Contacts of the helix formed by residues 77 - 88 (chain A) in PDB entry 2CWJ
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 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ASP 3.8 2.4 + - - -
76A ILE* 1.3 83.3 - - - +
78A ARG* 1.3 51.0 + - - +
79A PHE* 2.2 31.1 + - - +
80A SER* 2.8 24.1 + - - -
81A GLU* 5.4 0.2 - - - -
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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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40A GLY 5.3 2.1 + - - -
41A PHE* 3.4 49.3 - - - +
73A ILE* 4.4 7.8 - - + +
75A ASP* 2.6 58.4 + - + +
76A ILE 2.9 7.7 + - - +
77A SER* 1.3 74.3 - - - +
79A PHE* 1.3 57.4 + - - +
80A SER 3.2 0.7 - - - -
81A GLU* 2.6 44.6 + - + +
82A PHE* 3.0 28.9 + - - +
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Residues in contact with PHE 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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73A ILE* 4.7 9.9 - - + -
75A ASP 4.9 1.0 + - - -
77A SER* 2.2 32.7 + - - +
78A ARG* 1.3 68.1 - - - +
80A SER* 1.3 49.3 + - - +
82A PHE* 3.4 7.5 + + - +
83A ASN* 2.4 70.2 + - - +
97A ARG* 3.7 28.9 - - - -
99A VAL* 4.1 20.6 - - + -
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Residues in contact with SER 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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77A SER* 2.8 14.7 + - - -
79A PHE* 1.3 74.6 - - - +
81A GLU* 1.3 77.8 + - - +
82A PHE 2.8 5.8 + - - -
83A ASN* 3.5 8.1 - - - +
84A GLU* 2.8 25.6 + - - +
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Residues in contact with GLU 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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41A PHE* 3.7 19.2 - - + +
42A LYS* 4.6 15.2 - - + +
45A ALA* 5.9 0.2 - - - -
77A SER 5.4 0.2 - - - -
78A ARG* 2.6 54.0 + - + +
79A PHE 3.6 0.2 - - - -
80A SER* 1.3 88.6 + - - +
82A PHE* 1.3 59.3 + - - +
84A GLU* 3.6 21.6 - - - +
85A VAL* 4.0 11.4 + - - +
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Residues in contact with PHE 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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45A ALA* 4.7 22.4 - - + -
49A LEU* 3.8 27.6 - - + -
71A VAL* 4.3 22.4 - - + -
73A ILE* 4.3 19.7 - - + -
78A ARG 3.0 19.7 + - - +
79A PHE* 3.7 8.3 - + - -
80A SER 2.8 1.4 + - - -
81A GLU* 1.3 75.6 - - - +
83A ASN* 1.3 77.6 + - - +
84A GLU 2.4 17.7 + - - -
85A VAL* 2.6 17.2 + - + +
86A TYR* 3.1 43.7 + + + -
97A ARG* 4.4 9.0 - - - -
99A VAL* 4.8 6.7 - - + -
111A LEU* 5.0 8.5 - - + -
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Residues in contact with ASN 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 PHE* 2.4 54.0 + - - +
80A SER* 3.5 8.8 - - - +
82A PHE* 1.3 80.5 - - - +
84A GLU* 1.3 64.0 + - - +
86A TYR* 3.5 15.2 + - - +
87A ARG* 3.9 4.5 + - - +
97A ARG* 3.4 14.5 + - - +
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Residues in contact with GLU 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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42A LYS* 3.2 34.5 + - - -
80A SER 2.8 15.3 + - - +
81A GLU* 3.6 12.8 - - - +
82A PHE 2.4 5.3 + - - -
83A ASN* 1.3 74.0 - - - +
85A VAL* 1.3 60.4 + - - +
86A TYR 3.0 1.0 + - - -
87A ARG* 2.8 61.3 + - - +
88A GLU* 4.3 5.9 - - - +
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Residues in contact with VAL 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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42A LYS* 3.3 39.3 - - + +
45A ALA* 3.6 24.0 - - + +
46A LYS* 3.6 17.0 - - + -
49A LEU* 4.2 3.8 - - + -
81A GLU 4.1 8.3 - - - +
82A PHE* 2.6 13.7 + - + +
84A GLU* 1.3 75.9 - - + +
86A TYR* 1.3 56.9 + - - +
87A ARG 3.3 0.3 + - - -
88A GLU* 3.6 18.9 + - - +
89A TYR* 2.8 39.9 - - + +
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Residues in contact with TYR 86 (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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49A LEU* 4.3 13.7 - - + -
69A VAL* 2.9 21.2 - - + +
71A VAL* 5.0 1.8 - - + -
82A PHE* 3.1 38.9 + + + -
83A ASN* 3.6 14.8 - - - +
84A GLU 3.0 1.0 + - - -
85A VAL* 1.3 77.6 - - - +
87A ARG* 1.3 68.9 + - - +
89A TYR* 3.2 12.0 + - - +
90A PHE* 3.3 40.3 + + + -
94A TYR* 4.3 12.1 - + - -
95A PRO* 2.8 39.0 + - + +
97A ARG* 4.0 24.4 - - + +
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Residues in contact with ARG 87 (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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83A ASN 3.9 4.1 + - - +
84A GLU* 2.8 46.6 + - - +
86A TYR* 1.3 76.1 - - - +
88A GLU* 1.3 81.7 + - + +
89A TYR 2.3 20.8 + - - -
90A PHE 2.9 25.7 + - - +
94A TYR* 4.2 15.7 - - - +
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Residues in contact with GLU 88 (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 LYS* 5.9 0.9 - - - +
46A LYS* 4.3 19.2 - - - -
53A LYS* 4.4 9.2 + - - +
84A GLU* 4.1 9.9 - - - +
85A VAL* 3.6 26.8 + - - +
86A TYR 3.5 0.2 - - - -
87A ARG* 1.3 99.9 + - + +
89A TYR* 1.3 72.7 + - + +
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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