Contacts of the helix formed by residues 29 - 42 (chain A) in PDB entry 1XT9
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 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ASN* 1.3 71.6 - - - +
30A HIS* 1.3 68.0 + - - -
33A GLY* 2.8 29.5 + - - -
56A PRO* 3.8 31.6 - - + +
57A GLU* 4.2 14.8 - - + +
103A TRP* 3.8 2.4 - - - -
42B ARG* 2.8 49.4 + - - +
71B LEU 4.5 0.5 - - - +
72B ALA* 3.5 1.7 - - - -
73B LEU* 2.9 38.9 + - + +
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Residues in contact with HIS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 4.9 2.9 - - - -
12A LEU* 3.8 24.0 + - + +
13A LEU* 3.6 6.5 - - + +
14A ARG* 5.0 8.8 - - + +
17A ASP* 3.3 36.3 - - - +
28A ASN* 3.3 9.1 - - - +
29A ASP* 1.3 85.0 + - - +
31A ILE* 1.3 57.1 + - - +
33A GLY* 3.7 0.8 - - - -
34A PHE* 2.9 30.5 + - - +
57A GLU* 4.6 6.4 + - - -
27B LYS* 5.4 4.7 + - - -
39B GLN 5.1 1.0 + - - -
41B GLN 5.1 0.9 - - - -
42B ARG* 3.2 51.0 + - - -
52B ASP* 5.8 4.4 + - - -
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Residues in contact with ILE 31 (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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13A LEU* 4.4 16.2 - - + -
17A ASP* 3.6 36.8 - - + +
18A VAL* 4.4 2.5 - - - +
20A LEU* 4.5 1.6 - - + -
21A LEU* 4.3 21.5 - - + -
27A LEU* 3.8 41.5 - - + -
28A ASN* 3.1 22.3 + - - +
30A HIS* 1.3 74.6 - - - +
32A ILE* 1.3 65.4 + - + +
34A PHE* 3.2 8.3 + - + +
35A ALA* 3.1 20.1 + - + +
165A MET* 5.7 0.4 - - - -
168A ILE* 5.6 2.7 - - + -
206A ILE* 4.7 4.5 - - + -
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Residues in contact with ILE 32 (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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27A LEU* 4.1 9.4 - - + -
28A ASN 3.3 15.0 + - - +
31A ILE* 1.3 76.4 - - - +
33A GLY* 1.3 63.5 + - - +
35A ALA* 3.2 4.2 + - - +
36A PHE* 3.0 31.0 + - + +
56A PRO* 3.8 13.5 - - + -
89A ALA* 3.9 26.7 - - + -
103A TRP* 4.4 19.1 - - + +
164A GLY* 3.3 30.3 - - - +
167A VAL* 4.5 6.7 - - + -
168A ILE* 3.2 32.8 - - + -
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Residues in contact with GLY 33 (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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11A SER* 4.2 7.0 - - - -
29A ASP 2.8 19.4 + - - -
30A HIS* 3.7 1.1 - - - -
32A ILE* 1.3 75.0 - - - +
34A PHE* 1.3 64.7 + - - +
36A PHE* 3.3 6.0 + - - +
37A GLU* 2.9 26.3 + - - +
55A SER* 5.0 0.9 - - - -
56A PRO* 4.2 13.9 - - - +
57A GLU* 5.3 0.7 - - - -
49B GLN* 4.2 13.3 - - - +
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Residues in contact with PHE 34 (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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6A LEU* 3.7 16.4 - - + -
8A TYR* 3.8 27.4 - + + -
11A SER* 3.5 25.4 - - - +
13A LEU* 3.9 20.6 - - + -
30A HIS 2.9 17.7 + - - +
31A ILE* 3.6 6.3 - - + +
33A GLY* 1.3 74.7 - - - +
35A ALA* 1.3 67.3 + - - +
37A GLU* 2.9 4.9 + - - +
38A TYR* 2.8 26.2 + - + +
202A TRP* 3.6 31.9 - + - -
205A LEU* 3.9 9.6 - - + -
206A ILE* 3.7 29.4 - - + -
209A LEU* 3.9 20.2 - - + -
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Residues in contact with ALA 35 (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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31A ILE* 3.1 8.6 + - + +
32A ILE 3.4 8.5 - - - +
34A PHE* 1.3 79.5 - - - +
36A PHE* 1.3 58.2 + - - +
38A TYR* 3.2 4.7 + - - +
