Contacts of the strand formed by residues 58 - 65 (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 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLN* 3.4 27.7 + - + +
50A CYS 3.4 7.4 - - - +
51A ILE* 4.2 17.7 - - + +
56A GLY 3.7 5.4 + - - +
57A GLN* 1.3 95.7 + - - +
59A TYR* 1.3 69.3 + - - +
112A TYR* 3.4 39.3 + - + +
114A ALA* 5.4 0.9 - - - +
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Residues in contact with TYR 59 (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 TYR* 3.9 27.8 - + - -
49A GLN* 3.3 10.6 - - - +
50A CYS* 2.8 43.5 + - - +
52A SER* 4.2 8.5 - - - -
55A THR* 4.8 2.6 + - - -
57A GLN* 3.3 43.9 - - + +
58A GLU* 1.3 77.4 - - - +
60A ALA* 1.3 61.3 + - - +
97A HIS* 3.6 38.8 + + + -
109A ILE* 3.8 14.8 - - + -
110A LEU 3.5 15.3 - - - +
111A GLU* 4.5 2.7 - - - -
112A TYR* 3.9 8.8 - - - -
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Residues in contact with ALA 60 (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 3.3 47.1 - - + +
39A LEU* 3.9 13.9 - - + -
47A VAL* 3.9 5.2 - - + -
48A ARG 3.7 4.9 - - - -
59A TYR* 1.3 74.4 - - - +
61A ALA* 1.3 58.7 + - - +
62A LYS 3.8 0.6 + - - -
108A LEU 3.2 2.6 - - - +
110A LEU* 2.8 37.1 + - + +
112A TYR* 4.4 1.2 - - + +
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Residues in contact with ALA 61 (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* 4.5 1.8 - - + -
34A LEU* 4.2 6.1 - - + -
47A VAL* 3.3 3.4 - - - -
48A ARG 2.8 37.3 + - - +
50A CYS* 4.1 11.8 - - - -
59A TYR 4.0 1.4 - - - -
60A ALA* 1.3 69.8 - - - +
62A LYS* 1.3 59.7 + - - +
63A PHE* 3.4 29.3 - - + -
107A ILE* 4.2 2.9 - - + -
108A LEU 3.3 5.6 - - - -
109A ILE* 4.0 19.5 - - + -
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Residues in contact with LYS 62 (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 3.4 35.6 + - - +
2A CL 4.0 5.1 - - + +
45A ALA* 4.4 11.0 - - + -
46A VAL 3.6 4.0 - - - +
47A VAL* 3.9 16.6 - - + -
60A ALA 3.8 1.2 + - - -
61A ALA* 1.3 71.0 - - - +
63A PHE* 1.3 61.0 + - - +
64A LEU* 3.5 33.4 + - + +
80A GLU* 3.5 24.2 + - - -
106A ILE 3.6 2.6 - - - +
107A ILE* 3.3 3.7 - - - -
108A LEU* 2.8 46.8 + - + +
110A LEU* 3.9 17.7 - - + -
179A ASP* 3.6 18.1 + - - -
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Residues in contact with PHE 63 (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* 4.4 9.2 - - + -
28A PHE* 4.4 4.9 - + - -
34A LEU* 4.1 32.8 - - + -
44A PHE 4.0 0.3 - - - +
45A ALA* 3.2 7.1 - - - +
46A VAL* 2.9 52.0 + - + +
48A ARG* 4.6 8.5 - - + -
61A ALA* 3.4 29.8 - - + -
62A LYS* 1.3 71.6 - - - +
64A LEU* 1.3 60.5 + - - +
65A LYS* 4.2 1.3 + - - +
105A GLU* 3.4 31.0 - - + +
106A ILE 3.8 3.6 - - - -
107A ILE* 3.3 35.2 - - + +
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Residues in contact with LEU 64 (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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44A PHE 3.6 2.5 - - - -
45A ALA* 3.8 13.2 - - + -
62A LYS* 3.5 41.7 - - + +
63A PHE* 1.3 72.6 - - - +
65A LYS* 1.3 63.6 + - - +
68A ARG* 3.7 16.8 - - - +
77A ILE* 3.9 35.1 - - + +
80A GLU* 4.2 13.5 - - - +
105A GLU* 3.2 4.5 - - - +
106A ILE 2.9 38.6 + - - +
108A LEU* 4.1 23.3 - - + -
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Residues in contact with LYS 65 (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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43A LYS 5.6 0.7 - - - +
44A PHE* 3.0 36.4 + - + +
63A PHE 4.2 1.3 - - - +
64A LEU* 1.3 71.6 - - - +
66A LYS* 1.3 61.8 + - - +
67A ARG 3.4 14.8 - - - +
68A ARG* 3.0 29.6 + - - -
77A ILE* 3.7 2.6 - - - +
104A SER* 3.3 29.0 + - - +
105A GLU* 2.8 30.5 + - + -
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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