Contacts of the helix formed by residues 43 - 57 (chain A) in PDB entry 3PIK
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 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A PHE 4.3 0.2 - - - -
42A VAL* 1.3 79.7 - - - +
44A ASN* 1.3 59.6 + - - +
45A GLN* 2.9 14.0 + - - +
46A VAL* 2.8 54.9 + - + +
47A LYS* 3.8 8.0 - - - +
156A TYR* 3.7 12.2 + - - -
157A PHE* 4.7 2.9 - - + -
239A GLN* 2.7 36.8 + - - +
241A VAL* 4.0 6.8 - - - +
245A SER* 3.2 24.5 + - - +
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Residues in contact with ASN 44 (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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42A VAL 3.1 6.5 + - - +
43A ASP* 1.3 72.8 + - - +
45A GLN* 1.3 66.5 + - - +
46A VAL 3.3 0.2 - - - -
47A LYS* 3.3 23.2 + - - +
48A THR* 3.1 28.8 + - - -
239A GLN* 5.5 0.2 - - - +
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Residues in contact with GLN 45 (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 ASP* 2.9 9.1 + - - +
44A ASN* 1.3 78.3 - - - +
46A VAL* 1.3 62.9 + - - +
48A THR* 3.1 19.1 + - - +
49A LEU* 3.1 18.2 + - + +
156A TYR* 3.7 10.1 - - + +
236A PRO* 3.4 42.8 - - + +
237A GLN* 4.1 13.9 + - - +
239A GLN* 3.5 22.1 - - - +
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Residues in contact with VAL 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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41A PHE* 3.8 29.2 - - + -
43A ASP* 2.8 30.1 + - + +
45A GLN* 1.3 75.2 - - - +
47A LYS* 1.3 60.5 + - - +
49A LEU* 3.3 5.3 + - - +
50A ILE* 3.0 34.7 + - + +
152A VAL* 4.8 0.9 - - + +
153A ALA* 3.5 38.1 - - + +
156A TYR* 3.7 34.0 - - + -
157A PHE* 4.2 6.1 - - + -
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Residues in contact with LYS 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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37A TRP* 3.7 21.2 - - + +
38A ARG* 2.9 45.9 + - + +
41A PHE* 3.3 34.8 + - + +
42A VAL* 3.9 8.5 + - - +
43A ASP 3.8 11.0 - - - +
44A ASN* 3.3 24.3 + - - +
45A GLN 3.1 0.6 - - - -
46A VAL* 1.3 78.4 - - - +
48A THR* 1.3 61.9 + - - +
50A ILE* 3.3 4.0 + - - +
51A SER* 2.9 32.5 + - - -
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Residues in contact with THR 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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44A ASN* 3.1 24.2 + - - -
45A GLN* 3.4 15.1 + - - +
47A LYS* 1.3 77.9 - - - +
49A LEU* 1.3 63.8 - - + +
51A SER* 3.5 6.6 + - - +
52A GLU* 3.2 41.7 + - + +
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Residues in contact with LEU 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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45A GLN* 3.1 13.3 + - + +
46A VAL* 3.7 5.6 - - - +
48A THR* 1.3 77.8 - - + +
50A ILE* 1.3 61.0 + - - +
52A GLU* 3.3 11.6 + - - +
53A ALA* 2.9 24.9 + - - +
152A VAL* 4.0 11.9 - - + -
156A TYR* 3.5 40.8 - - + -
225A LEU* 4.3 11.7 - - + -
229A LEU* 3.1 38.5 - - + +
234A LYS 5.9 1.3 - - - +
236A PRO* 3.6 28.5 - - + -
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Residues in contact with ILE 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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37A TRP* 3.7 33.4 - - + -
41A PHE* 3.8 37.0 - - + -
46A VAL* 3.0 28.8 + - + +
47A LYS* 3.3 6.7 + - - +
49A LEU* 1.3 77.3 - - - +
