Contacts of the helix formed by residues 31 - 45 (chain F) in PDB entry 1XBT
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 GLY 31 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E ARG* 3.5 23.2 - - - -
42E ARG* 5.0 0.6 - - - +
29F PHE 3.4 1.6 - - - -
30F SER* 1.3 79.7 - - - +
32F LYS* 1.3 59.5 + - - +
33F SER 3.3 2.9 - - - -
34F THR* 3.2 10.9 + - - -
35F GLU* 2.9 26.2 + - - +
149F LEU* 3.9 1.6 - - - -
6195F TTP 3.0 14.7 + - - -
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Residues in contact with LYS 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ILE* 3.9 11.7 - - + +
25F LEU 3.8 11.2 - - - +
26F GLY 3.6 14.1 - - - +
27F PRO 2.9 24.4 + - - -
30F SER* 3.5 10.9 - - - +
31F GLY* 1.3 71.7 - - - +
33F SER* 1.3 55.5 + - - +
35F GLU* 3.3 4.2 + - - +
36F LEU* 2.9 28.1 + - - +
97F ASP* 5.6 1.1 - - - +
98F GLU* 6.5 0.4 - - - +
122F ALA* 3.8 16.2 - - + +
123F ALA* 3.2 33.2 - - - +
124F LEU* 3.3 11.9 - - - +
149F LEU* 3.9 9.1 - - + +
6195F TTP 2.6 61.7 + - - +
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Residues in contact with SER 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F LYS* 1.3 74.6 - - - +
34F THR* 1.3 60.4 + - - +
36F LEU* 3.4 8.0 + - - +
37F MET* 3.0 37.0 + - - +
97F ASP* 2.7 32.5 + - - -
122F ALA* 4.4 0.2 - - - +
6194F MG 2.6 21.7 - - - -
6195F TTP 3.3 10.7 + - - -
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Residues in contact with THR 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E THR* 3.7 25.1 - - + +
38E ARG* 3.8 26.1 - - + -
41E ARG* 4.1 21.7 + - - +
31F GLY* 3.2 14.5 + - - -
33F SER* 1.3 78.8 - - - +
35F GLU* 1.3 56.5 + - - +
37F MET* 3.3 6.5 + - + +
38F ARG* 2.9 27.5 + - - +
41F ARG* 6.2 0.2 - - - +
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Residues in contact with GLU 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E GLU* 3.9 12.8 - - - +
38E ARG* 4.3 7.5 + - - +
24F ILE* 3.9 15.3 - - + -
31F GLY 2.9 16.2 + - - +
32F LYS 3.7 4.0 - - - +
34F THR* 1.3 73.1 - - - +
36F LEU* 1.3 65.7 + - - +
38F ARG* 2.9 44.5 + - - +
39F ARG* 3.0 53.3 + - - +
149F LEU* 4.1 19.3 - - + -
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Residues in contact with LEU 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ILE* 3.8 9.5 - - + +
32F LYS 2.9 16.5 + - - +
33F SER 3.6 4.0 - - - +
34F THR 3.3 0.2 - - - -
35F GLU* 1.3 75.7 - - - +
37F MET* 1.3 73.1 + - + +
39F ARG* 3.3 4.3 + - - +
40F VAL* 2.9 36.1 + - + +
52F VAL* 4.9 1.1 - - + -
95F GLY* 3.8 13.0 - - - -
96F ILE 3.7 28.5 - - - +
97F ASP* 3.8 19.1 - - + +
120F ILE* 3.3 46.4 - - + +
121F VAL 4.5 0.4 - - - +
122F ALA* 4.0 10.8 - - + +
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Residues in contact with MET 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E THR* 5.8 0.2 - - + -
33F SER* 3.0 23.1 + - - +
34F THR* 3.7 6.1 - - - +
36F LEU* 1.3 84.7 - - + +
38F ARG* 1.3 61.7 + - - +
40F VAL* 3.7 6.0 - - - +
41F ARG* 2.8 68.2 + - - +
52F VAL* 3.4 45.3 - - + -
75F ALA* 5.9 2.5 - - + -
97F ASP* 5.6 3.6 - - + +
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Residues in contact with ARG 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E SER 2.7 28.5 + - - -
31E GLY* 3.4 35.8 - - - +
34E THR* 3.8 16.4 - - + +
35E GLU* 4.2 16.3 + - - +
