Contacts of the helix formed by residues 31 - 45 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C ARG* 3.4 21.8 - - - -
42C ARG* 5.0 0.6 - - - +
29D PHE 3.4 1.4 - - - -
30D SER* 1.3 80.1 - - - +
32D LYS* 1.3 64.2 + - - +
33D SER 3.3 2.9 - - - -
34D THR* 3.2 10.0 + - - -
35D GLU* 3.0 20.4 + - - +
149D LEU* 4.0 2.2 - - - -
4195D TTP 3.1 14.2 + - - -
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Residues in contact with LYS 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 4.0 8.4 - - + +
25D LEU 3.7 10.8 - - - +
26D GLY* 3.5 18.2 - - - +
27D PRO 2.9 19.2 + - - -
30D SER* 3.3 12.3 - - - +
31D GLY* 1.3 72.0 - - - +
33D SER* 1.3 56.4 + - - +
35D GLU* 3.3 2.8 + - - +
36D LEU* 2.9 28.1 + - - +
97D ASP* 5.9 0.2 - - - +
122D ALA* 3.7 18.3 - - + +
123D ALA* 3.4 32.1 - - - +
124D LEU* 3.2 11.7 - - - +
149D LEU* 3.9 11.9 - - + -
4195D TTP 2.7 62.8 + - - +
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Residues in contact with SER 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D GLY 3.3 0.6 - - - -
32D LYS* 1.3 74.5 - - - +
34D THR* 1.3 60.5 + - - +
36D LEU* 3.3 8.4 - - - +
37D MET* 3.0 34.7 + - - +
54D LYS* 5.3 3.6 - - - -
97D ASP* 3.0 30.9 + - - -
122D ALA* 4.4 0.6 - - - +
4194D MG 2.2 30.7 - - - -
4195D TTP 3.4 4.7 + - - -
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Residues in contact with THR 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C THR* 3.8 24.1 - - + +
38C ARG* 3.7 32.0 - - + -
41C ARG* 4.1 17.7 + - - +
31D GLY* 3.2 13.1 + - - -
33D SER* 1.3 79.3 - - - +
35D GLU* 1.3 57.2 + - - +
37D MET* 3.3 6.9 + - - +
38D ARG* 2.9 27.3 + - - +
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Residues in contact with GLU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLU* 3.6 16.3 - - - +
38C ARG* 4.1 6.8 + - - +
24D ILE* 4.0 15.9 - - + -
31D GLY 3.0 16.9 + - - +
32D LYS 3.8 4.0 - - - +
34D THR* 1.3 73.0 - - - +
36D LEU* 1.3 65.7 + - - +
38D ARG* 2.7 46.6 + - - +
39D ARG* 2.9 52.8 + - - +
147D VAL* 5.7 0.2 - - + -
149D LEU* 4.1 18.8 - - + -
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Residues in contact with LEU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 3.8 8.4 - - + +
32D LYS 2.9 14.5 + - - +
33D SER 3.3 7.6 - - - +
35D GLU* 1.3 75.8 - - - +
37D MET* 1.3 77.7 + - + +
39D ARG* 3.2 4.5 + - - +
40D VAL* 3.0 35.6 + - + +
52D VAL* 4.9 1.3 - - + -
95D GLY* 3.8 14.8 - - - -
96D ILE 3.7 29.2 - - - +
97D ASP* 3.8 16.4 - - + +
120D ILE* 3.6 40.6 - - + +
121D VAL 4.7 0.2 - - - +
122D ALA* 4.1 10.3 - - + +
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Residues in contact with MET 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D SER* 3.0 25.2 + - - +
34D THR* 3.3 10.1 + - - +
36D LEU* 1.3 94.6 - - + +
38D ARG* 1.3 60.8 + - - +
40D VAL* 3.7 5.0 - - - +
41D ARG* 2.8 69.9 + - + +
52D VAL* 3.9 35.2 - - + -
54D LYS* 4.4 14.8 - - - +
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Residues in contact with ARG 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C SER 2.8 28.9 + - - +
31C GLY* 3.4 33.8 - - - +
34C THR* 3.8 15.5 - - + -
35C GLU* 4.1 16.6 + - - +
149C LEU* 3.9 25.3 - - - +
150C THR 4.4 1.8 + - - +
34D THR 2.9 16.6 + - - +
