Contacts of the strand formed by residues 65 - 75 (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 ALA 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A TRP* 3.9 13.2 - - - +
26A TYR* 3.6 23.9 - - + -
27A PHE* 3.6 27.7 - - + +
59A LYS* 3.5 0.2 - - - -
60A SER* 2.8 28.6 + - - -
63A SER* 3.1 16.7 + - - +
64A ASP* 1.3 77.2 - - - +
66A ALA* 1.3 60.4 + - - +
95A GLY 3.5 7.4 - - - -
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Residues in contact with ALA 66 (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 TRP* 3.2 13.0 + - - +
27A PHE* 5.0 0.9 - - - -
58A LEU 3.2 14.4 - - - +
59A LYS* 4.0 5.2 - - + -
64A ASP 3.3 7.8 + - - +
65A ALA* 1.3 77.9 - - - +
67A PHE* 1.3 61.5 + - - +
95A GLY 2.9 30.7 + - - +
97A THR 4.0 4.7 - - - +
98A LEU* 3.8 18.2 - - + -
109A LEU* 3.7 19.5 - - + -
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Residues in contact with PHE 67 (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 TRP* 4.0 8.5 - + + -
27A PHE* 4.6 2.9 - + - -
56A TYR* 3.9 40.6 - + - -
57A ALA* 3.3 3.3 - - - +
58A LEU* 3.0 51.9 + - + +
66A ALA* 1.3 76.4 - - - +
68A ILE* 1.3 70.4 + - - +
69A ALA* 4.0 12.1 - - + -
92A ILE* 4.7 1.6 - - + -
93A ALA 3.2 13.0 - - - +
94A LEU* 3.5 18.2 - - + -
98A LEU* 4.2 0.9 - - - +
109A LEU* 4.5 1.8 - - - -
137A VAL* 4.1 12.8 - - + -
140A LEU* 3.4 57.0 - - + -
141A MET* 3.9 4.9 - - + -
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Residues in contact with ILE 68 (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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55A GLN* 3.7 30.3 - - + +
56A TYR 3.5 5.8 - - - +
57A ALA* 4.0 5.8 - - + -
67A PHE* 1.3 82.4 - - - +
69A ALA* 1.3 71.2 + - - +
70A GLY* 4.0 0.6 + - - +
91A SER* 3.9 1.9 + - - +
92A ILE* 3.5 2.5 - - - -
93A ALA* 2.9 40.8 + - + +
98A LEU* 3.8 12.6 - - + -
107A TYR* 3.7 7.9 - - + +
108A ALA* 3.6 43.7 - - - +
109A LEU* 3.8 13.7 - - + +
112A GLN* 5.8 1.3 - - - +
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Residues in contact with ALA 69 (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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55A GLN* 3.1 7.6 - - - +
56A TYR* 2.8 41.1 + - + +
67A PHE* 4.0 8.1 - - + -
68A ILE* 1.3 73.7 - - - +
70A GLY* 1.3 58.2 + - - +
73A LEU* 3.8 13.3 - - + +
89A LEU* 3.8 11.4 - - + -
91A SER 3.4 6.1 - - - -
92A ILE* 3.6 20.0 - - + -
137A VAL* 4.2 10.5 - - + -
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Residues in contact with GLY 70 (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 3.3 8.1 - - - -
55A GLN* 4.5 4.3 - - - -
68A ILE* 4.0 1.4 + - - +
69A ALA* 1.3 75.4 - - - +
71A GLY* 1.3 56.7 + - - -
73A LEU* 4.6 1.8 - - - -
88A LYS 4.5 0.2 - - - -
89A LEU* 3.7 7.2 - - - +
90A ASP* 2.8 26.1 + - - -
91A SER* 2.9 28.0 + - - -
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Residues in contact with GLY 71 (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* 2.9 32.2 + - - +
70A GLY* 1.3 73.7 - - - -
72A ASP* 1.3 61.3 + - - +
73A LEU* 4.0 3.0 - - - +
88A LYS* 3.2 10.1 - - - -
90A ASP* 3.6 20.2 - - - -
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Residues in contact with ASP 72 (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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53A GLY 3.8 6.0 - - - +
54A SER* 4.7 0.7 - - - +
71A GLY* 1.3 73.5 - - - +
73A LEU* 1.3 58.8 + - - +
74A HIS* 3.7 24.0 + - - -
87A GLY* 3.4 6.2 - - - -
88A LYS* 2.8 57.2 + - + +
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Residues in contact with LEU 73 (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* 4.3 11.9 - - + -
52A ASP* 3.2 4.1 - - - -
53A GLY 2.9 37.0 + - - +
55A GLN 4.7 1.6 - - - -
56A TYR* 4.2 13.9 - - + +
69A ALA* 3.8 41.7 - - + +
70A GLY 4.5 0.7 - - - +
71A GLY 4.6 3.8 - - - +
72A ASP* 1.3 75.9 + - - +
74A HIS* 1.3 70.3 + - - +
85A LEU* 4.1 10.5 - - + -
86A TRP 3.5 6.7 - - - +
88A LYS 3.3 22.7 - - - +
89A LEU* 4.4 8.1 - - + -
133A VAL* 3.8 28.3 - - + -
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Residues in contact with HIS 74 (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* 4.6 3.6 - - - -
51A PHE 3.7 2.0 - - - -
52A ASP* 2.8 31.2 - - + +
72A ASP* 3.7 38.0 + - - -
73A LEU* 1.3 79.9 - - - +
75A TYR* 1.3 61.5 + - - +
84A THR 3.5 0.7 - - - +
85A LEU* 3.2 7.3 - - - +
86A TRP* 2.9 88.1 + + + +
87A GLY* 4.1 1.3 - - - -
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Residues in contact with TYR 75 (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* 3.9 17.5 - + + -
51A PHE* 2.9 38.7 + + + +
52A ASP* 4.9 2.8 - - - +
74A HIS* 1.3 75.9 - - - +
76A THR* 1.3 62.7 + - - +
77A LEU* 3.4 40.4 + - + +
83A HIS* 3.3 50.7 + + - +
84A THR 3.3 13.9 - - - -
85A LEU* 3.9 17.0 - - + -
86A TRP* 5.0 0.2 - - - -
138A TYR* 5.0 15.5 - + - -
141A MET* 5.5 4.7 - - + -
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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