Contacts of the helix formed by residues 73 - 79 (chain A) in PDB entry 5E1O
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 GLY 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ASP* 4.7 0.2 - - - -
70A ALA 3.0 11.5 + - - -
71A GLY 3.1 1.6 + - - -
72A ILE* 1.3 80.4 - - - +
74A ARG* 1.3 59.8 + - - +
75A ILE 3.2 2.9 - - - -
76A THR* 3.7 9.2 - - - -
77A LYS* 2.8 33.8 + - - +
89A MET* 3.5 19.5 - - - -
103A TYR* 3.7 2.7 - - - -
104A LEU* 3.6 4.5 - - - +
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Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 4.0 23.8 - - + -
30A MET* 4.9 8.7 - - + +
31A LEU* 3.7 24.7 - - - +
38A SER* 2.9 38.3 + - - +
41A ASP* 2.8 32.9 + - - +
42A ILE* 3.9 8.6 - - + +
70A ALA 4.2 2.8 + - - -
72A ILE* 3.7 2.5 - - + +
73A GLY* 1.3 75.4 - - - +
75A ILE* 1.3 75.3 + - - +
77A LYS* 3.6 0.7 + - - +
78A ARG* 3.3 29.4 + - + +
103A TYR* 3.8 17.7 - - + +
135A GLN* 3.6 2.6 - - - +
136A TRP* 3.5 12.3 - - - -
301A SAH 2.8 43.4 + - - +
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE* 4.2 10.1 - - + -
67A ASP* 3.8 12.5 + - - +
70A ALA 5.3 0.8 + - - +
73A GLY* 3.2 0.4 - - - -
74A ARG* 1.3 95.4 - - - +
76A THR* 1.3 65.0 + - - +
79A LEU* 2.9 49.0 + - + -
80A LEU* 3.1 15.9 + - + -
133A TRP* 3.9 16.4 - - + +
135A GLN* 3.4 36.8 - - + +
301A SAH 3.4 30.4 + - - +
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Residues in contact with THR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ASP* 2.6 35.0 + - - +
73A GLY* 3.2 13.0 + - - -
75A ILE* 1.3 79.9 - - - +
77A LYS* 1.3 58.4 + - - +
80A LEU* 4.1 7.9 - - - -
81A LEU* 2.9 54.7 + - + +
87A VAL* 3.7 17.5 - - + +
89A MET* 3.6 14.4 - - - +
104A LEU* 4.2 4.3 - - + -
111A VAL* 4.0 13.7 - - + -
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLY 2.8 20.3 + - - +
74A ARG 3.9 2.5 - - - +
76A THR* 1.3 75.7 - - - +
78A ARG* 1.3 103.0 + - + +
81A LEU* 4.3 8.3 - - + +
82A PRO* 3.5 14.9 - - - +
103A TYR* 3.2 51.3 + - + +
104A LEU* 3.6 30.8 + - + +
105A GLY* 5.1 1.2 - - - -
107A GLU* 6.0 3.6 - - + +
95B ASP* 5.2 3.4 - - - -
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A SER* 5.8 1.1 - - - +
42A ILE* 4.0 23.6 - - + -
46A ARG* 2.9 24.6 + - - -
74A ARG* 3.3 19.3 + - + +
77A LYS* 1.3 118.1 + - + +
79A LEU* 1.3 61.0 + - - +
82A PRO* 3.8 10.7 - - - +
103A TYR* 4.3 7.2 + - - +
305A UNX 4.1 15.0 - - - -
21B LYS* 3.4 42.5 + - - +
22B GLN* 4.2 25.3 - - + +
23B ILE 5.7 0.8 + - - -
95B ASP* 3.8 17.4 + - - -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE* 4.3 13.0 - - + +
45A SER* 4.0 7.0 - - - -
46A ARG* 3.5 46.5 + - + +
49A LEU* 4.4 5.2 - - + -
75A ILE* 2.9 31.5 + - + +
78A ARG* 1.3 80.9 - - - +
80A LEU* 1.3 74.4 + - + +
82A PRO* 3.6 7.8 - - - +
83A LEU* 3.5 28.6 - - + +
133A TRP* 3.8 36.6 - - + -
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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