Contacts of the helix formed by residues 75 - 83 (chain A) in PDB entry 5CDW
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 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PHE* 3.2 10.9 - - - +
74A ASN* 1.3 82.5 - - - +
76A LEU* 1.3 63.0 + - - +
77A ASN* 2.9 23.0 + - - -
78A GLU* 3.2 27.4 + - - +
79A LEU* 3.4 15.2 + - - +
66E TYR* 3.6 13.7 - - - +
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Residues in contact with LEU 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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75A SER* 1.3 75.0 - - - +
77A ASN* 1.3 60.4 + - - +
79A LEU* 3.4 11.6 - - + +
80A VAL* 3.3 21.0 + - - +
6E HIS* 5.0 11.9 - - + +
8E TRP* 4.3 16.8 - - - +
9E PHE* 4.9 9.9 - - + -
33E ILE* 4.1 34.8 - - + -
43E PHE* 5.0 10.1 - - + -
58E VAL* 4.5 14.1 - - + -
66E TYR* 3.4 48.2 - - + +
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Residues in contact with ASN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A SER* 2.9 25.7 + - - -
76A LEU* 1.3 76.3 + - - +
78A GLU* 1.3 68.2 + - - +
79A LEU 3.1 1.6 - - - -
80A VAL* 3.2 2.9 + - - +
81A ASP* 2.9 40.1 + - - +
6E HIS* 3.8 22.2 + - + -
8E TRP* 3.3 34.5 - - + -
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 3.9 14.1 - - + -
74A ASN* 3.4 36.3 + - - +
75A SER* 3.2 27.4 + - - +
77A ASN* 1.3 82.7 - - - +
79A LEU* 1.3 62.4 + - - +
81A ASP* 4.4 5.3 - - - +
82A TYR* 3.1 26.3 + - - +
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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
----------------------------------------------------------
73A PHE* 3.7 32.2 - - + -
75A SER 3.4 8.8 + - - +
76A LEU* 3.4 16.8 + - + +
77A ASN 3.1 0.4 - - - -
78A GLU* 1.3 76.9 - - - +
80A VAL* 1.3 72.2 + - + +
82A TYR* 3.9 0.5 - - - +
83A HIS* 3.1 48.4 + - + +
33E ILE* 5.6 2.7 - - + -
45E LEU* 5.0 12.6 - - + -
58E VAL* 4.4 14.8 - - + -
66E TYR* 4.0 7.2 - - + -
67E PHE* 3.8 32.5 - - - +
68E LEU* 4.1 11.0 - - + +
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 3.3 15.7 + - + +
77A ASN* 3.2 8.6 + - - +
79A LEU* 1.3 82.5 - - + +
81A ASP* 1.3 64.6 + - - +
83A HIS* 3.0 14.6 + - - +
84A ARG* 3.4 22.2 + - - +
96A LEU* 4.1 9.7 - - + +
8E TRP* 3.8 37.7 - - + +
31E PHE* 3.4 37.2 - - + -
33E ILE* 4.5 13.5 - - + -
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Residues in contact with ASP 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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77A ASN* 2.9 29.2 + - - +
78A GLU* 4.4 4.6 - - - +
80A VAL* 1.3 79.3 - - - +
82A TYR* 1.3 63.5 + - - +
84A ARG* 3.0 52.6 + - - +
85A SER* 4.1 4.3 + - - -
26B ARG* 5.8 7.2 + - - +
8E TRP* 5.0 4.5 - - - -
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Residues in contact with TYR 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* 5.1 10.0 - - + +
73A PHE* 3.4 34.5 - + + -
78A GLU 3.1 20.6 + - - +
79A LEU 3.9 1.6 - - - +
81A ASP* 1.3 78.1 - - - +
83A HIS* 1.3 69.4 + + - +
84A ARG 3.1 4.5 + - - -
85A SER* 3.4 6.0 + - - -
86A THR* 3.3 48.4 + - + +
90E ARG* 5.2 10.6 - - - +
91E ASN* 6.1 0.9 - - - +
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Residues in contact with HIS 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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73A PHE* 4.7 6.2 - + - -
79A LEU* 3.1 44.3 + - + +
80A VAL 3.0 10.0 + - - +
82A TYR* 1.3 89.7 - + - +
84A ARG* 1.3 55.1 + - - +
86A THR* 3.1 22.0 + - + +
87A SER 3.4 10.4 + - - -
88A VAL* 3.2 37.4 - - + +
95A PHE* 3.9 1.9 - - - -
96A LEU* 3.2 27.8 + - + +
45E LEU* 5.6 0.2 - - + -
68E LEU* 3.1 36.8 - - + +
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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