Contacts of the strand formed by residues 69 - 77 (chain A) in PDB entry 1I04
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 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A LEU* 2.9 45.2 + - - +
67A GLU 3.5 1.0 - - - -
68A ASN* 1.3 82.4 - - - +
70A LEU* 1.3 72.5 + - - +
88A VAL* 3.1 26.3 - - - +
89A ALA 2.6 22.0 + - - -
90A ASP* 3.4 9.6 + - - -
91A LYS* 5.0 0.8 - - - +
98A TYR* 4.2 5.3 + - - -
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Residues in contact with LEU 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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30A VAL* 3.8 24.7 - - + -
33A ILE* 4.3 15.7 - - + -
63A ILE* 4.1 15.0 - - + -
64A HIS 3.5 2.2 - - - -
65A VAL* 4.0 18.6 - - + -
69A SER* 1.3 89.7 + - - +
71A VAL* 1.3 63.7 + - - +
72A LEU* 3.9 9.8 + - + -
87A MET 3.7 0.3 - - - +
88A VAL* 3.4 2.9 - - - -
89A ALA* 2.7 44.6 + - + +
98A TYR* 3.6 35.0 - - + +
108A PHE* 4.5 13.7 - - + -
110A ILE* 5.2 2.0 - - + -
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Residues in contact with VAL 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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62A GLN 3.7 0.7 - - - +
63A ILE* 3.4 5.5 - - - -
64A HIS* 2.9 61.0 + - + +
66A LEU* 4.1 25.4 - - + -
70A LEU* 1.3 76.1 - - - +
72A LEU* 1.3 68.6 + - - +
73A LYS* 4.6 12.1 - - + -
86A SER* 5.2 5.2 - - - -
87A MET 3.4 9.2 - - - +
88A VAL* 4.8 14.4 - - + -
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Residues in contact with LEU 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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60A LEU* 4.2 5.6 - - + -
62A GLN 3.7 2.0 - - - -
63A ILE* 3.9 33.7 - - + -
70A LEU* 4.4 19.3 - - + +
71A VAL* 1.3 78.7 - - - +
73A LYS* 1.3 59.7 + - - +
74A PHE* 3.3 33.7 - - + -
85A LEU 3.8 0.7 - - - +
86A SER* 3.3 7.3 - - - -
87A MET* 2.8 48.2 + - + +
89A ALA* 4.7 3.4 - - + -
100A VAL* 5.9 1.3 - - + -
108A PHE* 4.1 27.6 - - + -
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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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60A LEU* 3.5 4.0 - - - +
61A GLU* 2.8 35.3 + - + -
62A GLN* 2.9 26.3 + - + +
64A HIS* 4.2 27.8 - - + +
71A VAL* 4.6 9.9 - - + -
72A LEU* 1.3 74.1 - - - +
74A PHE* 1.3 56.0 + - - +
84A GLU* 2.8 30.6 + - + +
85A LEU 3.7 1.1 - - - +
86A SER* 2.7 31.0 + - - +
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Residues in contact with PHE 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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58A LEU* 3.6 29.2 - - + -
59A PHE 3.2 9.9 - - - +
60A LEU* 3.4 40.2 - - + -
61A GLU* 4.2 1.3 - - - -
72A LEU* 3.3 42.0 - - + -
73A LYS* 1.3 74.4 - - - +
75A HIS* 1.3 67.8 + - - +
84A GLU* 3.4 9.9 - - - +
85A LEU* 2.7 49.5 + - + +
87A MET* 3.6 34.5 - - + -
138A TYR* 5.2 7.6 - + - -
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Residues in contact with HIS 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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58A LEU* 4.1 1.4 - - - -
59A PHE* 3.1 36.0 + - + +
61A GLU* 2.8 39.4 + - + +
74A PHE* 1.3 75.8 + - - +
76A THR* 1.3 63.0 + - - +
82A CYS* 3.7 33.7 - - + +
83A SER* 3.0 27.1 - - - -
84A GLU* 3.5 21.9 + - + +
85A LEU 4.5 0.2 - - - +
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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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55A ASN* 5.4 0.7 - - - +
57A ARG 4.6 6.5 - - - +
58A LEU* 3.3 31.6 - - + -
75A HIS* 1.3 75.2 - - - +
77A VAL* 1.3 64.1 + - - +
78A ARG 4.3 0.2 + - - -
81A GLU 3.7 0.5 - - - +
82A CYS* 3.3 6.2 - - - -
83A SER* 2.9 46.2 + - - -
85A LEU* 3.9 19.3 - - + +
102A TYR* 4.8 2.7 - - - +
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Residues in contact with VAL 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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53A ASN* 4.2 17.8 + - - +
57A ARG* 4.9 7.5 + - - +
59A PHE* 3.6 29.8 - - + -
76A THR* 1.3 80.6 - - - +
78A ARG* 1.3 63.6 + - - +
79A ASP 4.5 0.7 - - - +
80A GLU* 4.1 20.0 - - - +
81A GLU 3.6 2.9 - - - +
82A CYS* 4.1 1.6 - - - -
174A ARG* 3.7 26.7 - - + -
175A CYS* 3.5 26.5 - - - -
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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