Contacts of the strand formed by residues 78 - 83 (chain A) in PDB entry 1LDS
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 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.6 24.9 - - + -
40A LEU 3.3 14.8 - - - +
41A LYS* 3.3 45.3 + - + +
46A ILE* 4.4 7.4 - - + -
70A PHE* 3.7 22.0 - + + +
71A THR 4.0 7.8 + - - -
72A PRO* 3.8 27.5 - - + +
76A ASP* 3.6 24.2 + - + +
77A GLU* 1.3 77.1 - - - +
79A ALA* 1.3 58.4 + - - +
94A LYS* 3.6 3.8 - - - +
95A TRP* 2.7 67.1 + + + +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.7 7.4 - - - -
23A LEU* 4.9 2.0 - - - +
39A LEU* 3.4 7.7 - - - +
40A LEU* 2.7 43.1 + - + +
77A GLU* 6.1 0.4 - - - +
78A TYR* 1.3 77.3 - - - +
80A CYS* 1.3 60.3 + - - +
92A ILE* 3.8 21.5 - - + -
93A VAL 3.3 13.7 - - - +
94A LYS* 3.7 12.1 - - + +
95A TRP 4.1 1.3 - - - +
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Residues in contact with CYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.5 2.5 - - + -
9A VAL* 3.5 17.0 - - + -
25A CYS* 2.0 52.3 - - + -
37A VAL* 3.6 19.3 - - - -
38A ASP 3.3 6.7 - - - -
39A LEU* 4.3 2.9 - - + +
79A ALA* 1.3 76.0 - - - +
81A ARG* 1.3 60.8 + - - +
82A VAL* 4.1 8.2 - - - +
91A LYS 3.5 1.9 - - - +
92A ILE* 3.3 3.7 - - - -
93A VAL* 2.8 32.3 + - - +
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Residues in contact with ARG 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU* 3.8 1.5 - - - +
37A VAL* 3.3 4.3 - - - -
38A ASP* 2.8 64.6 + - + +
40A LEU* 3.9 39.3 - - + +
43A GLY 4.8 6.3 + - - -
45A ARG* 4.2 14.1 - - - +
79A ALA 4.3 0.2 - - - -
80A CYS* 1.3 73.0 - - - +
82A VAL* 1.3 65.5 + - - +
83A ASN* 4.9 8.1 - - - +
90A PRO* 4.1 23.8 - - + -
91A LYS 3.3 3.1 - - - +
92A ILE* 3.9 24.8 - - + +
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Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 4.2 5.8 - - + -
7A ILE* 3.5 35.0 - - + -
27A VAL* 4.1 6.3 - - + -
35A ILE* 3.8 28.7 - - + -
36A GLU 3.4 3.8 - - - +
37A VAL* 4.1 10.8 - - + -
80A CYS* 4.1 18.4 - - - -
81A ARG* 1.3 80.4 - - - +
83A ASN* 1.3 67.1 + - - +
87A LEU* 3.6 17.2 - - + +
90A PRO* 3.4 3.9 - - - +
91A LYS 2.8 37.6 + - - +
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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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35A ILE* 3.3 8.5 - - - +
36A GLU* 2.9 60.1 + - + +
81A ARG* 4.4 10.3 - - - +
82A VAL* 1.3 72.9 - - - +
84A HIS* 1.3 61.2 + - - +
87A LEU* 4.6 3.3 - - - +
89A GLN 4.4 0.7 - - - -
90A PRO* 3.1 41.1 - - - +
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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