Contacts of the strand formed by residues 62 - 70 (chain M) in PDB entry 1MWA
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 PHE 62 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10I THR* 3.9 24.0 - - + -
94I THR* 4.2 2.9 - - + -
96I GLN* 3.2 22.0 - - + -
29M GLN 3.7 10.6 + - - -
30M PHE* 3.3 36.6 + - + +
31M HIS* 3.2 39.0 - + - -
33M PRO* 3.3 28.5 - - + -
54M MET* 3.2 43.3 - - + -
56M PHE* 3.7 19.7 - + + -
60M TRP 3.9 0.2 - - - -
61M SER* 1.3 76.9 + - - +
63M TYR* 1.3 65.3 + - - +
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Residues in contact with TYR 63 (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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27I TYR* 4.5 8.0 + - - -
26M TYR* 3.9 24.5 - + + -
27M VAL 3.4 5.4 - - - -
28M THR* 3.6 26.0 - - + -
30M PHE* 4.2 1.6 - - - -
53M ASP 5.1 0.5 - - - +
54M MET* 3.2 6.2 - - - +
55M SER* 3.0 45.9 + - - +
56M PHE 3.4 4.4 + - - -
57M SER* 3.2 42.0 - - - -
61M SER* 4.1 2.9 - - - +
62M PHE* 1.3 79.3 - - - +
64M ILE* 1.3 61.9 + - - +
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Residues in contact with ILE 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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25M CYS 4.1 0.5 - - - +
26M TYR* 4.0 3.6 - - - -
27M VAL* 3.1 32.6 + - + +
30M PHE* 4.4 13.4 - - + -
35M ILE* 4.2 16.4 - - + -
37M ILE* 4.2 18.4 - - + -
51M MET* 3.0 33.7 - - + -
52M SER* 3.7 8.7 - - - +
53M ASP 2.8 30.7 - - - +
54M MET* 4.0 15.9 - - + -
63M TYR* 1.3 76.8 - - - +
65M LEU* 1.3 63.6 + - - +
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Residues in contact with LEU 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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235I PRO* 3.8 25.4 - - + +
236I ALA 4.6 2.7 - - - +
237I GLY* 4.9 7.4 - - - -
10M TYR* 4.0 2.2 - - - +
24M ASN* 3.0 31.9 - - - +
25M CYS 3.0 36.6 - - - +
26M TYR* 3.4 25.1 - - + +
37M ILE* 5.3 0.9 - - - -
51M MET* 3.2 22.6 - - - +
52M SER* 3.4 19.1 + - - +
64M ILE* 1.3 80.8 - - - +
66M ALA* 1.3 61.4 + - - +
67M HIS* 4.7 7.1 + - + +
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Residues in contact with ALA 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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24M ASN* 3.4 3.8 - - - +
25M CYS* 2.8 54.0 + - + +
37M ILE* 4.2 26.2 - - + +
38M GLN* 6.0 0.4 - - - +
39M MET* 3.4 14.6 - - + +
49M VAL* 4.9 5.6 - - + +
50M GLU 4.1 5.2 - - - +
51M MET* 4.1 6.1 - - - -
65M LEU* 1.3 76.1 - - - +
67M HIS* 1.3 60.5 + - - +
80M CYS* 5.4 0.7 - - - -
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Residues in contact with HIS 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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237I GLY* 5.9 5.8 + - - -
12M ARG* 5.5 4.0 - - - -
22M ILE* 4.1 18.8 - - + -
23M LEU 3.2 16.8 - - - +
24M ASN* 3.7 14.8 + - - +
39M MET* 3.3 3.8 - - - -
49M VAL 4.7 0.2 + - - -
50M GLU* 3.0 53.3 + - + +
51M MET* 3.8 19.6 - - - -
52M SER 4.7 1.8 + - - -
65M LEU* 4.7 6.6 + - + +
66M ALA* 1.3 76.8 - - - +
68M THR* 1.3 59.7 + - - +
69M GLU 4.4 0.6 + - - -
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Residues in contact with THR 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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22M ILE* 4.8 2.7 - - - -
23M LEU* 3.1 28.4 + - - +
39M MET* 2.9 35.0 - - + +
46M ILE* 3.7 20.9 - - + +
48M LYS 2.9 26.9 - - - +
49M VAL* 3.3 26.5 - - + -
67M HIS* 1.3 73.8 - - - +
69M GLU* 1.3 72.2 + - - +
70M PHE* 5.3 0.5 - - - +
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Residues in contact with GLU 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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20M PRO* 5.4 5.0 - - - +
21M ASN 3.0 25.7 - - - +
22M ILE* 3.6 16.7 - - + +
46M ILE* 4.9 4.3 - - - +
48M LYS 5.1 1.2 + - - -
50M GLU* 5.9 2.7 - - - +
67M HIS* 4.4 0.8 + - - -
68M THR* 1.3 82.3 - - - +
70M PHE* 1.3 64.5 + - - +
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Residues in contact with PHE 70 (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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11M SER* 4.3 12.1 - - - -
20M PRO* 3.2 3.5 - - - +
21M ASN* 2.5 52.5 + - + -
22M ILE 3.0 25.1 - - - -
23M LEU* 3.0 48.2 - - + -
46M ILE* 5.6 2.0 - - + -
68M THR* 4.0 2.5 - - - +
69M GLU* 1.3 78.9 + - - +
71M THR* 1.3 56.8 + - - +
72M PRO* 4.3 20.6 - - + -
78M TYR* 3.4 44.0 - + + +
95M TRP* 4.6 8.1 - + - -
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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