Contacts of the strand formed by residues 45 - 52 (chain A) in PDB entry 1LMK
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 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A VAL* 4.1 9.2 - - + -
38A LYS 3.7 1.6 - - - -
39A GLN* 2.9 39.3 - - + -
44A GLY* 1.3 75.9 - - - -
46A GLU* 1.3 63.5 + - - +
95A TYR* 4.7 0.7 - - + -
241C TYR* 5.1 2.2 - - + -
243C LYS* 4.0 7.9 - - + -
249C PRO* 3.8 34.3 - - + -
292C PHE* 3.5 36.6 - - + -
303C PHE* 3.5 55.8 - - + +
304C GLY 5.0 0.7 - - - +
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Residues in contact with GLU 46 (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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37A VAL* 3.1 9.0 - - - +
38A LYS* 2.8 58.7 + - + +
40A ARG* 4.9 12.0 + - - +
43A HIS* 5.2 6.7 - - - +
44A GLY 3.8 6.8 + - - +
45A LEU* 1.3 78.2 - - - +
47A TRP* 1.3 60.8 + - - +
61A ASN* 5.4 2.9 - - - +
63A LYS* 2.7 42.9 + - + +
64A PHE* 4.4 11.9 - - + -
303C PHE* 4.1 5.8 - - - -
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Residues in contact with TRP 47 (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 GLU* 2.9 29.4 + - + +
36A TRP 3.5 12.1 - - - -
37A VAL* 4.4 8.7 - - + -
46A GLU* 1.3 74.1 - - - +
48A ILE* 1.3 58.2 + - - +
49A GLY* 3.5 26.2 + - - -
50A LYS* 3.5 23.1 - - + -
59A THR* 3.5 26.0 - - + -
60A TYR 4.1 1.3 - - - -
61A ASN* 3.0 53.8 + - + +
64A PHE* 4.1 0.8 - - - -
107A TYR* 4.1 3.8 - - - -
109A LEU* 4.9 2.0 - - + -
299C VAL* 5.0 1.1 - - + -
300C PRO* 3.5 25.4 - - + -
301C PHE* 3.3 59.5 - + + +
303C PHE* 4.2 5.3 - - + -
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Residues in contact with ILE 48 (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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36A TRP* 2.8 24.6 + - + +
37A VAL 4.1 2.9 - - - -
38A LYS* 3.8 22.2 - - + +
47A TRP* 1.3 73.0 - - - +
49A GLY* 1.3 56.1 + - - +
60A TYR* 3.8 3.3 - - - -
61A ASN* 2.9 25.6 + - - +
64A PHE* 3.7 30.3 - - + +
68A ALA* 3.3 33.4 - - + -
70A PHE* 4.3 6.1 - - + -
81A MET* 3.9 12.8 - - - -
83A LEU* 5.0 0.4 - - + -
94A TYR* 3.3 40.2 - - + -
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Residues in contact with GLY 49 (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 GLU* 3.3 5.0 - - - +
36A TRP* 2.7 32.8 + - - -
47A TRP* 3.5 21.9 + - - -
48A ILE* 1.3 81.2 - - - +
50A LYS* 1.3 57.8 + - - -
59A THR 3.1 14.4 - - - -
70A PHE* 3.5 9.4 - - - -
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Residues in contact with LYS 50 (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 TRP* 3.2 34.4 - - + -
34A ILE 3.1 13.2 - - - +
35A GLU* 2.7 35.1 + - + +
47A TRP* 3.5 20.0 - - + -
49A GLY* 1.3 75.0 - - - +
51A ILE* 1.3 61.6 + - - +
58A ASN* 3.1 17.2 - - - +
59A THR* 2.9 34.7 + - + +
70A PHE* 3.1 11.4 - - - -
100A GLU* 2.7 26.0 + - - +
107A TYR* 3.0 18.7 + - - +
299C VAL* 6.1 0.9 - - + -
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Residues in contact with ILE 51 (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 TRP* 3.1 7.7 - - - -
34A ILE* 2.7 59.3 + - + +
36A TRP* 4.7 5.6 - - - +
50A LYS* 1.3 75.3 - - - +
52A LEU* 1.3 65.1 + - - +
53A PRO* 3.7 2.3 - - + +
56A GLY* 4.2 18.4 - - - +
57A SER 3.6 10.8 - - - +
58A ASN* 4.2 5.2 - - - +
70A PHE* 3.8 17.3 - - + +
71A THR* 3.3 49.1 - - - +
72A ALA* 3.6 15.9 - - + +
79A ALA* 4.9 2.7 - - + -
80A TYR 5.7 0.2 - - - +
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Residues in contact with LEU 52 (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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30A SER 4.0 15.5 - - - +
31A ASN 4.9 1.6 - - - +
32A TYR 3.8 14.8 - - - +
33A TRP* 3.5 45.9 - - + +
51A ILE* 1.3 74.1 - - - +
53A PRO* 1.3 71.8 - - + +
55A GLY* 5.4 2.9 - - - +
56A GLY* 2.8 34.0 + - - -
57A SER* 3.1 23.8 + - - -
102A TYR* 4.0 27.8 - - + +
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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