Contacts of the strand formed by residues 58 - 67 (chain M) in PDB entry 4UJ3
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 LYS 58 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9M ASP* 3.5 17.8 - - + +
10M TYR* 4.1 27.6 - - + -
54M GLN* 3.5 2.2 - - - +
55M VAL 2.9 31.3 + - - +
56M ASP 2.9 9.3 + - - +
57M GLY* 1.3 81.9 - - - +
59M THR* 1.3 61.6 + - - +
60M ILE* 3.6 4.1 + - + +
173M TYR* 3.1 28.9 - - + +
180M GLN* 6.3 1.1 - - - +
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Residues in contact with THR 59 (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 GLU 4.3 4.4 + - - +
8M TYR* 3.5 11.8 - - - +
9M ASP* 2.8 48.4 + - - +
10M TYR 3.5 6.1 + - - -
52M SER* 5.6 6.3 - - - -
53M ILE 3.4 5.6 - - - -
54M GLN* 3.0 31.6 - - - +
57M GLY 4.7 2.7 - - - +
58M LYS* 1.3 70.1 - - - +
60M ILE* 1.3 61.7 + - - +
61M LYS 4.0 0.7 + - - -
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Residues in contact with ILE 60 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M TYR* 3.4 42.4 - - + +
12M PHE* 3.9 28.5 - - + -
51M ARG 3.7 0.3 - - - +
52M SER* 3.0 4.0 - - - -
53M ILE* 2.5 54.2 + - + +
55M VAL* 4.1 19.1 - - + -
58M LYS* 4.0 13.7 - - + +
59M THR* 1.3 75.3 - - - +
61M LYS* 1.3 70.8 + - - +
62M ALA 3.7 1.3 + - - +
169M LEU* 4.4 18.2 - - + +
173M TYR* 4.9 9.4 - - + -
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Residues in contact with LYS 61 (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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6M ASP 5.8 2.0 + - - -
8M TYR* 3.5 39.6 - - + +
10M TYR 3.0 8.0 + - - +
11M LEU* 3.2 31.9 - - + +
12M PHE 3.1 24.6 + - - -
50M THR* 4.1 28.7 + - - -
51M ARG 4.5 1.8 - - - +
52M SER* 3.6 21.6 + - - +
59M THR 4.0 1.4 + - - -
60M ILE* 1.3 72.7 - - - +
62M ALA* 1.3 62.9 + - - +
63M GLN* 5.8 1.3 - - - +
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Residues in contact with ALA 62 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M PHE 3.7 4.7 - - - +
14M VAL* 5.5 0.2 - - + -
31M PHE* 4.6 6.7 - - + -
49M ALA 3.8 0.7 - - - +
50M THR* 3.2 29.7 - - - +
51M ARG 2.7 21.1 + - - +
60M ILE 3.7 1.2 + - - +
61M LYS* 1.3 73.0 - - - +
63M GLN* 1.3 59.6 + - - +
64M ILE* 3.8 19.8 + - + +
169M LEU* 3.8 35.9 - - + -
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Residues in contact with GLN 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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11M LEU* 3.8 30.3 - - + +
12M PHE 2.8 18.4 + - - +
13M LYS* 4.0 14.0 - - - +
14M VAL 2.8 24.6 + - - +
48M PHE* 3.5 36.8 - - + -
49M ALA 4.0 1.8 - - - -
50M THR* 4.0 6.9 - - + +
61M LYS* 5.8 1.6 - - - +
62M ALA* 1.3 70.3 - - - +
64M ILE* 1.3 62.1 + - - +
65M TRP* 3.2 29.5 + - - +
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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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14M VAL* 3.3 28.5 - - + +
16M LEU* 3.9 27.4 - - + -
28M LEU* 3.5 27.8 - - + +
31M PHE* 4.4 15.5 - - + -
32M THR* 4.7 1.8 - - + -
48M PHE* 2.9 24.3 - - - -
49M ALA 2.9 18.6 + - - +
50M THR* 5.6 0.2 - - - -
62M ALA* 4.0 19.5 - - + +
63M GLN* 1.3 72.7 - - - +
65M TRP* 1.3 60.9 + - - +
165M PHE* 3.9 32.1 - - + -
169M LEU* 5.8 0.9 - - + -
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Residues in contact with TRP 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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13M LYS* 3.4 35.8 - - + +
14M VAL 2.9 9.9 + - - +
15M VAL* 3.7 7.8 - - + -
16M LEU* 2.9 32.1 + - - +
46M VAL* 3.4 21.5 - - + -
47M GLU 3.3 7.2 - - - -
48M PHE* 3.6 31.6 - + + +
63M GLN* 3.2 44.9 + - - +
64M ILE* 1.3 73.8 - - - +
66M ASP* 1.3 59.6 + - - +
80M TYR* 3.5 18.4 - + + -
746O MET* 3.4 39.9 - - + -
750O PRO* 4.0 21.1 - - + -
753O LEU* 3.9 7.6 - - + -
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Residues in contact with ASP 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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16M LEU* 4.2 10.7 - - + +
24M LYS* 4.0 11.4 - - - +
25M SER* 2.9 34.5 + - - -
28M LEU* 3.6 27.1 - - + +
43M THR* 3.9 10.9 + - - +
46M VAL* 3.9 4.5 - - - +
47M GLU* 2.9 33.5 + - + +
65M TRP* 1.3 75.6 - - - +
67M THR* 1.3 81.7 + - - +
80M TYR* 3.5 4.9 - - - -
201M MG 3.2 15.7 - - - -
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Residues in contact with THR 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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16M LEU 4.5 4.4 + - - +
17M ILE* 6.1 0.4 - - + -
24M LYS* 3.4 12.7 - - - -
43M THR* 4.2 8.7 - - - -
45M GLY 3.1 19.9 + - - -
46M VAL* 4.0 6.6 - - - +
66M ASP* 1.3 93.2 + - - +
68M ALA* 1.3 74.0 + - - +
69M GLY 3.4 2.3 + - - -
71M GLU* 3.5 25.2 + - - +
80M TYR* 3.5 33.0 + - + +
200M GNP 3.5 2.6 + - - -
201M MG 3.7 0.2 - - - -
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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