Contacts of the strand formed by residues 74 - 79 (chain A) in PDB entry 1A76
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 THR 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LYS 3.0 11.7 + - - -
23A LYS* 3.3 20.8 - - + +
24A VAL* 3.0 24.6 + - - +
69A LEU* 4.1 2.0 - - - -
72A ASP* 3.7 5.3 + - - -
73A ILE* 1.3 70.1 - - - +
75A PRO* 1.3 64.7 - - + +
76A ILE* 5.6 0.2 - - - +
276A LEU* 4.5 10.8 - - + +
278A LEU* 4.0 29.8 - - + +
315A LYS* 3.8 24.1 - - - +
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Residues in contact with PRO 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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24A VAL* 3.4 15.3 - - + +
26A ILE* 3.4 29.6 - - + -
65A THR* 4.1 23.6 - - + -
68A LEU* 4.3 11.9 - - + -
69A LEU* 3.8 15.9 - - + -
73A ILE 3.2 11.0 - - - +
74A THR* 1.3 92.4 - - + +
76A ILE* 1.3 61.1 + - - +
77A TRP* 4.7 2.9 - - - +
144A ILE* 4.0 16.1 - - + +
145A PRO* 4.2 8.7 - - - +
278A LEU* 4.5 2.0 - - + +
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Residues in contact with ILE 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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24A VAL 3.0 13.7 + - - +
25A ALA* 3.4 12.2 - - + -
26A ILE* 2.8 24.4 + - - -
74A THR 5.6 0.2 - - - +
75A PRO* 1.3 75.8 - - - +
77A TRP* 1.3 64.2 + - - +
78A VAL* 4.0 0.3 - - - +
145A PRO* 3.5 17.7 - - + +
146A TYR 4.8 0.9 - - - +
147A VAL* 3.9 28.0 - - + -
160A MET* 3.8 21.5 - - + -
166A VAL* 4.0 11.0 - - + -
274A TYR* 4.5 2.7 - - + -
275A SER 3.1 33.7 - - - +
276A LEU* 4.1 15.9 - - + -
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Residues in contact with TRP 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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26A ILE* 3.6 31.0 - - + +
28A GLY* 3.9 13.2 - - - -
31A ALA* 3.8 24.7 - - + -
32A LEU* 4.1 14.8 - - + -
35A PHE* 3.8 28.3 - + - -
60A GLY 5.2 0.4 - - - -
61A VAL* 4.1 15.0 - - + -
64A LYS* 5.6 0.9 - - + -
65A THR* 3.3 31.7 + - - +
75A PRO* 4.7 1.3 - - + +
76A ILE* 1.3 76.2 - - - +
78A VAL* 1.3 53.8 + - - +
79A PHE* 3.7 21.8 - + + -
139A LEU* 3.5 36.1 - - + +
144A ILE* 3.8 16.3 - - + +
145A PRO 3.0 7.3 + - - -
146A TYR* 2.9 8.8 - - + +
147A VAL* 2.7 34.3 + - - +
189A THR* 5.9 1.1 - - + -
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Residues in contact with VAL 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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25A ALA* 4.1 11.7 - - + -
26A ILE 2.9 17.0 + - - +
27A ASP* 3.9 1.3 - - - +
28A GLY* 2.8 28.5 + - - +
29A MET 4.3 1.0 + - - -
76A ILE 4.0 8.5 - - - +
77A TRP* 1.3 78.0 - - - +
79A PHE* 1.3 68.0 + - - +
147A VAL* 3.6 8.5 - - + +
149A ALA* 4.4 0.4 - - + -
153A GLY* 3.5 31.3 - - - +
156A GLN* 3.6 25.6 - - + -
157A ALA* 4.1 5.6 - - + -
160A MET* 4.0 24.7 - - + -
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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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28A GLY* 4.4 6.1 - - - -
29A MET* 3.2 34.5 - - + -
32A LEU* 3.8 15.3 - - + -
77A TRP* 3.7 17.7 - + + -
78A VAL* 1.3 78.3 - - - +
80A ASP* 1.3 63.5 + - - +
81A GLY 3.4 4.0 - - - +
82A GLU* 4.8 0.7 - - - +
132A VAL* 4.2 2.9 - - + -
135A CYS* 4.8 5.2 - - + -
136A LYS* 3.6 49.1 - - + +
139A LEU* 3.6 32.1 - - + -
146A TYR* 3.7 19.1 - + + -
147A VAL 2.7 17.7 + - - +
148A GLU* 4.6 1.3 - - - -
149A ALA* 2.9 30.9 + - - +
153A GLY* 3.9 2.3 - - - -
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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