149E LEU* 3.9 24.6 - - - +
150E THR 4.3 3.8 + - - +
34F THR 2.9 17.0 + - - +
35F GLU* 2.9 43.9 + - - +
36F LEU 3.3 0.2 - - - -
37F MET* 1.3 77.9 - - - +
39F ARG* 1.3 73.5 + - - +
41F ARG* 3.5 6.3 + - - +
42F ARG* 3.3 41.3 + - - +
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Residues in contact with ARG 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F GLN* 2.7 52.2 + - - +
23F VAL 4.9 1.6 + - - +
24F ILE* 3.6 19.5 - - - +
35F GLU* 3.0 43.6 + - - +
36F LEU 3.6 7.2 - - - +
38F ARG* 1.3 86.0 - - - +
40F VAL* 1.3 60.8 + - - +
42F ARG* 3.4 28.6 + - - +
43F PHE* 3.3 21.4 - - - -
120F ILE* 4.0 20.4 - - + -
145F SER* 4.2 10.7 + - - -
147F VAL* 3.6 30.5 - - - +
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Residues in contact with VAL 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F LEU* 2.9 33.3 + - + +
37F MET* 3.9 7.9 - - - +
39F ARG* 1.3 74.1 - - - +
41F ARG* 1.3 65.6 + - + +
43F PHE* 3.1 12.4 + - - +
44F GLN* 3.0 24.2 + - - +
50F CYS* 3.9 27.3 - - + -
51F LEU 5.5 0.9 - - - +
52F VAL* 4.1 19.7 - - + -
93F VAL* 4.6 4.9 - - + -
95F GLY* 4.3 15.5 - - - +
120F ILE* 4.1 16.6 - - + -
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Residues in contact with ARG 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E THR* 4.1 24.1 + - - +
37F MET* 2.8 57.3 + - - +
38F ARG* 4.0 5.3 - - - +
40F VAL* 1.3 71.3 - - + +
42F ARG* 1.3 60.5 + - - +
44F GLN* 3.7 19.2 - - - +
45F ILE* 2.9 34.0 + - - +
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Residues in contact with ARG 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E PHE 3.7 19.9 - - - +
30E SER 3.9 6.3 - - - +
31E GLY* 5.5 0.4 - - - -
150E THR* 2.7 49.5 + - - +
151E ALA* 3.9 9.4 + - - +
152E VAL* 3.6 29.3 + - + +
159E GLU* 4.1 7.1 + - - +
22F GLN* 5.9 1.6 + - - +
38F ARG* 3.3 40.1 + - - +
39F ARG* 3.4 30.1 + - - +
40F VAL 3.2 0.6 - - - -
41F ARG* 1.3 75.8 - - - +
43F PHE* 1.3 79.4 + - - +
45F ILE* 3.3 20.5 - - - +
46F ALA* 3.6 3.8 + - - +
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Residues in contact with PHE 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E VAL* 3.9 18.4 - - + -
157E PHE 5.8 1.8 - - - -
20F GLN* 5.3 2.0 - - - -
22F GLN* 4.9 8.5 - - - -
39F ARG* 3.3 24.9 - - + -
40F VAL 3.1 6.3 + - - +
42F ARG* 1.3 92.9 - - - +
44F GLN* 1.3 66.0 + - - +
46F ALA* 3.0 12.2 + - - -
47F GLN 3.3 0.3 + - - -
48F TYR* 3.1 49.6 + + + +
50F CYS* 4.3 1.6 - - - -
93F VAL* 3.9 34.1 - - + -
118F THR* 4.2 22.4 - - + -
120F ILE* 4.2 16.2 - - + -
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Residues in contact with GLN 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F VAL* 3.0 20.3 + - - +
41F ARG* 3.8 18.3 - - - +
43F PHE* 1.3 77.4 - - - +
45F ILE* 1.3 58.4 + - - +
47F GLN* 2.9 22.5 + - - +
48F TYR 3.8 13.5 - - - +
50F CYS* 3.8 25.1 + - + +
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Residues in contact with ILE 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E PHE* 4.1 39.3 - - + +
152E VAL 6.2 0.4 - - - +
154E MET* 3.6 25.4 - - + +
178E ALA* 4.9 11.1 - - + +
41F ARG 2.9 20.5 + - - +
42F ARG* 3.3 16.6 - - - +
44F GLN* 1.3 76.0 - - - +
46F ALA* 1.3 56.7 + - + +
47F GLN* 3.2 7.5 + - - +
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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