Contacts of the strand formed by residues 45 - 58 (chain M) in PDB entry 5DM6
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 45 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38M LYS* 4.1 28.3 - - + -
39M VAL 3.3 11.2 - - - +
40M ARG* 4.6 7.7 - - + +
43M ASN 3.9 4.7 + - - -
44M ARG* 1.3 80.8 + - - +
46M ARG* 1.3 65.1 + - - +
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Residues in contact with ARG 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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116H ARG* 5.3 0.7 - - - +
119H ARG* 5.3 2.8 - - - +
38M LYS* 3.4 7.1 - - - +
39M VAL* 2.9 37.3 + - + +
41M GLU* 3.0 38.2 + - + +
44M ARG* 3.1 50.3 + - - +
45M THR* 1.3 76.5 - - - +
47M SER* 1.3 81.1 + - - +
48M GLN* 4.7 9.6 - - + +
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Residues in contact with SER 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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36M ASP* 4.6 12.6 + - - +
37M THR 3.5 10.2 + - - -
38M LYS* 4.5 2.1 - - - +
45M THR 5.5 0.2 - - - -
46M ARG* 1.3 83.9 - - - +
48M GLN* 1.3 60.2 + - - +
49M ALA* 5.5 0.4 - - - +
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Residues in contact with GLN 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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116H ARG* 4.3 0.8 + - - -
132H GLU* 4.3 14.3 + - - +
133H VAL 3.4 23.8 + - - +
134H LEU* 3.5 40.0 - - - +
36M ASP* 4.0 1.1 - - - +
37M THR* 2.8 42.4 + - - +
38M LYS* 4.9 0.2 - - - +
39M VAL* 3.9 20.1 - - + +
46M ARG* 4.1 11.3 + - - -
47M SER* 1.3 74.6 - - - +
49M ALA* 1.3 66.8 + - - +
50M PHE* 4.2 1.3 - - - -
79M ARG* 4.1 12.0 + - - -
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Residues in contact with ALA 49 (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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34M ARG* 4.8 11.6 - - + -
35M VAL 3.3 6.1 - - - +
36M ASP* 3.3 23.8 - - - +
47M SER 5.5 0.2 - - - +
48M GLN* 1.3 85.2 - - - +
50M PHE* 1.3 63.7 + - - +
51M GLU* 3.8 4.4 + - - +
70M LYS* 6.0 1.7 - - - -
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Residues in contact with PHE 50 (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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134H LEU* 3.7 29.2 - - + -
34M ARG* 3.6 0.2 - - - -
35M VAL* 2.8 42.7 + - + +
37M THR* 4.5 1.5 - - + +
48M GLN* 4.2 1.7 + - - -
49M ALA* 1.3 72.9 - - - +
51M GLU* 1.3 59.3 + - - +
68M VAL* 3.4 44.4 - - + -
70M LYS* 3.2 37.2 - - + +
77M VAL* 3.5 28.0 - - + -
79M ARG* 3.8 36.6 - - + +
81M PHE* 4.4 14.6 - + + -
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Residues in contact with GLU 51 (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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32M THR* 4.5 8.1 - - + +
33M VAL 3.2 17.9 - - - +
34M ARG* 3.4 34.3 + - + +
49M ALA 3.8 3.8 + - - +
50M PHE* 1.3 78.8 - - - +
52M GLY* 1.3 60.8 + - - +
68M VAL* 4.3 2.0 - - - -
70M LYS* 3.6 24.5 - - - +
94M VAL* 4.3 20.8 - - - +
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Residues in contact with GLY 52 (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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32M THR* 3.2 11.7 - - - +
33M VAL* 2.9 33.3 + - - +
51M GLU* 1.3 76.0 - - - +
53M VAL* 1.3 64.1 + - - -