39A PHE* 2.9 35.5 + - + -
168A ILE* 3.6 39.3 - - + -
202A TRP* 3.6 24.7 - - + -
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Residues in contact with PHE 36 (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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32A ILE* 3.0 26.4 + - + +
33A GLY* 3.7 9.2 - - - +
35A ALA* 1.3 73.3 - - - +
37A GLU* 1.3 66.1 + - - +
39A PHE* 3.3 18.7 + + - +
40A ALA* 3.0 24.6 + - - +
53A PHE* 3.7 27.6 - - + +
54A ILE 3.2 35.2 - - - -
55A SER* 4.2 6.7 - - - +
87A PHE* 4.1 17.0 - - + -
89A ALA* 4.1 21.5 - - + -
105A LEU* 4.4 7.4 - - + -
167A VAL* 4.5 2.7 - - + -
168A ILE* 4.5 6.7 - - + -
171A THR* 3.7 30.1 - - + -
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Residues in contact with GLU 37 (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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8A TYR* 3.9 13.0 - - + +
9A MET* 3.1 7.4 - - - +
10A ASP* 2.7 35.3 + - - +
11A SER* 3.8 26.9 - - - +
33A GLY 2.9 15.8 + - - +
34A PHE 2.9 7.4 + - - +
36A PHE* 1.3 75.9 - - - +
38A TYR* 1.3 59.2 + - - +
40A ALA* 3.3 5.0 + - - +
41A ASN* 2.9 44.7 + - - +
48B LYS* 2.7 29.8 + - - -
49B GLN* 4.5 7.6 + - - +
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Residues in contact with TYR 38 (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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8A TYR* 3.8 19.4 - + + -
34A PHE* 2.8 16.6 + + + +
35A ALA 3.4 8.5 - - - +
37A GLU* 1.3 75.7 - - - +
39A PHE* 1.3 59.6 + - - +
42A SER* 2.9 53.7 + - - -
43A GLN* 3.0 44.5 + - + +
202A TRP* 3.9 21.1 - + + -
205A LEU* 3.9 39.7 - - + +
209A LEU* 4.4 12.8 - - + -
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Residues in contact with PHE 39 (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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35A ALA 2.9 20.5 + - - -
36A PHE* 3.5 23.1 - + - +
38A TYR* 1.3 76.4 - - - +
40A ALA* 1.3 61.3 + - - +
43A GLN* 3.7 24.9 - - - -
44A PHE* 2.7 45.4 + + + +
53A PHE* 3.7 20.6 - + + -
168A ILE* 3.7 13.5 - - + -
171A THR* 3.7 35.2 - - + -
172A GLU* 3.6 28.9 - - + -
202A TRP* 3.6 30.7 - + - -
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Residues in contact with ALA 40 (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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36A PHE 3.0 17.0 + - - +
37A GLU* 3.8 9.0 - - - +
38A TYR 3.3 0.2 - - - -
39A PHE* 1.3 77.8 - - - +
41A ASN* 1.3 68.7 + - - +
44A PHE 4.1 1.9 - - - +
45A HIS* 3.3 19.9 - - - +
48A SER* 5.5 4.5 - - - -
53A PHE* 3.7 24.0 - - + +
48B LYS* 5.9 1.8 - - - +
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Residues in contact with ASN 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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8A TYR* 4.2 6.4 + - - +
9A MET* 3.5 46.4 - - + +
37A GLU* 2.9 41.0 + - - +
40A ALA* 1.3 81.5 + - - +
42A SER* 1.3 60.1 + - - +
45A HIS* 3.4 15.2 - - - +
48B LYS* 4.8 4.0 + - - +
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Residues in contact with SER 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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8A TYR* 3.3 22.6 + - - -
38A TYR* 2.9 31.6 + - - -
40A ALA 3.6 0.8 - - - -
41A ASN* 1.3 78.3 - - - +
43A GLN* 1.3 69.0 + - - +
44A PHE 3.1 1.9 + - - -
45A HIS* 3.2 22.2 + - - -
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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