Contacts of the strand formed by residues 105 - 111 (chain A) in PDB entry 3LM0
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 GLU 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A MET* 4.9 0.9 - - - +
63A PHE* 3.4 31.5 - - + +
64A LEU 3.2 11.4 - - - +
65A LYS* 2.8 33.7 + - + +
66A LYS* 4.1 2.9 - - - -
101A GLU* 3.5 3.8 - - - +
102A ASN* 2.9 57.2 + - - +
104A SER* 1.3 89.6 + - - +
106A ILE* 1.3 65.3 + - - +
107A ILE* 4.3 7.8 - - + +
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Residues in contact with ILE 106 (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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22A PHE* 4.1 16.8 - - + -
62A LYS 3.6 2.3 - - - +
63A PHE 3.8 0.3 - - - -
64A LEU* 2.9 36.2 + - - +
66A LYS* 4.0 15.4 - - + +
74A ARG* 3.8 28.7 - - + +
77A ILE* 3.7 37.9 - - + -
78A LEU* 5.5 0.9 - - + +
81A ILE* 4.2 3.4 - - + -
99A VAL* 3.7 24.0 - - + -
100A TYR 3.5 4.0 - - - +
101A GLU* 4.0 13.9 - - + +
105A GLU* 1.3 78.3 - - - +
107A ILE* 1.3 64.3 + - - +
108A LEU* 4.2 9.2 - - + -
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Residues in contact with ILE 107 (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 MET* 3.5 33.4 - - + -
28A PHE* 4.6 7.2 - - + -
61A ALA* 4.2 6.1 - - + -
62A LYS 3.3 8.3 - - - +
63A PHE* 3.3 47.3 - - + -
99A VAL* 3.4 7.4 - - - +
100A TYR* 2.7 52.0 + - + +
101A GLU 5.0 0.7 - - - +
102A ASN* 3.9 7.0 - - - +
105A GLU* 4.3 7.0 - - + -
106A ILE* 1.3 76.7 - - - +
108A LEU* 1.3 63.8 + - - +
109A ILE* 3.9 20.5 + - + -
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Residues in contact with LEU 108 (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 ALA 3.2 5.7 - - - +
61A ALA* 3.3 1.7 - - - -
62A LYS* 2.8 53.2 + - + +
64A LEU* 4.1 23.8 - - + -
80A GLU* 4.6 10.8 - - - +
81A ILE* 3.9 34.3 - - + -
84A LEU* 4.3 22.2 - - + -
96A LEU* 3.9 15.5 - - + -
98A GLU 3.9 1.6 - - - -
99A VAL* 4.0 9.6 - - + -
106A ILE* 4.2 5.2 - - + -
107A ILE* 1.3 75.9 - - - +
109A ILE* 1.3 63.9 + - - +
110A LEU* 3.4 14.2 + - + +
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Residues in contact with ILE 109 (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 PHE* 3.5 33.4 - - + -
32A TYR* 3.6 22.0 - - + +
50A CYS* 4.5 3.6 - - - -
59A TYR* 3.8 30.5 - - + -
60A ALA 3.8 1.1 - - - -
61A ALA* 4.0 12.6 - - + -
96A LEU* 3.8 2.0 - - - +
97A HIS* 2.9 32.3 + - + +
98A GLU* 2.9 25.0 + - + +
100A TYR* 3.8 23.6 - - + -
107A ILE* 4.2 6.3 - - + -
108A LEU* 1.3 76.8 - - - +
110A LEU* 1.3 58.3 + - - +
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Residues in contact with LEU 110 (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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1A EBD 4.0 18.6 - - + -
2A CL 3.8 20.9 - - + -
59A TYR* 3.5 7.6 - - - +
60A ALA 2.8 30.1 + - - +
62A LYS* 3.9 27.6 - - + -
84A LEU* 3.9 26.9 - - + -
94A ILE* 4.1 15.3 - - + -
95A ASN 3.4 14.4 - - - +
96A LEU* 4.0 10.8 - - + -
97A HIS* 4.2 2.9 - - - -
108A LEU* 4.0 12.3 - - + +
109A ILE* 1.3 76.1 - - - +
111A GLU* 1.3 70.6 + - - +
112A TYR 3.4 0.3 + - - -
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Residues in contact with GLU 111 (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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1A EBD 3.0 18.9 + - - -
59A TYR* 4.5 2.5 - - - -
93A VAL 4.1 0.5 - - - +
94A ILE* 3.3 29.3 - - + +
95A ASN* 2.9 54.2 + - + +
97A HIS* 3.6 17.0 - - - +
110A LEU* 1.3 72.3 - - - +
112A TYR* 1.3 68.9 + - - +
113A ALA* 6.2 0.2 - - - -
167A SER* 5.6 1.2 - - - -
176A LYS* 2.7 36.7 + - + +
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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