Contacts of the strand formed by residues 41 - 48 (chain M) in PDB entry 3D29
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 THR 41 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36M PRO* 3.3 5.0 - - - +
37M VAL* 2.9 34.5 + - + +
39M ASP 3.7 0.6 - - - -
40M ASN* 1.3 86.5 + - - +
42M VAL* 1.3 73.4 + - - +
43M VAL* 4.3 5.6 - - + -
76M PRO* 3.0 30.4 - - + +
79M ILE* 3.6 22.3 - - + +
101M VAL* 3.7 24.0 - - + -
102M ALA 3.3 11.0 - - - +
103M GLY* 4.2 0.2 - - - -
178M ILE* 4.5 1.4 - - - +
184M LEU* 4.3 2.3 - - - +
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Residues in contact with VAL 42 (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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14M ILE* 3.8 26.7 - - + +
34M LEU* 4.1 26.0 - - + -
35M ILE 3.5 8.3 - - - +
36M PRO* 4.3 7.9 - - + -
41M THR* 1.3 78.9 - - - +
43M VAL* 1.3 64.9 + - - +
44M GLY 3.9 0.2 + - - -
100M ILE 3.9 1.4 - - - +
102M ALA* 2.7 38.4 + - - +
176M ALA* 4.1 14.6 - - + -
178M ILE* 3.2 28.5 - - + -
184M LEU* 3.9 11.9 - - + -
186M PHE* 4.8 1.6 - - + -
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Residues in contact with VAL 43 (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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33M ARG 3.6 1.9 - - - +
35M ILE* 2.6 48.2 + - + +
37M VAL* 4.0 19.1 - - + -
41M THR* 4.3 5.8 - - + -
42M VAL* 1.3 77.0 - - - +
44M GLY* 1.3 57.5 - - - +
45M ILE* 4.0 14.4 - - + -
59M LEU* 4.1 13.7 - - + -
79M ILE* 4.2 16.4 - - + -
83M LEU* 4.1 11.4 - - + -
99M ILE* 3.5 30.7 - - + -
100M ILE 3.6 4.5 - - - +
101M VAL* 4.3 8.5 - - + -
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Residues in contact with GLY 44 (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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3M VAL* 4.0 12.1 - - - +
14M ILE* 3.7 11.3 - - - +
33M ARG 3.4 7.4 - - - -
34M LEU* 3.8 16.6 - - - -
43M VAL* 1.3 69.5 - - - +
45M ILE* 1.3 64.5 + - - +
98M ALA 4.0 0.3 - - - +
99M ILE* 3.5 5.5 - - - +
100M ILE* 2.9 35.5 + - - -
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Residues in contact with ILE 45 (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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3M VAL* 3.7 4.3 - - - +
33M ARG* 3.0 37.3 + - - +
35M ILE* 4.1 13.0 - - + -
43M VAL* 4.0 19.5 - - + +
44M GLY* 1.3 80.0 - - - +
46M SER* 1.3 66.0 + - - +
52M MET* 3.8 34.8 - - + +
55M ILE* 3.8 33.2 - - + -
56M GLU 5.3 0.2 - - - +
59M LEU* 5.1 1.3 - - + -
97M ASN* 3.6 34.5 - - + +
98M ALA 3.8 2.7 - - - +
99M ILE* 4.2 7.9 - - + -
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Residues in contact with SER 46 (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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-1M GLY* 3.7 2.7 - - - -
1M THR 3.0 26.0 - - - -
3M VAL* 3.8 2.7 - - - +
33M ARG* 3.7 4.5 - - - +
45M ILE* 1.3 75.2 - - - +
47M GLY* 1.3 61.0 + - - +
49M ILE* 6.2 0.2 - - - -
97M ASN* 3.1 30.2 + - - +
98M ALA* 3.0 27.9 + - - +
127M THR* 3.0 24.4 + - - -
128M GLY* 5.2 0.4 + - - -
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Residues in contact with GLY 47 (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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-2M THR* 3.2 12.9 - - - -
-1M GLY 2.9 36.3 + - - +
46M SER* 1.3 76.6 - - - +
48M ASP* 1.3 66.1 + - - -
49M ILE* 3.2 4.0 + - - +
52M MET* 5.7 0.2 - - - +
96M TRP* 3.4 11.4 - - - -
97M ASN* 4.3 1.3 - - - -
98M ALA 5.1 0.2 - - - -
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Residues in contact with ASP 48 (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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-7M GLN* 4.9 1.1 - - - -
-6M GLN 4.4 1.2 - - - +
-5M PRO* 3.1 10.7 - - + +
-4M ILE* 2.9 32.9 + - - +
-3M VAL 3.3 7.7 + - - +
-2M THR* 4.1 4.1 - - - +
47M GLY* 1.3 68.3 - - - -
49M ILE* 1.3 61.0 + - - +
50M SER* 2.6 31.0 + - - -
51M ASP* 3.0 22.7 + - + +
52M MET* 2.9 13.0 + - - +
96M TRP* 2.8 31.6 + - + +
97M ASN* 2.9 20.1 + - - -
91N LYS* 3.7 6.2 + - - -
116N GLY* 5.4 0.7 - - - -
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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