Contacts of the strand formed by residues 37 - 45 (chain A) in PDB entry 5D8F
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 GLU 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.5 30.6 - - + +
30A THR 3.4 2.5 - - - -
31A LYS* 3.4 36.7 - - + +
35A GLY 4.0 2.8 + - - +
36A HIS* 1.3 73.9 - - - +
38A VAL* 1.3 57.7 + - - +
39A ARG 4.3 0.2 - - - -
55A TRP* 3.2 7.3 - - - -
56A ASP* 2.6 45.3 + - - +
60A ASN* 4.8 12.2 + - - +
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG 3.8 0.7 - - - +
29A VAL* 3.5 2.6 - - - -
30A THR* 2.9 51.1 + - + +
32A THR* 5.5 0.4 - - + -
37A GLU* 1.3 74.8 - - - +
39A ARG* 1.3 65.3 + - - +
40A THR* 4.1 3.1 + - - +
53A SER* 3.7 30.1 - - - +
54A VAL 3.3 15.3 - - - +
55A TRP* 3.5 40.2 - - + +
78A PHE* 6.1 6.1 - - + -
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Residues in contact with ARG 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A THR* 3.0 40.8 + - - -
27A GLY 3.2 15.7 + - - -
28A ARG* 3.1 11.4 - - - +
29A VAL* 3.3 31.6 - - + +
37A GLU 4.3 0.6 - - - -
38A VAL* 1.3 74.4 - - - +
40A THR* 1.3 61.1 + - - +
41A CYS* 4.3 5.0 - - - -
53A SER* 3.6 0.2 - - - -
54A VAL* 2.9 50.3 + - + +
59A GLY 3.1 25.4 + - - +
60A ASN* 3.7 21.8 + - - +
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Residues in contact with THR 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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27A GLY* 3.0 25.3 - - - -
28A ARG 2.9 13.4 + - - -
38A VAL* 4.1 4.5 + - - +
39A ARG* 1.3 73.4 - - - +
41A CYS* 1.3 67.7 + - - +
51A ASN* 3.9 30.1 - - + +
52A ILE 3.4 10.5 - - - +
53A SER* 3.0 21.4 + - - +
78A PHE* 4.3 16.0 - - + -
79A LYS* 5.4 1.8 + - - -
83A THR* 5.2 1.3 - - + +
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Residues in contact with CYS 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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23A VAL* 4.8 2.2 - - + -
25A GLU 3.1 13.7 - - - +
26A THR* 3.4 25.6 - - - -
27A GLY* 5.2 0.2 - - - -
39A ARG* 4.3 17.0 - - - -
40A THR* 1.3 76.0 - - - +
42A LYS* 1.3 59.1 + - - +
43A VAL* 4.0 7.4 - - + -
51A ASN* 3.3 8.7 - - - +
52A ILE* 2.9 44.5 + - + +
54A VAL* 4.4 12.1 - - - -
62A ILE* 4.3 20.0 - - + -
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Residues in contact with LYS 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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24A LEU* 2.8 46.4 + - + +
25A GLU* 2.9 58.1 + - + +
27A GLY* 5.2 0.4 - - - -
41A CYS* 1.3 71.2 - - - +
43A VAL* 1.3 56.3 + - - +
49A SER* 3.7 30.7 + - - -
50A ILE 3.7 5.8 - - - +
51A ASN* 4.2 13.2 - - - +
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Residues in contact with VAL 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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21A PHE* 3.5 39.5 - - + -
22A ILE 3.2 10.1 - - - +
23A VAL* 3.9 18.8 - - + -
24A LEU* 4.1 1.3 - - - +
41A CYS* 4.0 4.9 - - + -
42A LYS* 1.3 79.5 - - - +
44A ALA* 1.3 66.8 + - - +
49A SER* 3.2 3.3 - - - -
50A ILE* 2.9 55.0 + - + +
52A ILE* 3.7 29.4 - - + -
84A LEU* 4.8 0.9 - - + -
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Residues in contact with ALA 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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7A VAL* 4.5 3.8 - - - -
21A PHE* 3.5 7.9 - - - +
22A ILE* 2.9 40.6 + - + +
24A LEU* 3.7 26.5 - - + -
43A VAL* 1.3 78.9 - - - +
45A ASP* 1.3 64.0 + - - +
48A GLY 3.3 15.9 - - - +
49A SER* 3.7 7.9 - - - +
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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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6A PHE* 3.4 19.3 - - + -
7A VAL* 2.9 31.7 + - + +
19A LEU* 4.1 5.5 - - - +
20A ILE 4.2 13.8 - - - +
21A PHE* 5.1 0.2 - - - -
22A ILE* 5.3 1.6 - - - -
44A ALA* 1.3 76.9 - - - +
46A LYS* 1.3 66.6 + - - +
47A THR* 2.7 27.9 + - - -
48A GLY* 2.9 26.6 + - - +
200A PEG 5.8 4.3 - - - +
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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