Contacts of the strand formed by residues 49 - 59 (chain A) in PDB entry 1LKF
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 ASP 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ILE 4.2 3.7 - - - +
42A LYS* 3.0 45.0 + - + +
43A ASP 5.4 0.9 + - - -
48A LYS* 1.3 73.6 - - - +
50A THR* 1.3 61.7 + - - +
230A SER* 3.4 5.9 + - - -
231A HIS* 2.9 43.7 + - + +
233A GLN* 3.3 30.1 + - - +
282A TRP* 3.6 21.7 - - + +
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Residues in contact with THR 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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40A PHE* 3.6 3.3 - - - +
41A ILE* 2.7 59.6 + - + +
48A LYS* 4.0 8.3 + - - +
49A ASP* 1.3 78.1 + - - +
51A LEU* 1.3 63.3 + - - +
52A VAL* 4.2 1.8 - - + -
116A TYR* 3.7 31.1 + - + -
120A GLY* 5.5 0.3 + - - -
122A ILE* 4.3 3.1 - - + -
228A VAL* 3.6 28.0 - - + -
229A LEU 3.6 2.7 - - - +
230A SER* 5.0 4.7 + - - -
282A TRP* 4.0 3.1 - - - -
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Residues in contact with LEU 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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38A PHE* 3.8 38.4 - - + -
39A ASN 3.4 12.3 - - - +
40A PHE* 4.0 12.8 - - + +
50A THR* 1.3 74.9 - - - +
52A VAL* 1.3 66.3 - - - +
53A LEU* 4.5 5.8 - - + +
227A SER 3.6 1.0 - - - +
228A VAL* 3.3 6.6 - - - +
229A LEU* 2.8 44.0 + - + +
241A ILE* 5.2 1.1 - - + -
280A ILE* 3.6 37.5 - - + -
282A TRP* 3.4 30.3 - - + -
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASN* 2.8 48.9 + - + +
41A ILE* 3.8 19.1 - - + -
50A THR* 4.3 7.6 - - + -
51A LEU* 1.3 74.3 - - - +
53A LEU* 1.3 58.7 + - - +
114A LEU* 4.2 20.9 - - + -
116A TYR* 5.7 0.2 - - + -
122A ILE* 5.2 1.3 - - + -
138A PHE* 3.6 37.7 - - + -
140A GLU* 4.8 0.2 - - + -
226A LEU* 3.9 25.6 - - + -
227A SER 3.7 5.4 - - - +
228A VAL* 4.6 7.2 - - + -
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Residues in contact with LEU 53 (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 LEU* 3.9 20.4 - - + -
37A THR 3.4 13.0 - - - +
38A PHE* 3.7 35.9 - - + +
51A LEU* 3.8 6.8 - - + -
52A VAL* 1.3 72.6 - - - +
54A LYS* 1.3 63.6 + - - +
55A ALA* 4.0 1.0 + - - +
86A ILE* 3.9 20.6 - - + +
225A PHE 3.6 1.2 - - - +
226A LEU* 3.3 7.3 - - - +
227A SER* 2.9 52.8 + - - +
229A LEU* 5.2 1.6 - - + -
241A ILE* 3.8 28.9 - - + -
243A VAL* 4.3 7.2 - - + -
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Residues in contact with LYS 54 (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 ILE 3.5 4.2 - - - +
36A LEU* 3.5 1.2 - - - -
37A THR* 2.9 50.1 + - - +
39A ASN* 4.8 5.8 - - - +
52A VAL 3.8 1.0 + - - -
53A LEU* 1.3 75.1 - - - +
55A ALA* 1.3 60.1 + - - +
56A THR* 3.8 26.3 - - + +
140A GLU* 3.3 31.3 + - + +
141A THR* 3.0 30.4 + - - +
142A ILE* 5.0 0.7 - - + +
224A GLU* 3.8 18.6 + - - -
225A PHE 3.4 7.2 - - - +
226A LEU* 3.5 16.6 - - + -
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Residues in contact with ALA 55 (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 ILE 3.5 4.5 - - - -
36A LEU* 3.7 14.8 - - + -
53A LEU* 4.0 1.9 + - + -
54A LYS* 1.3 70.6 - - - +
56A THR* 1.3 59.9 + - - +
84A VAL* 4.8 2.0 - - + -
86A ILE* 4.5 19.1 - - + -
223A PRO 3.6 2.3 - - - +
224A GLU* 3.4 4.9 - - - -
225A PHE* 2.7 44.4 + - + +
245A TYR* 3.3 22.4 - - + +
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Residues in contact with THR 56 (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 ILE* 2.8 46.6 + - - +
37A THR* 5.6 1.4 + - - +
54A LYS* 3.8 27.4 - - + +
55A ALA* 1.3 79.2 - - - +
57A GLY* 1.3 61.0 + - - +
223A PRO* 3.1 20.2 - - - +
224A GLU* 3.8 19.3 - - + +
245A TYR* 2.6 24.9 + - - -
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Residues in contact with GLY 57 (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 SER* 3.3 8.3 - - - -
35A ILE* 3.8 21.1 - - - +
56A THR* 1.3 83.5 + - - +
58A ASN* 1.3 60.5 + - - -
222A ASN* 3.1 28.1 + - - +
223A PRO* 3.8 5.8 + - - -
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Residues in contact with ASN 58 (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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31A LYS* 3.3 21.4 + - - +
32A ILE* 3.3 2.3 - - - +
33A SER* 2.7 47.9 + - - +
57A GLY* 1.3 75.4 - - - +
59A ILE* 1.3 69.0 + - - +
60A ASN* 3.6 9.7 - - - +
220A ASN* 2.6 36.6 + - - +
221A PHE 3.5 4.7 - - - -
222A ASN* 3.1 7.3 + - - +
223A PRO* 4.0 1.4 - - - +
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Residues in contact with ILE 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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31A LYS 4.1 2.0 - - - -
32A ILE* 4.2 14.8 - - + -
58A ASN* 1.3 82.2 - - - +
60A ASN* 1.3 68.8 + - - +
82A TYR* 3.4 32.1 - - + -
84A VAL* 3.9 19.1 - - + -
220A ASN* 3.4 0.4 - - - -
221A PHE* 2.8 49.5 + - + +
223A PRO* 4.4 3.4 - - + -
245A TYR* 3.7 36.8 - - + -
246A GLN 4.0 20.9 - - - +
247A ARG* 4.1 7.0 - - + -
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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