51A SER* 1.3 63.4 + - - +
53A ALA* 3.2 4.8 + - - +
54A LEU* 2.9 32.1 + - + +
149A VAL* 3.9 38.1 - - + +
152A VAL* 4.0 18.8 - - + -
153A ALA 4.7 0.2 - - - +
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Residues in contact with SER 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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37A TRP* 3.6 14.6 - - - -
38A ARG* 5.1 4.0 + - - -
47A LYS 2.9 19.2 + - - -
48A THR* 3.8 7.6 - - - -
49A LEU 3.3 0.2 - - - -
50A ILE* 1.3 79.0 - - - +
52A GLU* 1.3 62.9 + - - +
54A LEU* 3.4 16.8 + - - +
55A VAL* 3.4 19.5 + - - +
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Residues in contact with GLU 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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48A THR* 3.2 32.0 + - + +
49A LEU* 3.7 13.0 - - - +
51A SER* 1.3 76.0 - - - +
53A ALA* 1.3 66.8 + - - +
55A VAL* 3.0 17.4 + - - +
56A ASN* 3.0 22.3 + - - +
229A LEU* 3.9 23.9 - - + +
231A SER* 4.3 12.8 + - - +
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Residues in contact with ALA 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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49A LEU 2.9 18.3 + - - +
50A ILE 3.5 4.3 - - - +
52A GLU* 1.3 75.9 - - - +
54A LEU* 1.3 60.6 + - - +
57A ASN* 2.8 32.8 + - - +
60A LEU* 4.9 0.3 - - - +
148A LEU* 3.9 8.9 - - + +
152A VAL* 3.6 28.0 - - + -
228A LEU 4.0 8.5 - - - +
229A LEU* 3.9 20.1 - - + +
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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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37A TRP* 3.9 20.9 - - + -
38A ARG* 5.5 1.8 - - - +
50A ILE* 2.9 25.9 + - + +
51A SER* 3.6 10.5 - - - +
52A GLU 3.3 0.2 - - - -
53A ALA* 1.3 76.2 - - - +
55A VAL* 1.3 61.3 + - + +
57A ASN 5.1 0.2 + - - -
60A LEU* 3.7 29.9 - - + +
145A HIS* 3.7 29.4 - - + +
148A LEU* 4.1 11.9 - - + -
149A VAL* 4.3 9.6 - - + -
451A SO4 3.9 21.5 - - - +
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Residues in contact with VAL 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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51A SER 3.4 16.2 - - - +
52A GLU* 3.0 9.5 + - - +
54A LEU* 1.3 83.1 - - + +
56A ASN* 1.3 77.6 + - - +
57A ASN 3.6 1.9 + - - +
58A ARG* 4.6 5.2 + - - -
61A ARG* 5.7 2.8 - - - +
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Residues in contact with ASN 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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52A GLU* 3.0 22.2 + - - +
55A VAL* 1.3 93.1 - - - +
57A ASN* 1.3 66.2 + - - +
58A ARG* 3.1 27.1 + - - +
229A LEU 3.2 17.0 - - - +
230A GLY* 3.6 17.9 - - - +
231A SER* 4.1 17.9 + - - -
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Residues in contact with ASN 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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53A ALA 2.8 17.9 + - - +
54A LEU 5.8 0.2 - - - +
55A VAL 3.6 1.6 - - - +
56A ASN* 1.3 77.5 - - - +
58A ARG* 1.3 60.0 + - - +
59A ASP* 3.0 16.0 + - - +
60A LEU* 3.0 31.3 + - + +
61A ARG* 3.1 26.3 + - - +
144A VAL* 5.7 0.2 - - - +
148A LEU* 3.5 30.2 - - + +
227A LEU 4.3 2.8 + - - -
228A LEU* 2.6 41.0 + - - +
229A LEU 3.6 3.7 + - - -
230A GLY 4.7 0.9 - - - +
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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