Contacts of the strand formed by residues 37 - 44 (chain A) in PDB entry 3C0I
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 GLN 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ARG* 2.8 44.6 - - + +
29A CYS 3.3 5.8 - - - +
30A ILE* 4.5 4.7 - - + +
35A GLY 4.9 3.6 - - - +
36A GLN* 1.3 75.0 - - - +
38A PHE* 1.3 75.9 + - - +
93A PHE* 3.5 39.6 + - + +
95A ASP* 5.0 5.3 + - - +
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Residues in contact with PHE 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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12A TYR* 3.7 29.8 - + - -
28A ARG* 3.3 9.9 - - - +
29A CYS* 2.9 36.4 + - - -
31A ASN* 4.2 7.0 - - + -
36A GLN* 3.2 52.7 - - + -
37A GLN* 1.3 78.0 - - - +
39A ALA* 1.3 61.3 + - - +
78A LEU* 4.1 20.0 - - + -
90A VAL* 3.7 24.5 - - + -
91A PHE 3.6 13.5 - - - +
92A GLU* 4.7 4.5 - - - -
93A PHE* 3.6 10.5 - - - -
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Residues in contact with ALA 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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18A ILE* 5.9 0.9 - - + -
26A VAL* 4.4 9.6 - - + -
27A ARG 3.5 8.3 - - - +
28A ARG* 4.6 0.4 - - - +
38A PHE* 1.3 74.3 - - - +
40A VAL* 1.3 57.5 + - - +
41A LYS 4.1 0.2 - - - -
89A MET 3.7 0.3 - - - +
90A VAL* 3.6 0.9 - - - -
91A PHE* 2.6 43.9 + - + +
92A GLU 3.7 4.5 - - - +
93A PHE* 3.9 7.2 - - + +
338A 3AM 3.3 43.5 - - + +
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Residues in contact with VAL 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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8A PHE* 3.7 25.6 - - + -
14A LEU* 4.3 1.1 - - + -
25A VAL 3.6 2.3 - - - +
26A VAL* 3.3 5.3 - - - -
27A ARG* 2.8 59.7 + - + +
29A CYS* 4.0 24.4 - - + -
38A PHE 4.1 0.8 - - - -
39A ALA* 1.3 73.7 - - - +
41A LYS* 1.3 71.4 + - - +
42A ILE* 4.1 14.6 - - + -
88A TYR* 4.1 9.0 - - + -
89A MET 3.3 20.0 - - - +
90A VAL* 4.2 3.4 - - + -
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Residues in contact with LYS 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 SER* 4.0 17.0 - - - -
25A VAL 3.5 4.0 - - - +
26A VAL* 4.1 17.0 - - + +
39A ALA 4.1 0.6 + - - -
40A VAL* 1.3 72.1 - - - +
42A ILE* 1.3 61.2 + - - +
43A VAL* 4.1 10.1 - - + -
62A GLU* 2.6 33.3 + - - +
87A LEU 3.5 2.1 - - - +
88A TYR* 3.5 1.9 - - - -
89A MET* 2.8 57.7 + - + +
91A PHE* 3.9 25.0 - - + -
164A GLY* 4.6 4.8 - - - -
338A 3AM 3.0 39.6 + - - +
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Residues in contact with ILE 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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14A LEU* 4.5 10.5 - - + -
23A PHE 4.0 0.2 - - - +
24A SER* 3.2 4.9 - - - -
25A VAL* 2.8 45.5 + - + +
27A ARG* 3.9 32.5 - - + +
40A VAL* 4.1 13.7 - - + -
41A LYS* 1.3 75.0 - - - +
43A VAL* 1.3 63.8 + - - +
44A ASP 4.1 0.7 + - - -
86A MET* 4.1 22.0 - - + -
87A LEU 3.3 4.9 - - - +
88A TYR* 3.8 37.5 - - + -
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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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23A PHE* 3.6 12.1 - - + +
24A SER* 3.7 14.4 - - - -
41A LYS* 4.1 7.9 - - - -
42A ILE* 1.3 75.2 - - - +
44A ASP* 1.3 69.6 + - - +
45A VAL* 3.2 8.7 + - - +
48A PHE* 4.3 14.1 - - + -
59A LEU* 4.1 25.6 - - + -
62A GLU* 5.8 0.9 - - - +
86A MET* 3.4 6.3 - - - -
87A LEU* 2.7 46.6 + - + +
89A MET* 3.3 30.7 - - + -
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Residues in contact with ASP 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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23A PHE 3.2 14.5 + - - +
42A ILE* 4.1 1.0 + - - +
43A VAL* 1.3 68.1 - - - +
45A VAL* 1.3 64.1 + - - +
46A ALA* 3.3 20.8 + - - +
47A LYS* 3.3 49.3 + - + +
48A PHE* 3.1 23.4 + - - +
85A GLY 4.3 0.2 - - - +
86A MET* 3.7 29.7 - - + +
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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