35D GLU* 2.7 43.4 + - - +
36D LEU 3.3 0.2 - - - -
37D MET* 1.3 76.8 - - - +
39D ARG* 1.3 73.1 + - - +
41D ARG* 3.5 7.9 + - - +
42D ARG* 3.3 38.6 + - - +
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Residues in contact with ARG 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D GLN* 2.9 43.9 + - - +
23D VAL 4.9 1.4 + - - +
24D ILE* 3.9 16.8 - - - +
35D GLU* 2.9 41.7 + - - +
36D LEU 3.6 6.7 - - - +
38D ARG* 1.3 83.9 - - - +
40D VAL* 1.3 63.1 + - - +
42D ARG* 3.4 28.7 + - - +
43D PHE* 3.3 20.5 - - - -
120D ILE* 4.0 23.3 - - + -
145D SER* 4.2 8.1 + - - -
147D VAL* 3.7 34.8 - - - +
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Residues in contact with VAL 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LEU* 3.0 39.1 + - + +
37D MET* 3.9 7.6 - - - +
39D ARG* 1.3 75.9 - - - +
41D ARG* 1.3 65.2 + - + +
43D PHE* 3.1 12.0 + - - +
44D GLN* 3.0 22.9 + - + +
50D CYS* 3.9 26.8 - - + -
51D LEU 5.4 1.1 - - - +
52D VAL* 4.1 20.6 - - + -
93D VAL* 4.7 5.4 - - + -
95D GLY* 4.3 14.8 - - - +
120D ILE* 4.3 12.3 - - + -
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Residues in contact with ARG 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C THR* 4.1 26.9 + - - +
37D MET* 2.8 56.0 + - + +
38D ARG* 4.0 5.1 - - - +
40D VAL* 1.3 73.2 - - + +
42D ARG* 1.3 60.4 + - - +
44D GLN* 3.8 19.8 - - - +
45D ILE* 2.9 34.5 + - + +
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Residues in contact with ARG 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C PHE 3.6 23.3 - - - +
30C SER 3.9 6.3 - - - +
31C GLY 4.8 0.7 - - - +
150C THR* 2.8 46.7 + - - +
151C ALA* 4.0 9.8 + - - +
152C VAL* 3.5 26.2 + - + +
159C GLU* 4.5 6.7 + - - +
22D GLN* 5.8 1.4 + - - +
38D ARG* 3.3 38.3 + - - +
39D ARG* 3.5 26.8 + - - +
40D VAL 3.2 0.8 - - - -
41D ARG* 1.3 77.9 - - - +
43D PHE* 1.3 80.2 + - - +
45D ILE* 3.7 7.0 - - - +
46D ALA* 3.6 13.2 + - - +
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Residues in contact with PHE 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C VAL* 3.9 14.1 - - + -
157C PHE 5.7 1.3 - - - -
20D GLN* 5.3 2.5 - - - -
22D GLN* 5.0 8.5 - - - -
39D ARG 3.3 19.5 - - - -
40D VAL 3.1 6.7 + - - +
42D ARG* 1.3 98.7 - - - +
44D GLN* 1.3 66.0 + - - +
46D ALA 3.0 9.9 + - - -
48D TYR* 3.1 59.1 + + + -
50D CYS* 4.3 2.5 - - - -
93D VAL* 3.8 32.5 - - + -
118D THR* 4.2 27.8 - - + -
120D ILE* 4.3 8.3 - - + -
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Residues in contact with GLN 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D VAL* 3.0 19.0 + - + +
41D ARG* 3.8 18.7 - - - +
43D PHE* 1.3 77.4 - - - +
45D ILE* 1.3 59.3 + - - +
47D GLN* 2.9 23.0 + - - +
48D TYR 3.8 13.1 - - - +
50D CYS* 3.8 20.7 - - + +
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Residues in contact with ILE 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C PHE* 3.9 28.5 - - + +
152C VAL 6.0 0.4 - - - +
154C MET* 3.4 28.3 - - + +
178C ALA* 4.2 23.6 - - + +
183C SER* 5.5 0.4 - - - +
41D ARG* 2.9 16.0 + - + +
42D ARG 3.7 12.6 - - - +
44D GLN* 1.3 79.3 + - - +
46D ALA* 1.3 57.8 + - + +
47D GLN* 3.3 8.6 + - - +
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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