Contacts of the strand formed by residues 66 - 74 (chain A) in PDB entry 1C88
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 TYR 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.7 20.6 - - + -
35A ALA* 3.3 23.3 - - - +
40A ASN* 3.5 30.5 - - + +
43A ARG* 2.8 45.5 + - + -
44A ASN* 2.7 30.6 + - - -
51A PRO* 3.0 38.2 - - + +
56A ARG* 3.7 15.0 - - - +
59A LEU* 3.6 5.1 - - - +
64A ASN* 3.1 17.4 + - - +
65A ASP* 1.3 78.0 + - - +
67A ILE* 1.3 70.6 + - - +
68A ASN* 3.6 12.2 - - - -
94A HIS* 4.6 1.6 + - - -
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Residues in contact with ILE 67 (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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43A ARG* 5.6 1.8 - - - +
51A PRO* 4.0 2.1 - - - +
56A ARG* 5.0 1.7 - - - +
57A ILE* 3.3 24.7 + - + +
59A LEU* 3.8 20.4 - - + -
65A ASP 3.5 1.0 + - - -
66A TYR* 1.3 91.0 - - - +
68A ASN* 1.3 69.9 + - + +
69A ALA* 2.8 25.2 + - + +
84A THR* 4.3 4.5 - - - +
85A GLN* 6.3 0.9 - - + -
91A THR* 5.1 5.4 - - + +
94A HIS* 3.6 31.6 - - + +
95A PHE* 3.7 21.3 - - + +
98A MET* 4.0 22.9 - - + -
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Residues in contact with ASN 68 (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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43A ARG 3.9 3.7 + - - +
44A ASN* 3.0 26.4 + - - +
49A VAL 2.9 26.3 + - - +
51A PRO* 3.6 10.3 - - - +
66A TYR* 3.6 11.9 + - - -
67A ILE* 1.3 72.9 - - - +
69A ALA* 1.4 51.6 + - - +
84A THR* 2.5 25.3 + - - -
85A GLN* 3.4 42.6 + - + +
257A ARG* 2.8 35.7 + - - -
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Residues in contact with ALA 69 (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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51A PRO* 3.7 6.7 - - - +
56A ARG* 3.3 6.9 - - - +
57A ILE* 2.9 27.1 + - + -
67A ILE* 2.8 14.3 + - + +
68A ASN* 1.4 76.2 + - - +
70A SER* 1.3 63.8 + - - +
82A ILE* 4.1 1.3 - - + -
83A LEU 3.3 8.1 - - - +
84A THR* 3.4 15.3 - - - +
98A MET* 3.6 28.7 - - - -
257A ARG* 4.0 2.7 - - - +
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Residues in contact with SER 70 (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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51A PRO* 3.9 10.6 - - - +
55A SER* 3.3 10.8 + - - -
57A ILE* 4.0 6.1 - - - -
69A ALA* 1.3 76.4 + - - +
71A LEU* 1.3 61.2 - - - +
72A ILE* 3.7 12.0 + - - +
82A ILE* 3.2 4.5 - - - -
83A LEU 2.9 31.2 + - - -
256A PHE 3.5 22.4 + - - -
257A ARG* 3.0 32.4 + - - +
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Residues in contact with LEU 71 (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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55A SER* 2.8 22.7 + - - +
57A ILE* 3.7 18.2 - - + +
70A SER* 1.3 72.0 - - - +
72A ILE* 1.3 58.0 + - - +
73A LYS* 3.7 23.9 + - + +
80A SER* 3.8 16.8 - - - +
81A TYR 3.6 13.9 - - - +
82A ILE* 4.3 3.6 - - + +
210A PRO* 3.8 28.0 - - + -
256A PHE* 3.5 23.7 - - - +
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Residues in contact with ILE 72 (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 SER* 3.8 15.3 - - - +
71A LEU* 1.3 79.1 - - - +
73A LYS* 1.3 55.7 + - - +
74A MET* 3.7 30.4 + - + -
80A SER* 3.1 5.2 - - - -
81A TYR* 2.7 48.2 + - + +
83A LEU* 4.1 22.4 - - + -
226A CYS* 5.9 1.1 - - + -
253A MET* 4.3 13.2 - - + -
256A PHE* 3.9 17.3 - - + -
257A ARG* 3.8 28.5 - - + -
260A LEU* 4.4 14.6 - - + -
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Residues in contact with LYS 73 (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 LEU* 3.7 22.9 + - + +
72A ILE* 1.3 73.5 - - - +
74A MET* 1.3 61.1 + - - +
75A GLU* 3.6 18.6 + - - +
80A SER* 3.5 18.8 - - - +
252A ASP* 5.2 0.2 - - - +
256A PHE* 3.3 36.4 - - + -
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Residues in contact with MET 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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72A ILE* 3.7 22.0 - - + -
73A LYS* 1.3 71.7 - - - +
75A GLU* 1.3 56.3 + - - +
76A GLU 3.5 0.9 - - - -
77A ALA* 4.0 18.2 - - + +
78A GLN* 2.8 30.8 + - - -
79A ARG* 2.9 25.8 + - + +
81A TYR* 4.2 2.2 - - + -
230A THR* 3.8 20.0 - - + +
234A LEU* 5.9 0.7 - - + -
249A VAL* 3.8 24.9 - - + +
252A ASP* 3.6 25.8 - - + +
253A MET* 3.6 35.4 - - + -
256A PHE* 4.5 2.0 - - - -
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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