Contacts of the strand formed by residues 45 - 51 (chain M) in PDB entry 5X6E
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 ILE 45 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44M GLY* 1.3 80.9 - - - +
46M THR* 1.3 66.8 + - - +
62M TYR* 4.3 13.2 - - + -
63M TYR 3.4 6.7 - - - +
64M LYS* 3.7 29.8 - - + -
87M VAL 3.8 0.2 - - - -
88M ILE* 2.8 40.4 + - + -
89M SER* 3.0 31.8 + - - +
92M ALA* 4.3 0.4 - - - +
154M TYR* 4.1 19.5 - - + +
166M LEU* 4.5 13.5 - - + -
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Residues in contact with THR 46 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M ILE* 4.4 10.3 - - + -
41M LEU* 3.4 27.0 - - + +
45M ILE* 1.3 78.9 - - - +
47M LYS* 1.3 57.5 + - - +
62M TYR* 3.4 6.9 - - - +
63M TYR* 2.6 63.4 + - - +
85M LEU* 3.7 18.0 - - + +
86M GLU 3.2 13.0 - - - +
87M VAL* 4.1 20.9 - - + -
88M ILE* 4.0 3.1 - - - +
92M ALA* 4.7 2.0 - - + -
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Residues in contact with LYS 47 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M THR* 1.3 74.1 - - - +
48M LEU* 1.3 60.3 + - - +
49M THR* 3.6 18.6 + - + +
57M ILE* 5.6 1.4 - - - +
59M ASN* 3.3 30.2 + - - +
61M GLN 3.6 11.9 - - - +
62M TYR* 4.3 11.7 - - + +
63M TYR* 4.6 0.4 - - - +
84M ASN 3.6 0.2 - - - +
85M LEU* 3.4 7.7 - - - +
86M GLU* 2.7 66.1 + - + +
88M ILE* 3.6 28.0 - - + +
173M GLU* 3.1 26.7 + - - +
176M TYR* 4.9 4.9 - - - -
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Residues in contact with LEU 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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29M PHE* 4.2 12.8 - - + -
47M LYS* 1.3 71.8 - - - +
49M THR* 1.3 60.2 + - - +
59M ASN* 3.9 1.1 - - - -
60M LEU* 3.0 54.1 + - + +
61M GLN* 3.0 26.9 + - - +
62M TYR* 5.0 0.2 - - - +
63M TYR* 4.1 20.6 - - + +
69M ILE* 4.9 5.8 - - + -
83M TYR* 3.8 21.1 - - + -
84M ASN 3.2 18.8 - - - +
85M LEU* 4.2 12.6 - - + -
128N LEU* 4.0 18.6 - - + -
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Residues in contact with THR 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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27M LEU* 5.4 0.2 - - - +
47M LYS* 3.6 28.7 - - + +
48M LEU* 1.3 75.5 - - - +
50M SER* 1.3 66.2 + - - +
51M ILE* 4.9 4.6 - - - +
57M ILE* 5.5 4.9 - - + -
58M MET 3.3 9.0 - - - -
59M ASN* 3.5 20.9 - - - +
60M LEU* 4.8 0.7 - - - -
83M TYR* 3.4 9.5 - - - +
84M ASN* 2.8 56.7 + - - +
86M GLU* 4.5 10.1 + - + +
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Residues in contact with SER 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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31M GLN* 4.0 5.6 - - - -
49M THR* 1.3 77.8 - - - +
51M ILE* 1.3 65.5 + - - +
52M SER 4.2 0.7 + - - -
56M THR 4.1 0.5 - - - +
57M ILE* 3.2 4.0 - - - +
58M MET* 2.8 40.8 + - - +
60M LEU* 4.7 4.7 - - - -
82M TYR 4.5 1.6 - - - -
83M TYR* 3.7 22.2 - - - -
132N ASN* 4.3 7.9 + - - -
220N LYS* 3.1 27.8 - - - +
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Residues in contact with ILE 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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29D T 3.7 25.1 - - + +
31M GLN* 3.1 37.3 + - - +
32M TRP* 4.5 14.1 - - + -
49M THR* 4.9 4.0 - - - +
50M SER* 1.3 82.5 + - - +
52M SER* 1.3 74.5 + - - +
55M GLY* 3.9 25.6 - - - +
56M THR 4.0 2.0 - - - -
57M ILE* 3.6 19.5 - - + -
84M ASN* 4.1 10.5 - - - +
220N LYS* 5.6 2.0 - - - -
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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