Contacts of the strand formed by residues 61 - 69 (chain M) in PDB entry 4M75
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 LEU 61 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L PRO* 4.5 1.6 - - - -
30M LEU* 3.9 18.4 - - + -
38M ILE* 4.9 0.7 - - + -
40M VAL* 5.0 2.0 - - + -
52M LEU* 4.3 7.2 - - + -
54M GLY 3.6 11.9 - - - +
55M TYR* 4.3 3.6 - - + +
59M MSE 2.9 24.2 - - + +
60M ASN* 1.3 73.6 - - - +
62M VAL* 1.3 65.3 + - - +
63M LEU* 4.0 10.1 + - + -
92M THR 3.8 0.2 - - - +
93M VAL* 3.3 4.1 - - - +
94M ILE* 2.7 78.7 + - + +
96M GLY 5.8 0.4 - - - +
99M LEU* 4.8 10.1 - - + -
102M LEU* 3.5 31.2 - - + -
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Residues in contact with VAL 62 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L LEU* 4.1 11.4 - - + -
8L PRO* 3.6 41.3 - - + -
11L VAL* 4.2 9.2 - - + -
53M LYS* 3.1 26.0 + - + -
54M GLY* 3.0 19.8 + - - +
61M LEU* 1.3 72.2 - - - +
63M LEU* 1.3 73.7 + - - +
91M LEU* 3.6 29.4 - - + -
92M THR 3.2 10.8 - - - +
93M VAL* 4.4 5.4 - - + -
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Residues in contact with LEU 63 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M ILE* 3.7 26.7 - - + -
40M VAL* 4.5 3.1 - - + -
48M VAL* 4.3 11.0 - - + -
49M ILE 4.6 0.2 - - - -
50M GLY* 3.9 20.0 - - - +
51M VAL 3.5 2.2 - - - +
52M LEU* 3.6 25.6 - - + -
53M LYS* 6.0 0.4 - - - -
61M LEU* 4.5 7.0 - - + +
62M VAL* 1.3 92.8 - - - +
64M ASP* 1.3 59.5 + - - +
66M THR* 3.1 17.9 - - + +
90M GLY 3.3 0.7 - - - +
91M LEU* 3.4 2.2 - - - -
92M THR* 3.0 40.1 + - - +
94M ILE* 3.8 30.1 - - + -
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Residues in contact with ASP 64 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M GLY* 3.3 1.6 - - - -
51M VAL* 2.9 46.4 + - + +
53M LYS* 5.5 9.2 - - + +
63M LEU* 1.3 73.2 - - - +
65M ASP* 1.3 100.1 + - - +
66M THR 3.0 2.1 + - - -
90M GLY* 4.0 7.2 - - - +
91M LEU* 4.3 23.1 - - + +
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Residues in contact with ASP 65 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37M LYS* 5.3 12.4 + - - -
49M ILE 3.9 2.8 - - - +
50M GLY* 4.0 3.8 - - - -
51M VAL* 5.2 7.4 - - + +
64M ASP* 1.3 90.9 + - - +
66M THR* 1.3 66.2 + - - +
67M VAL* 3.7 14.0 + - - +
88M LYS* 6.0 0.9 - - - -
89M LEU 3.9 5.4 + - - -
90M GLY* 3.7 6.3 + - - -
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Residues in contact with THR 66 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80L ILE* 6.5 0.2 - - - -
48M VAL* 4.1 11.0 - - + -
49M ILE 3.2 10.3 - - - -
63M LEU* 3.1 30.7 - - + +
64M ASP 4.0 0.2 - - - -
65M ASP* 1.3 80.7 - - - +
67M VAL* 1.3 59.7 + - - +
87M ARG 4.5 0.2 - - - -
88M LYS* 3.3 4.9 - - - +
89M LEU* 2.7 58.4 + - - +
90M GLY 3.3 4.9 - - - +
92M THR* 2.8 30.9 - - - +
94M ILE* 6.0 0.2 - - + -
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Residues in contact with VAL 67 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47M LEU 3.7 0.3 - - - +
48M VAL* 2.0 38.6 - - - +
49M ILE* 3.1 15.8 + - + +
65M ASP* 3.7 17.0 - - - +
66M THR* 1.3 78.1 - - - +
68M GLU* 1.3 57.3 - - - +
69M TYR* 3.8 27.4 - - + +
86M ALA* 3.9 12.6 - - + -
87M ARG 3.5 22.7 - - - +
88M LYS* 4.6 5.4 - - + +
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Residues in contact with GLU 68 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L VAL* 4.2 9.0 - - - +
29L GLU* 4.8 0.5 - - - +
80L ILE* 4.3 11.2 - - + +
46M LYS* 3.3 38.6 + - + -
47M LEU 3.5 6.3 - - - +
48M VAL* 4.0 8.7 - - + -
67M VAL* 1.3 75.0 - - - +
69M TYR* 1.3 70.9 + - - +
70M MSE 3.5 11.8 - - - +
86M ALA* 3.5 1.7 - - - -
87M ARG* 2.9 69.4 + - + +
89M LEU* 3.6 22.9 - - + +
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Residues in contact with TYR 69 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45M GLY 5.5 0.4 - - - -
46M LYS* 3.6 7.8 - - - +
47M LEU* 3.1 45.8 + - + +
49M ILE* 3.7 30.8 - - + +
67M VAL* 3.8 36.1 - - + +
68M GLU* 1.3 78.8 - - - +
70M MSE 1.3 73.8 + - - +
86M ALA* 3.8 28.7 - - + +
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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