Contacts of the helix formed by residues 41 - 56 (chain A) in PDB entry 1X3A
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 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ASN* 4.0 11.5 + - - +
40A PHE* 1.3 80.0 - - - +
42A PHE* 1.3 61.2 + - - +
43A ASP* 3.6 8.9 - - - +
44A GLN* 3.0 26.0 + - + +
45A MET* 2.8 30.8 + - + +
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Residues in contact with PHE 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 PHE* 3.3 21.1 + - + -
41A ASP* 1.3 64.7 - - - +
43A ASP* 1.3 68.6 + - + +
44A GLN 2.4 12.6 + - - -
45A MET 2.5 2.9 + - - -
46A TYR* 2.4 69.3 + + + -
73A GLU* 4.3 8.7 - - + -
74A GLU* 3.3 69.5 - - + +
77A TRP* 4.0 22.0 - + + -
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Residues in contact with ASP 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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41A ASP* 4.3 9.9 - - - +
42A PHE* 1.3 92.5 + - + +
44A GLN* 1.3 81.2 + - - +
46A TYR* 3.6 10.2 - - - +
47A PRO* 3.2 17.7 - - - +
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Residues in contact with GLN 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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41A ASP* 3.0 30.7 + - + +
42A PHE 2.4 9.3 + - - -
43A ASP* 1.3 91.6 + - - +
45A MET* 1.3 65.3 + - + +
46A TYR 3.2 3.0 + - - -
47A PRO* 3.5 11.3 - - - +
48A VAL* 3.7 14.4 - - - +
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Residues in contact with MET 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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40A PHE* 3.6 26.5 - - + -
41A ASP 2.8 13.9 + - - +
42A PHE* 2.5 8.8 + - - -
44A GLN* 1.3 78.9 - - + +
46A TYR* 1.3 61.9 + - - +
47A PRO 3.6 0.2 - - - -
48A VAL* 4.2 24.5 - - + -
49A ALA* 3.4 19.4 + - - +
77A TRP* 4.9 2.1 - - - -
81A PHE* 3.1 49.8 - - + -
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Residues in contact with TYR 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 PHE* 2.4 59.7 + + + +
43A ASP* 3.6 11.0 - - - +
45A MET* 1.3 76.7 - - - +
47A PRO* 1.3 83.0 - - + +
49A ALA* 3.4 14.1 - - - +
50A LEU* 3.8 27.6 + - + +
73A GLU* 3.6 20.0 - - - -
77A TRP* 4.6 6.6 + - - -
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Residues in contact with PRO 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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43A ASP 3.2 13.5 - - - +
44A GLN 3.5 9.0 - - - +
46A TYR* 1.3 107.3 - - + +
48A VAL* 1.3 61.8 + - + +
49A ALA 2.9 4.7 - - - -
50A LEU* 2.6 51.0 + - + +
51A VAL* 3.8 4.2 + - - +
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Residues in contact with VAL 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 GLN 3.7 17.3 - - - +
45A MET* 4.2 31.9 - - + -
46A TYR 3.5 0.4 - - - -
47A PRO* 1.3 80.2 - - + +
49A ALA* 1.3 58.7 + - - +
50A LEU 3.6 0.2 + - - -
51A VAL* 3.6 18.3 + - + +
52A MET* 3.7 13.4 - - + +
81A PHE* 4.8 4.0 - - + -
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Residues in contact with ALA 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 MET 3.4 10.8 + - - +
46A TYR 3.4 10.7 + - - +
47A PRO 2.8 0.8 + - - -
48A VAL* 1.3 75.9 - - - +
50A LEU* 1.3 65.0 + - - +
51A VAL 3.1 2.0 - - - -
52A MET* 3.0 21.0 + - - +
53A LEU* 3.1 15.5 + - - +
77A TRP* 3.3 49.4 - - + -
81A PHE* 4.2 6.3 - - + -
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Residues in contact with LEU 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 TYR* 4.2 25.6 - - + +
47A PRO* 2.6 38.7 + - + +
49A ALA* 1.3 73.0 - - - +
51A VAL* 1.3 60.2 + - + +
53A LEU* 3.2 30.4 + - + +
54A GLN* 3.4 15.1 + - - +
63A ARG* 5.9 3.4 - - - +
77A TRP* 6.0 0.4 - - + +
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Residues in contact with VAL 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 PRO 3.8 5.4 + - - +
48A VAL* 3.6 13.4 + - + +
49A ALA 3.1 0.6 - - - -
50A LEU* 1.3 78.9 - - + +
52A MET* 1.3 61.3 - - + +
54A GLN* 2.8 46.6 + - - +
55A GLU* 3.2 12.9 - - - +
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Residues in contact with MET 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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18A ILE* 4.5 28.5 - - + -
48A VAL* 3.7 17.9 - - + +
49A ALA* 3.0 13.1 + - - +
51A VAL* 1.3 77.0 - - + +
53A LEU* 1.3 59.0 + - - +
55A GLU* 3.0 34.7 - - - +
56A ASP* 3.0 31.4 + - - +
59A LEU* 3.6 17.0 - - + +
77A TRP* 5.2 1.3 - - + -
80A TYR* 5.0 6.5 - - + +
81A PHE* 4.4 22.7 - - + -
84A VAL* 5.3 5.2 - - + -
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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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49A ALA 3.1 6.4 + - - +
50A LEU* 3.4 36.1 - - + +
51A VAL 3.2 0.2 - - - -
52A MET* 1.3 74.9 - - - +
54A GLN* 1.3 67.8 + - - +
55A GLU 3.1 1.1 - - - -
56A ASP 2.5 29.4 + - - +
57A GLU* 3.6 0.5 + - - -
59A LEU* 3.7 11.2 - - + +
60A SER* 3.5 38.6 + - - +
63A ARG* 4.1 19.3 - - - +
77A TRP* 3.5 37.0 - - + -
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Residues in contact with GLN 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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50A LEU 3.4 10.9 + - - +
51A VAL* 2.8 39.2 + - - +
53A LEU* 1.3 75.5 - - - +
55A GLU* 1.3 91.7 + - - +
57A GLU* 4.4 6.1 + - - +
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Residues in contact with GLU 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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15A GLN* 4.0 15.2 + - - +
51A VAL* 3.2 20.9 - - - +
52A MET* 3.0 37.4 - - - +
53A LEU 3.1 0.8 - - - -
54A GLN* 1.3 96.2 + - - +
56A ASP* 1.3 84.8 + - - +
57A GLU* 3.8 9.9 + - - +
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Residues in contact with ASP 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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15A GLN* 4.1 2.8 + - - -
18A ILE* 5.7 2.4 - - - +
19A LEU* 3.1 33.6 - - + +
22A SER* 4.6 4.0 - - - +
52A MET* 3.0 19.6 - - - +
53A LEU 2.5 17.8 + - - +
55A GLU* 1.3 100.1 - - - +
57A GLU* 1.3 68.7 + - - +
58A LEU* 3.2 2.0 - - + +
59A LEU* 3.2 29.0 + - + +
60A SER 3.3 6.6 + - - -
80A TYR* 4.7 4.5 + - - -
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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