Contacts of the helix formed by residues 79 - 85 (chain A) in PDB entry 2CMF
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 SER 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLY 3.4 4.9 + - - -
78A PHE* 1.3 76.4 - - - +
80A GLY* 1.3 64.8 + - - +
81A SER 3.0 1.6 + - - -
82A GLU* 4.4 4.7 - - - +
83A MET* 3.1 31.1 + - - +
431A VAL* 3.8 22.9 - - - +
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Residues in contact with GLY 80 (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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78A PHE* 3.3 20.9 - - - -
79A SER* 1.3 81.3 + - - +
81A SER* 1.3 57.6 + - - +
83A MET* 3.7 4.1 - - - +
84A TRP* 3.2 22.0 + - - -
431A VAL* 3.6 9.1 - - - +
432A TRP* 3.0 26.8 - - - -
442A TYR* 3.2 6.3 + - - -
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Residues in contact with SER 81 (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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72A ASP* 3.3 26.2 + - - +
75A PHE* 3.6 28.0 + - - +
78A PHE* 3.4 7.2 + - - -
79A SER 3.1 0.4 - - - -
80A GLY* 1.3 77.1 - - - +
82A GLU* 1.3 68.3 + - - +
83A MET 3.2 2.2 - - - -
84A TRP* 3.2 23.0 + - - +
85A ASN* 3.7 10.4 + - - -
334A TYR* 3.5 13.5 - - - -
432A TRP* 3.5 10.0 - - - -
1536A F11 4.9 1.5 - - - -
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Residues in contact with GLU 82 (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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71A VAL* 5.6 0.5 - - - +
72A ASP 3.8 6.9 - - - +
73A GLU* 5.1 3.3 - - - +
75A PHE 4.7 2.9 - - - +
76A PRO* 4.5 5.3 - - - +
77A GLY* 2.6 42.9 + - - +
78A PHE 2.9 15.5 + - - +
79A SER* 4.4 2.9 - - - +
81A SER* 1.3 76.1 + - - +
83A MET* 1.3 60.7 + - - +
84A TRP 3.0 7.6 + - - -
85A ASN* 3.1 43.6 + - + +
87A ASN* 6.1 0.3 - - - +
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Residues in contact with MET 83 (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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79A SER* 3.1 17.2 + - - +
80A GLY* 3.7 5.6 - - - +
82A GLU* 1.3 77.0 - - - +
84A TRP* 1.3 91.9 + - + +
85A ASN 4.6 0.7 - - - -
127A LEU* 3.5 25.7 - - - +
128A ASP 5.2 1.2 + - - -
129A VAL* 3.6 41.5 - - + +
442A TYR* 3.2 33.0 - - + +
445A GLU* 4.2 7.0 - - + +
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Residues in contact with TRP 84 (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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69A GLN* 5.0 4.0 - - - +
80A GLY 3.2 17.7 + - - -
81A SER 3.2 8.2 + - - +
82A GLU 3.0 1.0 - - - -
83A MET* 1.3 104.3 - - + +
85A ASN* 1.3 66.1 - - - +
86A PRO* 3.9 1.0 - - - +
122A SER* 5.3 3.2 + - - +
123A GLY* 5.1 5.5 + - - -
124A SER* 4.9 2.1 + - - -
127A LEU* 3.4 19.2 - - + +
129A VAL* 4.6 6.3 - - + -
130A TYR* 3.6 28.3 - + - -
441A GLY* 3.6 27.8 - - - -
442A TYR* 3.2 32.6 + + - -
444A ILE* 4.2 8.3 - - + -
1536A F11 3.1 79.7 - + + +
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Residues in contact with ASN 85 (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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70A TYR 4.8 0.5 - - - +
71A VAL* 3.2 15.4 - - + +
72A ASP* 2.7 51.8 + - - +
81A SER* 3.7 6.3 + - - -
82A GLU* 3.1 49.1 + - + +
84A TRP* 1.3 78.8 - - - +
86A PRO* 1.3 75.1 - - + +
87A ASN* 3.3 1.9 + - - +
127A LEU* 3.1 18.0 - - - +
1536A F11 5.8 0.9 - - - -
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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