Contacts of the strand formed by residues 122 - 128 (chain A) in PDB entry 2LS8
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 ALA 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ASP 2.9 16.4 - - - +
21A ASN* 4.6 2.2 - - - +
22A LYS* 2.9 20.2 + - - +
59A SER* 3.5 20.6 - - - +
61A PHE* 3.3 20.8 - - + -
103A VAL* 5.3 2.9 - - + -
120A PHE* 3.9 14.4 - - + -
121A GLU* 1.3 75.8 - - - +
123A SER* 1.3 66.1 + - - +
124A ARG* 4.9 0.3 - - - +
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Residues in contact with SER 123 (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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18A LEU 3.2 13.5 - - - -
19A THR* 3.6 18.6 + - - -
20A ASP 3.4 8.2 + - - -
58A LEU* 3.6 21.7 - - - +
59A SER 2.9 17.6 + - - +
60A TYR* 3.6 14.4 - - - -
61A PHE* 2.8 28.8 + - - -
122A ALA* 1.3 75.9 - - - +
124A ARG* 1.3 62.4 + - - +
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Residues in contact with ARG 124 (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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18A LEU* 2.7 65.5 + - + +
20A ASP* 2.6 43.4 + - - +
22A LYS* 3.7 18.3 - - - +
27A SER* 3.5 32.9 - - - +
30A ASN* 2.7 42.6 + - - +
31A CYS* 4.4 12.7 - - - -
34A MET* 5.8 1.2 - - - +
38A LEU* 4.6 5.2 - - + -
60A TYR* 3.5 5.3 - - - -
61A PHE* 3.7 15.0 - - + +
122A ALA 4.9 1.1 - - - +
123A SER* 1.3 76.1 - - - +
125A ILE* 1.3 62.4 + - - +
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Residues in contact with ILE 125 (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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15A TYR* 4.3 3.6 - - + -
16A PHE 3.5 15.9 - - - +
17A PRO* 4.4 2.0 - - + -
18A LEU* 4.6 0.2 - - - -
38A LEU* 3.4 11.6 - - - +
39A MET* 2.8 60.0 + - + -
50A ILE* 3.8 23.1 - - + -
54A LEU* 3.5 41.1 - - + -
60A TYR* 3.5 17.5 - - + -
61A PHE 3.7 5.5 + - - +
62A LEU* 4.7 1.3 - - + -
104A LEU* 4.5 5.8 - - + -
124A ARG* 1.3 79.9 - - - +
126A CYS* 1.3 67.7 + - - +
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Residues in contact with CYS 126 (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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7A TRP* 3.1 15.3 - - + -
15A TYR* 3.4 0.5 - - - -
16A PHE 2.7 44.5 + - - +
18A LEU* 4.1 11.6 - - + +
31A CYS* 2.0 50.9 - - - -
34A MET* 3.6 12.8 - - + -
36A ALA* 3.6 17.5 - - - -
37A HIS 3.4 9.2 - - - -
125A ILE* 1.3 73.8 - - - +
127A LYS* 1.3 59.8 + - - +
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Residues in contact with LYS 127 (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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13A ASN* 3.5 34.9 + - + +
14A CYS 3.1 6.5 - - - +
15A TYR* 3.4 33.7 - - + -
36A ALA* 3.3 2.0 - - - -
37A HIS* 2.6 43.8 + - + +
38A LEU 4.1 6.7 - - - +
39A MET* 4.4 4.0 - - - -
40A THR* 3.0 29.0 + - - +
42A SER* 5.0 2.8 + - - -
77A ASP* 2.7 35.0 + - - +
79A THR* 4.3 4.2 + - - -
125A ILE 4.2 0.8 + - - -
126A CYS* 1.3 73.0 - - - +
128A ILE* 1.3 59.5 + - - +
129A PRO* 4.1 9.3 - - - +
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Residues in contact with ILE 128 (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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3A CYS* 3.8 12.1 - - + -
4A PRO* 5.7 6.1 - - + -
7A TRP* 3.4 29.5 - - + -
13A ASN* 3.5 1.2 - - - -
14A CYS* 2.7 52.7 + - + -
34A MET* 3.5 23.6 - - + +
35A GLY 3.7 9.9 - - - +
36A ALA* 3.6 9.6 - - + -
127A LYS* 1.3 77.3 - - - +
129A PRO* 1.3 77.5 - - + +
131A THR* 4.1 15.9 - - + -
132A THR* 5.3 5.8 - - - +
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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