Contacts of the strand formed by residues 40 - 45 (chain A) in PDB entry 1MCA
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 ALA 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A CYS* 4.6 12.1 - - + -
12A CYS* 3.6 37.0 - - + +
15A PHE* 4.8 5.2 - - + -
30A ARG* 4.0 0.2 - - - +
31A ILE* 3.1 39.2 + - + +
32A THR 5.4 0.2 + - - -
36A CYS* 5.2 1.3 - - - -
38A LYS 4.0 1.6 + - - -
39A GLU* 1.3 74.9 - - - +
41A VAL* 1.3 67.3 + - - +
42A ILE* 4.9 5.4 - - + +
53A ALA 5.1 0.2 - - - -
55A PRO* 5.4 0.4 - - - -
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Residues in contact with VAL 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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28A TYR* 3.4 26.2 - - + +
29A ARG 3.6 3.8 - - - +
30A ARG* 4.2 9.0 - - + +
39A GLU* 3.0 30.3 - - + +
40A ALA* 1.3 78.2 - - - +
42A ILE* 1.3 68.8 + - - +
52A CYS* 3.6 4.3 - - - +
53A ALA 2.9 38.0 + - - +
55A PRO* 4.1 16.2 - - + -
60A VAL* 5.9 0.7 - - + -
64A MET* 3.1 36.8 - - + -
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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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12A CYS* 3.9 20.9 - - - -
29A ARG* 2.8 87.8 + - + +
31A ILE* 4.5 23.6 - - + -
40A ALA* 5.2 6.1 - - + +
41A VAL* 1.3 81.1 - - - +
43A PHE* 1.3 74.9 + - - +
50A GLU* 5.0 4.5 - - + -
51A ILE 3.7 11.7 - - - +
52A CYS* 4.0 4.9 - - - -
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Residues in contact with PHE 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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20A ILE* 6.5 0.4 - - + -
25A LEU* 3.3 38.4 - - + -
27A SER 4.1 4.9 - - - -
28A TYR* 3.5 16.8 - + - -
41A VAL 4.4 0.2 + - - -
42A ILE* 1.3 85.4 - - - +
44A LYS* 1.3 62.3 + - - +
45A THR* 4.1 5.7 + - + +
49A LYS 4.1 0.5 - - - +
50A GLU* 3.4 3.1 - - - +
51A ILE* 2.8 41.6 + - + +
52A CYS 5.3 0.6 - - - -
53A ALA* 5.1 8.7 - - + -
59A TRP* 6.4 1.8 - + - -
60A VAL* 5.2 1.8 - - + -
63A SER* 4.1 16.8 - - - -
64A MET* 3.1 58.8 - - + -
67A LEU* 4.6 5.6 - - + -
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Residues in contact with LYS 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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25A LEU* 3.9 4.0 - - - +
26A ALA* 3.1 20.8 + - + -
27A SER* 3.1 36.6 + - - +
29A ARG* 4.3 28.0 - - - +
42A ILE* 4.1 0.8 + - + +
43A PHE* 1.3 74.2 - - - +
45A THR* 1.3 68.3 + - - +
48A ALA* 5.7 4.3 - - - +
49A LYS 3.6 7.4 - - - +
50A GLU* 3.6 31.2 - - + +
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Residues in contact with THR 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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20A ILE* 6.3 3.4 - - + -
24A ARG* 3.4 19.3 - - + +
25A LEU* 4.1 15.0 - - + +
26A ALA* 4.4 5.2 - - - +
43A PHE* 4.8 6.5 - - + +
44A LYS* 1.3 84.8 - - - +
46A ILE* 1.3 61.0 + - - +
47A VAL* 3.1 15.4 + - - +
48A ALA* 3.6 8.7 + - - -
49A LYS* 2.9 39.7 + - + +
51A ILE* 5.2 11.9 - - + -
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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