Contacts of the strand formed by residues 69 - 73 (chain A) in PDB entry 2L80
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 LEU 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 3.5 26.2 - - - +
4A TYR* 3.6 35.4 - - + -
5A ALA* 5.1 0.7 - - - +
8A LEU* 3.6 24.2 - - + -
36A ASN* 2.9 24.0 + - - +
37A LEU* 3.2 23.6 + - + -
38A THR* 5.6 5.6 - - - +
67A TYR* 3.2 6.6 + - + -
68A PRO* 1.3 84.0 - - + +
70A ALA* 1.3 62.6 + - - +
83A VAL* 5.3 4.0 - - + -
84A TYR 3.7 4.0 - - - +
85A SER* 3.5 24.9 - - - +
87A GLN* 5.7 0.2 - - + -
92A VAL* 4.7 2.9 - - + -
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Residues in contact with ALA 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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34A TRP* 3.3 36.0 - - + +
35A LEU 3.1 13.5 - - - +
36A ASN* 3.7 4.3 - - + +
37A LEU* 3.4 7.0 - - - +
43A LEU* 6.5 1.1 - - + -
69A LEU* 1.3 76.9 - - - +
71A VAL* 1.3 60.9 + - - +
83A VAL* 3.2 3.3 - - - +
84A TYR* 2.8 36.0 + - - +
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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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33A LEU 3.9 0.2 - - - -
34A TRP* 3.1 3.2 - - - -
35A LEU* 2.7 44.7 + - + +
37A LEU* 3.4 30.7 - - + -
70A ALA* 1.3 71.0 - - - +
72A LYS* 1.3 69.9 + - - +
73A LEU* 3.0 17.5 + - + +
76A ILE* 4.6 2.2 - - + -
81A ALA* 4.1 16.8 - - + -
82A ASP 3.7 10.8 - - - +
83A VAL* 4.0 14.6 - - + +
97A LEU* 4.9 3.6 - - + -
101A LEU* 4.2 25.1 - - + -
104A PHE* 5.8 1.3 - - + -
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Residues in contact with LYS 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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32A ASN* 3.2 38.6 + - - +
33A LEU 3.0 13.0 - - - +
34A TRP* 3.5 29.9 - - + +
45A GLY 3.2 20.6 + - - -
46A LYS 5.5 0.2 - - - -
47A TRP* 5.6 2.0 - - - +
70A ALA 3.7 3.4 + - - -
71A VAL* 1.3 71.4 - - - +
73A LEU* 1.3 61.5 + - - +
75A THR* 2.6 48.5 + - + -
76A ILE* 4.4 1.2 - - - +
82A ASP* 2.7 39.8 + - + +
83A VAL* 4.8 0.2 - - - -
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Residues in contact with LEU 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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21A GLY 5.0 0.9 - - - +
22A TRP* 3.4 38.1 - - + -
31A GLU* 5.8 0.4 - - - -
32A ASN* 3.9 8.2 + - - -
33A LEU* 2.7 46.4 + - + +
35A LEU* 3.5 38.4 - - + +
42A VAL* 3.5 17.5 - - + -
71A VAL* 3.5 13.0 - - + +
72A LYS* 1.3 80.6 - - - +
74A GLY* 1.3 60.5 + - - +
75A THR* 3.2 2.3 + - - +
76A ILE* 3.6 23.6 - - + -
106A ILE* 4.2 4.7 - - + -
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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