Contacts of the strand formed by residues 51 - 58 (chain A) in PDB entry 1KP5
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 LYS 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A GLY* 3.2 1.7 - - - -
46A ASP* 2.6 45.5 + - + +
49A TYR* 3.1 11.6 - - + +
50A GLY* 1.3 77.8 - - - +
52A LEU* 1.3 67.9 + - - +
53A THR* 4.3 18.2 - - + -
81A PHE* 5.0 1.9 - - - +
231A LEU* 4.4 9.0 - - + -
232A GLU 3.4 5.6 - - - +
233A PHE* 3.6 32.0 - - + -
901A SO4 3.0 38.3 + - - -
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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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24A ILE* 4.4 4.5 - - + -
44A GLU 3.2 12.1 - - - +
45A GLY* 4.0 5.6 - - - -
50A GLY 5.4 1.3 - - - +
51A LYS* 1.3 77.2 - - - +
53A THR* 1.3 68.4 + - - +
54A LEU* 4.2 17.0 - - + -
76A GYS 3.9 14.1 - - - +
78A VAL* 3.9 28.9 - - + +
81A PHE* 4.3 15.0 - - + -
230A LEU* 4.6 5.8 - - + -
231A LEU* 3.7 0.9 - - - +
232A GLU* 3.0 66.4 + - + +
234A VAL* 5.2 8.7 - - + -
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Residues in contact with THR 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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43A GLY* 3.1 4.7 - - - -
44A GLU* 2.9 42.8 + - - +
51A LYS* 4.3 14.1 - - + -
52A LEU* 1.3 73.2 - - - +
54A LEU* 1.3 65.0 + - - +
230A LEU 3.3 5.2 - - - +
231A LEU* 3.3 30.7 - - + -
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Residues in contact with LEU 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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24A ILE* 3.6 33.9 - - + -
26A VAL* 4.4 11.2 - - + -
42A GLU* 3.4 8.3 - - - +
43A GLY* 3.6 21.5 - - - +
52A LEU* 4.2 20.0 - - + -
53A THR* 1.3 83.9 - - - +
55A LYS* 1.3 59.5 + - - +
56A PHE* 3.5 35.0 - - + -
76A GYS 4.4 14.8 - - - +
78A VAL* 4.9 1.6 - - + -
228A MET 3.9 0.3 - - - +
229A VAL* 3.5 4.5 - - - +
230A LEU* 2.7 43.1 + - + +
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Residues in contact with LYS 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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40A SER 3.9 0.3 - - - +
41A GLY* 3.0 21.0 - - - -
42A GLU* 2.9 14.6 + - + +
54A LEU* 1.3 73.2 - - - +
56A PHE* 1.3 68.2 + - - +
57A ILE* 4.2 12.6 - - + +
220A ASP* 3.2 26.2 + - - +
222A ASN 5.7 0.2 + - - -
223A GLU* 3.1 36.1 + - - +
227A HIS* 4.3 9.2 - - + -
228A MET 3.4 7.4 - - - +
229A VAL* 4.2 16.4 - - + +
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Residues in contact with PHE 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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26A VAL* 3.7 22.4 - - + -
39A VAL* 4.1 5.2 - - + -
40A SER 3.3 2.9 - - - +
41A GLY* 3.5 18.2 - - - -
54A LEU* 3.5 38.6 - - + -
55A LYS* 1.3 75.5 - - - +
57A ILE* 1.3 62.7 + - - +
67A TRP* 3.8 21.3 - - + -
74A PHE* 3.4 44.6 - + + -
227A HIS* 3.0 25.8 - - - +
228A MET* 2.8 41.1 + - + +
230A LEU* 4.0 20.9 - - + -
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Residues in contact with ILE 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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39A VAL* 3.4 0.6 - - - -
40A SER* 2.7 37.9 + - - +
55A LYS* 4.2 13.7 - - + +
56A PHE* 1.3 81.7 - - - +
58A CYS* 1.3 73.0 + - - +
59A THR* 3.1 20.7 + - + +
67A TRP* 4.1 3.4 - - - -
223A GLU* 3.2 19.1 - - - +
225A ARG* 3.1 48.9 - - + +
226A ASP 3.7 2.7 - - - -
227A HIS* 4.0 11.9 - - + -
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Residues in contact with CYS 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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37A PHE* 4.7 5.2 - - - -
38A SER 3.5 12.3 - - - +
39A VAL* 4.2 4.7 - - + -
57A ILE* 1.3 73.5 - - - +
59A THR* 1.3 60.8 + - - +
60A THR* 3.4 22.6 + - - -
61A GLY 3.5 31.2 + - - +
62A LYS 3.9 3.1 - - - -
63A LEU* 3.7 27.4 - - + +
67A TRP* 3.7 16.3 - - + -
225A ARG* 4.8 6.9 - - - +
226A ASP* 3.0 17.9 + - + +
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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