Contacts of the helix formed by residues 40 - 51 (chain A) in PDB entry 4PIM
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A TRP 4.6 1.4 + - - +
38A PHE 3.5 1.0 + - - +
39A TYR* 1.3 77.7 - - - +
41A ALA* 1.3 68.9 + - - +
42A VAL* 3.7 14.2 + - - +
43A GLY* 2.9 25.8 + - - -
44A SER* 2.8 22.1 + - - -
219A ASN* 3.1 13.4 + - - +
223A VAL* 3.6 20.8 - - + +
226A ARG* 2.8 36.8 + - - +
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Residues in contact with ALA 41 (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 ASP* 1.3 75.5 + - - +
42A VAL* 1.3 66.4 + - + +
44A SER* 3.5 4.2 + - - -
45A ASP* 3.2 31.7 + - - +
115A ASP* 6.0 2.5 - - - +
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Residues in contact with VAL 42 (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 ASP* 3.2 14.1 + - - +
41A ALA* 1.3 78.8 - - + +
43A GLY* 1.3 63.5 + - - +
45A ASP* 3.2 1.4 + - - -
46A LEU* 3.0 30.4 + - + +
219A ASN* 3.5 24.0 - - - +
226A ARG* 5.7 2.9 - - - +
49B GLN* 3.0 25.0 + - - +
53B LEU* 3.8 24.0 - - + -
54B PRO* 5.7 4.0 - - + -
210B ALA* 3.9 17.0 - - + -
212B VAL* 4.0 4.5 - - + -
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Residues in contact with GLY 43 (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 11.9 - - - -
39A TYR* 4.5 1.3 - - - -
40A ASP* 2.9 18.5 + - - -
42A VAL* 1.3 77.1 - - - +
44A SER* 1.3 57.2 + - - +
46A LEU* 3.4 3.6 + - - -
47A PHE* 2.9 24.9 + - - +
216A PHE* 3.5 22.5 - - - -
219A ASN* 3.5 12.1 - - - +
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Residues in contact with SER 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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39A TYR* 3.2 26.3 + - - +
40A ASP 2.8 19.9 + - - -
41A ALA* 3.9 5.4 - - - -
43A GLY* 1.3 75.8 - - - +
45A ASP* 1.3 61.5 + - - +
47A PHE* 3.3 9.9 + - - +
48A ASP* 3.0 26.5 + - - +
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Residues in contact with ASP 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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41A ALA* 3.2 16.7 + - - +
44A SER* 1.3 78.9 - - - +
46A LEU* 1.3 64.4 + - - +
48A ASP* 3.4 9.7 + - - +
49A GLN* 3.1 30.9 + - - +
49B GLN* 3.5 24.4 + - + +
52B ARG* 3.3 35.0 + - - +
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Residues in contact with LEU 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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42A VAL* 3.0 32.4 + - + +
43A GLY* 3.7 7.6 - - - +
45A ASP* 1.3 73.7 - - - +
47A PHE* 1.3 65.8 + - - +
49A GLN* 3.1 8.7 + - - +
50A ILE* 3.0 25.5 + - - +
212A VAL* 4.0 10.6 - - + +
215A ALA* 3.9 24.9 - - + +
216A PHE* 3.9 31.4 - - + -
219A ASN* 4.3 6.3 - - + -
46B LEU* 4.1 21.5 - - + -
49B GLN* 3.3 21.5 - - - +
210B ALA 5.6 0.2 - - - +
212B VAL* 4.5 9.2 - - + -
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Residues in contact with PHE 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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39A TYR* 4.4 26.9 - + + -
43A GLY 2.9 14.6 + - - +
44A SER* 3.6 10.1 - - - +
45A ASP 3.3 0.2 - - - -
46A LEU* 1.3 77.9 - - - +
48A ASP* 1.3 65.2 + - + +
50A ILE* 2.9 33.1 + - + +
51A THR* 3.1 33.1 + - + +
56A TYR* 4.2 24.0 - + - -
163A THR* 6.1 0.9 - - - -
216A PHE* 4.3 6.1 - + + -
401A ACT 4.7 17.0 - - + -
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Residues in contact with ASP 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 SER 3.0 14.2 + - - +
45A ASP* 3.4 13.3 - - - +
47A PHE* 1.3 78.1 - - - +
49A GLN* 1.3 61.1 + - - +
51A THR* 2.4 35.0 + - - +
52A ARG* 2.9 38.8 + - - -
89A THR* 5.9 2.4 - - - +
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Residues in contact with GLN 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 ASP* 3.1 15.4 + - - +
46A LEU* 3.1 10.2 + - - +
48A ASP* 1.3 73.4 - - - +
50A ILE* 1.3 66.6 + - - +
52A ARG* 3.0 37.2 + - - +
53A LEU* 3.5 14.2 + - + +
212A VAL* 4.2 11.5 - - + +
42B VAL* 4.4 0.9 - - - +
45B ASP* 3.6 18.1 + - + +
46B LEU* 3.3 36.1 + - - +
49B GLN* 2.8 44.2 + - - +
52B ARG* 5.6 1.4 - - - +
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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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46A LEU 3.0 18.1 + - - +
47A PHE* 2.9 25.6 + - + +
49A GLN* 1.3 75.1 - - - +
51A THR* 1.3 58.0 + - - +
53A LEU* 2.9 31.3 + - + +
56A TYR* 3.3 40.4 - - + +
205A ALA 4.6 2.7 - - - +
206A TYR* 6.1 1.8 - - + -
212A VAL* 3.8 14.3 - - + +
213A THR* 3.9 38.4 - - + +
216A PHE* 4.0 22.4 - - + -
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Residues in contact with THR 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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47A PHE* 3.1 43.4 + - + +
48A ASP* 2.4 31.3 + - - +
50A ILE* 1.3 74.4 - - - +
52A ARG* 1.3 64.2 + - - +
53A LEU 3.5 0.2 - - - -
56A TYR* 3.7 16.1 - - + +
59A THR* 3.4 38.9 - - + +
60A ARG* 4.2 8.3 + - - -
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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