR 3.6 1.6 - - - +
30A LEU* 3.3 3.5 - - - +
31A THR* 2.8 50.9 + - - +
37A PHE* 5.0 0.9 - - - -
38A ILE* 1.3 75.3 - - - +
40A ILE* 1.3 63.5 + - - +
41A ARG* 5.9 0.4 - - - -
50A VAL* 4.0 11.9 - - + -
51A VAL 3.3 3.4 - - - -
52A ILE* 4.1 12.8 - - - -
71A ALA* 4.3 7.0 - - + +
73A MET* 3.9 45.8 - - - -
80A ILE* 4.3 9.9 - - - -
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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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15A LEU* 4.4 3.4 - - + -
20A ILE* 3.7 39.5 - - + -
24A ASN* 3.6 32.1 - - + +
29A THR 3.3 3.8 - - - +
30A LEU* 3.8 22.7 - - + -
38A ILE* 4.0 4.3 - - + -
39A CYS* 1.3 78.8 - - - +
41A ARG* 1.3 71.8 - - - +
42A GLU* 3.7 9.9 + - + -
50A VAL* 3.4 3.0 - - - +
51A VAL* 2.8 43.1 + - + +
53A ILE* 4.0 22.2 - - + -
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Residues in contact with ARG 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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24A ASN* 3.5 22.9 - - - +
28A SER* 2.8 32.3 + - - -
29A THR* 2.8 38.4 + - + +
39A CYS 5.9 0.4 - - - -
40A ILE* 1.3 72.4 - - - +
42A GLU* 1.3 60.7 + - - +
49A GLN 3.4 7.2 - - - +
50A VAL* 4.7 2.0 - - + -
66A ILE* 3.9 25.3 - - + +
68A ALA 3.7 10.9 + - - -
69A ASP* 3.0 26.5 + - - +
70A SER* 3.7 24.6 - - - +
71A ALA* 4.0 15.5 - - + +
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Residues in contact with GLU 42 (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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19A GLY 4.2 0.7 - - - +
20A ILE* 3.6 13.3 - - - +
21A ASN* 2.9 32.4 + - - +
24A ASN* 3.2 23.8 + - - +
40A ILE* 3.7 11.6 + - + -
41A ARG* 1.3 76.2 - - - +
43A LYS* 1.3 58.7 + - - +
44A VAL* 4.0 8.2 - - + +
48A ALA* 3.5 3.7 - - - +
49A GLN* 2.8 38.1 + - - +
51A VAL* 3.7 8.5 - - + +
63A ARG* 2.7 49.3 + - - +
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Residues in contact with LYS 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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24A ASN* 4.6 3.7 + - - +
42A GLU* 1.3 74.3 - - - +
44A VAL* 1.3 61.1 + - - +
45A GLY 3.5 20.0 + - - +
46A GLU* 3.3 34.5 + - - +
47A GLN 3.5 12.1 - - - +
48A ALA* 4.2 9.6 - - + +
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Residues in contact with VAL 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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42A GLU* 4.0 9.6 + - + +
43A LYS* 1.3 73.5 - - - +
45A GLY* 1.3 62.6 + - - +
46A GLU 3.7 0.2 + - - -
47A GLN* 3.0 22.9 + - - +
49A GLN* 3.3 32.3 + - - +
63A ARG* 3.7 15.7 - - - +
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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