Contacts of the strand formed by residues 47 - 56 (chain A) in PDB entry 1MMA
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 TYR 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A TRP* 3.6 44.6 - - + -
37A TYR 2.8 15.5 - - - +
38A ASN* 4.3 10.5 - - - -
44A ARG* 2.8 28.1 + - - +
45A ASP* 3.5 23.4 + - - -
46A SER* 1.3 78.0 + - - +
48A GLU* 1.3 71.8 + - - +
78A ASN* 3.2 25.1 + - - -
99A GLU* 4.5 17.0 + - - +
100A PRO* 3.6 21.7 - - + +
103A PHE* 6.5 1.3 - + - -
107A ARG* 5.7 2.3 + - - -
669A ASP* 4.8 2.9 + - - +
673A LEU* 4.6 10.7 - - + +
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Residues in contact with GLU 48 (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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36A TRP* 3.1 10.8 - - - -
37A TYR* 2.3 66.5 + - + +
39A PRO* 3.7 22.2 - - + -
46A SER 5.1 0.2 - - - +
47A TYR* 1.3 81.4 - - - +
49A CYS* 1.3 60.7 + - - +
65A SER* 3.3 23.7 + - - -
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Residues in contact with CYS 49 (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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34A TYR* 3.4 41.7 - - - -
35A ILE 2.8 7.9 - - - +
36A TRP* 3.5 24.9 - - + -
37A TYR* 3.1 12.3 + - - -
48A GLU* 1.3 80.2 + - - +
50A GLY* 1.3 60.5 + - - +
63A LYS 4.5 1.7 - - - +
65A SER* 4.9 3.8 + - - -
80A ARG* 3.7 20.0 - - - +
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Residues in contact with GLY 50 (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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34A TYR* 3.2 7.3 - - - -
35A ILE* 2.7 35.7 + - - +
37A TYR* 3.6 9.9 - - - -
49A CYS* 1.3 76.9 - - - +
51A GLU* 1.3 63.6 + - - -
62A PHE* 4.1 7.2 - - - -
63A LYS 3.6 16.4 - - - -
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A LYS* 2.9 42.2 + - - +
33A ARG 3.6 4.9 - - - -
34A TYR* 3.0 32.6 + - + -
50A GLY* 1.3 73.2 - - - -
52A ILE* 1.3 52.5 - - - +
53A VAL* 3.4 4.8 + - + +
62A PHE* 2.8 28.4 - - - +
63A LYS* 2.9 38.5 + - + +
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Residues in contact with ILE 52 (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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32A LYS* 3.2 18.7 + - - -
33A ARG* 2.8 42.8 + - + +
34A TYR 4.1 0.2 - - - +
35A ILE* 3.3 42.2 - - + -
51A GLU* 1.3 70.2 - - - +
53A VAL* 1.3 62.2 + - - +
54A SER* 3.2 32.3 - - - +
55A GLU* 4.3 4.5 - - - +
60A PHE* 4.1 22.4 - - + -
61A THR 3.5 5.8 - - - +
62A PHE* 3.9 4.0 - - + +
79A GLN* 3.9 15.5 - - - +
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Residues in contact with VAL 53 (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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32A LYS* 4.9 3.1 - - - +
51A GLU* 4.0 4.9 - - + +
52A ILE* 1.3 71.7 - - - +
54A SER* 1.3 66.0 + - - +
61A THR* 2.7 18.9 + - + +
62A PHE 3.8 20.4 - - - +
63A LYS* 4.3 10.3 - - + -
69A ASP* 4.7 10.3 - - - +
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Residues in contact with SER 54 (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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52A ILE* 3.2 12.9 - - - +
53A VAL* 1.3 84.6 + - - +
55A GLU* 1.3 77.8 + - - +
56A THR* 5.5 0.4 - - - -
61A THR* 2.8 38.5 + - - -
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Residues in contact with GLU 55 (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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52A ILE* 5.1 3.6 - - - +
54A SER* 1.3 95.5 + - - +
56A THR* 1.3 80.7 + - - +
57A SER* 5.3 0.4 - - - +
59A SER 3.5 13.5 - - - +
60A PHE* 3.6 24.7 - - + +
753A ARG* 5.8 3.1 + - - -
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Residues in contact with THR 56 (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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54A SER 5.5 0.4 - - - -
55A GLU* 1.3 90.6 - - - +
57A SER* 1.3 55.1 + - - +
58A ASP* 2.5 19.8 + - - +
59A SER* 2.6 43.7 + - - +
61A THR* 5.9 2.9 - - - +
71A GLN* 4.9 6.1 + - - +
74A LYS* 5.6 0.5 - - - +
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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