Contacts of the strand formed by residues 52 - 59 (chain A) in PDB entry 3MOK
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 ASP 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PHE* 3.7 7.9 - - - +
48A PRO* 3.8 1.8 - - - +
49A GLY* 2.9 29.1 + - - +
50A PRO* 3.8 0.9 - - - +
51A PHE* 1.3 89.4 + - - +
53A GLY* 1.3 60.1 + - - +
73A LEU 3.2 9.2 - - - +
74A HIS* 2.8 35.9 - - + +
75A TYR 4.2 2.7 + - - +
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Residues in contact with GLY 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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46A PHE* 3.8 3.0 - - - -
47A ASN 3.1 13.9 - - - -
48A PRO* 3.6 7.0 - - - -
52A ASP* 1.3 77.1 - - - +
54A SER* 1.3 64.8 + - - -
55A GLN 3.2 6.5 + - - -
72A ASP* 3.8 4.2 - - - -
73A LEU* 2.9 37.3 + - - +
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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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47A ASN* 2.8 21.0 + - - -
48A PRO* 4.1 5.4 - - - +
53A GLY* 1.3 71.9 - - - -
55A GLN* 1.3 65.1 + - - +
70A GLY* 3.3 4.5 - - - -
71A GLY 2.9 42.0 + - - -
72A ASP* 4.7 0.4 - - - +
73A LEU* 5.2 0.9 - - - -
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Residues in contact with GLN 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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45A GLY 4.5 0.2 - - - -
46A PHE* 3.5 8.6 - - - -
47A ASN* 2.9 55.6 + - + +
53A GLY* 4.2 2.7 - - - -
54A SER* 1.3 85.8 - - - +
56A TYR* 1.3 60.9 + - - +
68A ILE* 3.7 23.5 - - + +
69A ALA 3.1 8.5 - - - +
70A GLY* 4.8 2.7 - - - -
73A LEU* 4.7 2.2 - - - -
106A GLY* 3.5 2.6 - - - -
107A TYR* 2.8 51.2 + - + +
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Residues in contact with TYR 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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45A GLY* 3.5 14.8 - - - -
46A PHE* 3.5 48.9 - + + -
55A GLN* 1.3 73.4 - - - +
57A ALA* 1.3 67.7 + - - +
58A LEU* 3.7 29.0 - - + +
67A PHE* 3.9 22.5 - + - -
68A ILE* 3.5 1.5 - - - -
69A ALA* 2.8 37.4 + - + +
73A LEU* 4.2 13.2 - - + +
85A LEU* 4.7 2.7 - - + -
137A VAL* 4.0 16.6 - - + -
141A MET* 3.8 30.8 - - + +
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Residues in contact with ALA 57 (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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44A GLY* 3.5 1.7 - - - -
45A GLY* 2.8 31.5 + - - +
55A GLN 4.2 0.4 - - - -
56A TYR* 1.3 79.6 - - - +
58A LEU* 1.3 65.8 + - - +
67A PHE 3.3 10.8 - - - +
68A ILE* 4.0 6.1 - - + -
98A LEU* 4.0 15.3 - - + -
107A TYR* 3.6 38.6 - - + -
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Residues in contact with LEU 58 (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 PHE* 4.7 4.4 - - + -
43A THR* 3.5 19.3 - - - +
44A GLY 5.6 0.2 - - - -
45A GLY* 5.5 1.3 - - - +
56A TYR* 3.7 23.8 - - + +
57A ALA* 1.3 76.9 - - - +
59A LYS* 1.3 71.5 + - - +
66A ALA* 3.2 3.6 - - - +
67A PHE* 3.0 51.5 + - + -
98A LEU* 3.8 5.3 - - - +
141A MET* 3.6 42.4 - - + +
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Residues in contact with LYS 59 (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 PHE* 4.4 0.7 - - - -
38A VAL* 3.8 10.7 - - - +
40A GLY* 3.6 24.8 + - - -
42A ASN 3.7 25.1 - - - +
43A THR* 3.2 27.2 + - - +
58A LEU* 1.3 89.6 - - - +
60A SER* 1.3 87.9 + - - +
61A THR* 3.7 7.5 + - - +
63A SER 3.0 10.3 + - - -
64A ASP* 2.9 40.8 + - + +
65A ALA 3.5 11.2 - - - +
66A ALA* 4.0 4.0 - - + -
97A THR* 5.1 5.2 - - - -
98A LEU* 3.9 5.1 - - + +
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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