54M VAL 3.9 0.2 + - - -
68M VAL* 3.6 12.2 - - - +
69M ARG 3.5 12.6 - - - -
70M LYS* 4.7 0.9 - - - -
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Residues in contact with VAL 53 (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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30M GLY* 4.1 14.8 - - - +
31M ASP 3.9 2.9 - - - -
32M THR* 4.2 15.3 - - + +
52M GLY* 1.3 74.4 - - - -
54M VAL* 1.3 76.9 + - - +
55M ILE* 3.5 14.7 + - + -
68M VAL* 3.2 3.9 - - - -
69M ARG* 2.9 38.4 + - + +
104M LEU* 4.4 7.2 - - + -
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Residues in contact with VAL 54 (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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27M PHE* 4.1 13.7 - - + -
28M ARG 3.7 17.7 - - - +
29M PRO* 3.4 9.6 - - + +
30M GLY 2.7 29.3 + - - -
31M ASP 3.0 15.4 + - - +
33M VAL* 3.5 30.3 - - + -
53M VAL* 1.3 72.9 - - - +
55M ILE* 1.3 58.4 + - - +
56M ALA 4.3 9.2 - - - +
57M ILE* 4.3 11.2 - - + -
66M PHE* 3.9 24.2 - - + -
67M THR 3.5 4.9 - - - +
68M VAL* 4.5 4.7 - - + -
104M LEU* 3.1 4.3 - - - +
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Residues in contact with ILE 55 (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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29M PRO* 4.7 2.7 - - - -
53M VAL* 4.1 17.5 - - + +
54M VAL* 1.3 75.5 - - - +
56M ALA* 1.3 61.6 + - + +
67M THR* 2.9 36.8 + - + +
69M ARG* 4.0 20.6 - - + -
78M GLU* 3.9 26.5 - - - +
102M ALA 3.8 1.0 - - - +
103M LYS* 2.3 37.0 - - - +
104M LEU* 3.6 32.3 - - + +
105M TYR* 4.9 8.1 - - + -
107M GLY* 6.2 1.3 - - - -
108M LYS* 4.5 10.1 - - + -
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Residues in contact with ALA 56 (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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29M PRO* 4.6 1.6 - - - -
54M VAL* 3.7 2.5 - - - +
55M ILE* 1.3 86.3 - - + +
57M ILE* 1.3 66.6 + - - +
58M ASN* 4.3 6.2 - - - +
65M SER 4.0 0.2 - - - +
66M PHE* 3.3 3.5 - - - +
67M THR* 2.9 36.7 + - + +
102M ALA 4.2 5.6 - - - -
103M LYS* 4.0 26.2 - - + +
105M TYR* 4.4 10.8 - - + +
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Residues in contact with ILE 57 (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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27M PHE* 3.6 33.0 - - + +
28M ARG* 4.9 4.0 - - - +
29M PRO* 3.5 33.5 - - + +
54M VAL* 4.3 5.8 - - + -
56M ALA* 1.3 77.8 - - - +
58M ASN* 1.3 82.7 + - - +
64M LYS* 3.9 17.9 - - - +
65M SER 3.3 12.1 - - - +
66M PHE* 4.2 2.9 - - + -
83M PHE* 3.9 23.6 - - + -
102M ALA 4.7 0.8 + - - +
103M LYS* 3.5 9.0 + - - -
2846X G 4.9 2.1 + - - -
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Residues in contact with ASN 58 (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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56M ALA* 4.3 6.1 - - - +
57M ILE* 1.3 102.7 + - - +
59M GLY* 1.3 64.8 + - - +
63M ARG 4.9 0.2 - - - -
64M LYS* 3.2 4.7 - - - +
65M SER* 2.9 48.4 + - - +
103M LYS* 3.1 29.5 - - - +
105M TYR* 5.2 1.7 + - - -
201M MG 3.4 21.8 - - - -
2684X U 5.3 4.3 - - - +
2685X G 5.2 3.8 + - - -
2719X G 4.9 1.0 + - - +
2720X U 5.6 0.9 + - - -
2846X G 4.7 6.7 + - - -
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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