Contacts of the helix formed by residues 73 - 83 (chain X) in PDB entry 1M6E
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 LEU 73 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36X THR* 3.3 30.1 - - + +
37X GLU* 4.7 3.1 - - - +
40X ILE* 3.1 36.1 - - + -
55X ILE* 3.4 27.6 - - + -
69X ALA* 3.3 19.3 - - + +
70X VAL* 4.5 2.7 - - - +
72X GLU* 1.3 86.5 - - - +
74X ILE* 1.3 61.1 + - - +
75X LYS 2.9 0.9 - - - -
76X THR* 3.4 4.5 + - - +
77X VAL* 2.8 37.4 + - - +
142X PHE* 3.3 28.5 - - + -
144X HIS* 5.0 3.8 - - + -
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Residues in contact with ILE 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X ILE* 4.0 8.5 - - + -
70X VAL* 3.3 24.2 + - + +
71X THR* 4.9 3.6 - - - -
73X LEU* 1.3 73.4 - - - +
75X LYS* 1.3 69.4 + - - +
78X GLU* 3.0 28.4 + - + +
92X TYR* 3.2 62.5 + - + -
94X ILE* 3.6 26.0 - - + -
118X ASP 3.7 15.9 - - - +
121X CYS* 3.9 11.0 - - - -
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Residues in contact with LYS 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71X THR* 3.5 23.9 + - - +
72X GLU* 3.5 32.3 - - - +
73X LEU 2.9 1.2 - - - +
74X ILE* 1.3 77.0 - - - +
76X THR* 1.3 58.8 + - - +
78X GLU* 2.7 31.4 + - - +
79X GLU* 3.1 17.5 + - + +
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Residues in contact with THR 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X LYS* 5.0 5.2 + - - -
37X GLU* 2.4 32.8 + - - +
40X ILE* 5.0 9.9 - - + -
41X THR* 4.6 9.6 - - - +
72X GLU 3.3 13.6 + - - -
73X LEU* 3.4 9.1 + - - -
75X LYS* 1.3 82.1 - - - +
77X VAL* 1.3 62.7 + - - +
79X GLU* 3.1 21.1 + - + +
80X LEU* 3.1 27.7 + - + +
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Residues in contact with VAL 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40X ILE* 3.4 31.6 - - + -
44X TYR* 3.8 33.2 - - + +
53X LEU* 3.7 19.3 - - + -
73X LEU 2.8 24.6 + - - +
74X ILE 4.1 0.4 - - - +
76X THR* 1.3 72.0 - - + +
78X GLU* 1.3 65.8 + - - +
80X LEU* 3.0 19.2 + - - +
81X ARG* 3.0 12.8 + - - +
90X PRO* 4.4 5.4 - - + -
92X TYR* 3.2 24.5 - - + +
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Residues in contact with GLU 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74X ILE* 3.0 18.8 + - + +
75X LYS* 2.7 15.6 + - - +
77X VAL* 1.3 75.4 - - - +
79X GLU* 1.3 61.6 + - - +
80X LEU 3.1 1.6 + - - -
81X ARG* 3.3 10.2 + - - +
82X LYS* 3.2 32.1 + - + +
89X SER* 2.8 39.5 + - - -
90X PRO* 4.1 0.7 - - - +
92X TYR* 2.3 31.7 + - + +
118X ASP* 5.0 4.8 - - + +
119X GLY* 4.6 8.2 - - - -
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Residues in contact with GLU 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75X LYS* 3.1 16.4 + - + +
76X THR* 3.1 14.5 + - - +
78X GLU* 1.3 75.7 - - - +
80X LEU* 1.3 60.3 + - - +
82X LYS* 4.2 4.8 - - - +
83X LYS* 3.0 50.3 + - + +
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Residues in contact with LEU 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40X ILE 4.4 1.6 - - - +
41X THR* 4.0 34.3 - - + +
44X TYR* 3.4 37.7 - - + -
45X SER 5.5 0.4 - - - +
76X THR* 3.1 25.0 + - + +
77X VAL* 3.0 10.3 + - - +
79X GLU* 1.3 76.3 - - + +
81X ARG* 1.3 56.2 + - - +
82X LYS 2.7 15.9 + - - -
83X LYS* 2.9 11.8 + - + -
84X MET 2.8 30.2 + - - +
85X GLY* 6.1 0.2 - - - -
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Residues in contact with ARG 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X TYR* 3.0 25.5 - - + +
77X VAL* 3.0 11.3 + - + +
78X GLU* 3.8 10.4 + - - +
80X LEU* 1.3 78.1 - - - +
82X LYS* 1.3 95.0 + - - +
84X MET* 3.8 4.9 + - - +
86X ARG 2.6 35.1 - - - +
87X GLU* 2.7 29.2 + - - -
88X ASN* 3.2 28.1 + - - +
89X SER* 2.7 37.7 + - - +
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Residues in contact with LYS 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78X GLU* 3.2 19.1 + - + +
79X GLU* 4.6 4.5 - - - +
80X LEU 2.7 5.3 + - - -
81X ARG* 1.3 110.9 - - - +
83X LYS* 1.3 54.6 + - + +
84X MET* 2.6 32.2 + - - +
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Residues in contact with LYS 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79X GLU* 3.0 55.7 + - + +
80X LEU* 2.9 13.0 + - + +
82X LYS* 1.3 74.3 - - + +
84X MET* 1.3 67.2 + - - +
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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