Contacts of the helix formed by residues 44 - 59 (chain A) in PDB entry 1X2W
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 SER 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A TYR* 4.8 1.2 + - - -
10A GLU* 5.0 5.2 + - - -
42A ILE* 3.6 2.1 - - - +
43A GLU* 1.3 79.0 - - - +
45A ALA* 1.3 59.6 + - - +
46A GLY* 3.5 4.4 + - - -
47A GLU* 2.9 25.9 + - - +
48A ALA* 2.8 28.2 + - - +
87B TYR* 3.6 16.1 - - - -
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Residues in contact with ALA 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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44A SER* 1.3 73.1 - - - +
46A GLY* 1.3 58.8 + - - +
48A ALA* 3.1 2.9 + - - +
49A ASP* 2.8 29.6 + - - +
112A ARG* 3.9 16.1 + - - +
87B TYR* 3.6 26.0 - - + -
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Residues in contact with GLY 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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9A TYR* 3.1 24.8 + - - -
44A SER* 3.2 5.0 + - - -
45A ALA* 1.3 78.9 - - - +
47A GLU* 1.3 55.5 + - - +
49A ASP* 3.3 9.2 + - - +
50A PHE* 3.0 23.7 + - - +
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Residues in contact with GLU 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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9A TYR* 3.4 19.3 + - + -
12A HIS* 4.9 3.3 + - - -
14A TYR* 2.7 29.7 + - + +
41A SER* 3.1 20.9 + - - +
42A ILE* 4.4 3.8 - - - -
43A GLU* 2.4 42.9 + - - +
44A SER* 2.9 20.0 + - - +
46A GLY* 1.3 73.2 - - - +
48A ALA* 1.3 60.4 + - - +
50A PHE* 3.3 2.4 + - - +
51A VAL* 2.9 40.4 + - + +
128A GLU* 3.8 7.3 - - - +
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Residues in contact with ALA 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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42A ILE* 3.4 24.4 - - + +
44A SER 2.8 15.9 + - - +
45A ALA 3.1 5.8 + - - +
47A GLU* 1.3 72.3 - - - +
49A ASP* 1.3 66.2 + - - +
51A VAL* 3.4 4.7 + - - +
52A ALA* 3.0 24.8 + - - +
111A PHE 4.8 1.2 - - - +
112A ARG* 3.5 22.4 - - - +
114A TRP* 5.9 1.3 - - - +
87B TYR* 3.8 14.1 - - + +
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Residues in contact with ASP 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 ALA 2.8 13.5 + - - +
46A GLY* 3.4 11.9 - - - +
47A GLU 3.2 0.2 - - - -
48A ALA* 1.3 76.7 - - - +
50A PHE* 1.3 65.4 + - - +
52A ALA* 3.1 5.6 + - - +
53A GLN* 2.9 30.5 + - - +
112A ARG* 3.6 21.8 + - - +
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Residues in contact with PHE 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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7A SER* 3.9 22.0 - - - -
8A SER 3.5 23.3 - - - -
9A TYR* 3.4 43.3 - + + -
14A TYR* 3.6 34.8 - + + -
46A GLY 3.0 10.0 + - - +
47A GLU 3.3 8.3 + - - +
49A ASP* 1.3 83.8 + - - +
51A VAL* 1.3 63.0 + - - +
53A GLN* 3.1 48.4 + - - +
54A LEU* 3.2 12.9 + - + +
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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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14A TYR* 4.5 9.9 - - + -
40A VAL* 3.9 34.5 - - + -
42A ILE* 4.5 11.2 - - + -
47A GLU* 2.9 31.3 + - + +
48A ALA* 3.8 5.8 - - - +
49A ASP 3.1 0.4 - - - -
50A PHE* 1.3 75.8 - - + +
52A ALA* 1.3 64.0 + - - +
54A LEU* 3.1 8.1 + - + +
55A VAL* 2.9 36.5 + - + +
66A VAL* 6.3 0.2 - - + -
105A LEU* 4.0 23.8 - - + -
126A VAL* 5.1 6.7 - - + -
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Residues in contact with ALA 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 ALA 3.0 16.9 + - - +
49A ASP* 3.5 5.2 - - - +
51A VAL* 1.3 75.9 - - - +
53A GLN* 1.3 54.0 + - - +
55A VAL* 3.4 1.8 + - - +
56A THR* 2.6 39.4 + - - +
110A GLY 3.7 15.0 - - - +
111A PHE* 3.7 28.1 + - - +
112A ARG* 3.8 11.0 - - + +
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Residues in contact with GLN 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 ASP* 2.9 21.6 + - - +
50A PHE* 3.1 53.0 + - - -
52A ALA* 1.3 77.5 - - - +
54A LEU* 1.3 71.0 + - - +
56A THR* 3.3 6.2 + - - -
57A GLU* 3.1 32.8 + - + +
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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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7A SER* 4.1 21.5 - - - +
14A TYR* 4.0 27.4 - - + +
15A LYS 4.5 0.2 - - - +
16A PRO* 3.7 31.8 - - + +
50A PHE* 3.2 17.7 + - + +
51A VAL* 3.1 10.9 + - - +
53A GLN* 1.3 87.2 - - - +
55A VAL* 1.3 58.1 + - - +
57A GLU* 5.2 0.4 - - - -
58A ASN* 3.0 58.8 + - - +
126A VAL* 4.2 16.2 - - + -
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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 VAL* 2.9 35.0 + - + +
52A ALA* 3.7 5.2 - - - +
54A LEU* 1.3 72.5 - - - +
56A THR* 1.3 65.9 + - - +
59A ILE* 2.8 47.7 + - + +
66A VAL* 3.9 21.8 - - + -
105A LEU* 4.7 5.2 - - + -
111A PHE* 3.6 38.6 - - + -
126A VAL* 4.1 18.8 - - + -
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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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52A ALA* 2.6 27.0 + - - +
53A GLN* 3.3 8.2 + - - -
55A VAL* 1.3 76.8 - - - +
57A GLU* 1.3 70.9 + - - +
59A ILE 5.2 0.4 - - - -
60A GLN* 2.9 34.6 + - - +
110A GLY 5.1 0.9 + - - -
111A PHE* 3.7 24.1 - - + -
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Residues in contact with GLU 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 GLN* 3.1 23.2 + - + +
54A LEU* 5.2 0.2 - - - -
56A THR* 1.3 91.6 - - - +
58A ASN* 1.3 73.4 + - - +
60A GLN* 3.7 16.8 + - - +
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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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16A PRO* 3.6 23.4 - - + +
18A LYS* 4.9 11.4 + - - +
54A LEU* 3.0 47.6 + - - +
57A GLU* 1.3 89.2 - - - +
59A ILE* 1.3 62.2 + - - +
60A GLN* 3.8 4.5 + - - -
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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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16A PRO* 3.7 21.3 - - + -
17A PHE 4.5 7.2 - - - +
18A LYS* 4.2 6.7 - - + +
55A VAL* 2.8 38.1 + - + +
58A ASN* 1.3 77.0 - - - +
60A GLN* 1.3 62.6 + - - +
62A THR* 4.1 15.3 + - + +
66A VAL* 4.1 20.4 - - + -
111A PHE* 4.6 9.0 - - - -
124A PRO* 3.8 31.0 - - + -
125A PHE 3.7 24.2 - - - +
126A VAL* 3.9 10.3 - - + -
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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