Contacts of the helix formed by residues 31 - 45 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PHE 3.4 1.4 - - - -
30A SER* 1.3 79.7 - - - +
32A LYS* 1.3 59.5 + - - +
33A SER 3.3 2.2 - - - -
34A THR* 3.2 9.7 + - - -
35A GLU* 2.9 26.7 + - - +
149A LEU* 4.0 1.6 - - - -
1195A TTP 3.1 13.4 + - - -
38B ARG* 3.5 22.3 - - - -
42B ARG* 5.0 0.6 - - - +
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Residues in contact with LYS 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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24A ILE* 4.0 11.1 - - + +
25A LEU 3.8 11.7 - - - +
26A GLY 3.5 15.9 - - - +
27A PRO 2.8 23.8 + - - -
30A SER* 3.5 10.1 - - - +
31A GLY* 1.3 72.7 - - - +
33A SER* 1.3 57.4 + - - +
35A GLU* 3.3 2.9 + - - +
36A LEU* 2.9 27.7 + - - +
122A ALA* 3.8 17.9 - - + +
123A ALA* 3.4 31.4 - - - +
124A LEU* 3.0 13.7 - - - +
149A LEU* 4.0 9.6 - - + -
1195A TTP 2.8 55.8 + - - +
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Residues in contact with SER 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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31A GLY 3.3 0.2 - - - -
32A LYS* 1.3 74.7 - - - +
34A THR* 1.3 60.8 + - - +
36A LEU* 3.4 7.0 + - - +
37A MET* 3.0 35.5 + - - +
97A ASP* 2.8 37.4 + - - -
122A ALA* 4.4 0.4 - - - +
1194A MG 3.2 9.0 - - - -
1195A TTP 3.1 18.4 + - - -
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Residues in contact with THR 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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31A GLY* 3.2 14.1 + - - -
33A SER* 1.3 78.6 - - - +
35A GLU* 1.3 58.5 + - - +
37A MET* 3.3 6.9 + - - +
38A ARG* 2.9 27.3 + - - +
34B THR* 3.8 23.7 - - + +
37B MET* 5.9 0.2 - - + -
38B ARG* 3.7 28.3 - - + -
41B ARG* 3.8 22.7 + - - +
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Residues in contact with GLU 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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24A ILE* 3.8 23.8 - - + -
31A GLY 2.9 16.6 + - - +
32A LYS 3.7 4.5 - - - +
34A THR* 1.3 74.7 - - - +
36A LEU* 1.3 64.6 + - - +
38A ARG* 2.8 47.1 + - - +
39A ARG* 3.0 44.7 + - - +
149A LEU* 4.0 18.8 - - + -
35B GLU* 3.8 12.1 - - - +
38B ARG* 4.2 6.5 - - - +
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Residues in contact with LEU 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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24A ILE* 3.8 9.1 - - + +
32A LYS 2.9 14.2 + - - +
33A SER* 3.4 8.5 - - - +
35A GLU* 1.3 76.7 - - - +
37A MET* 1.3 62.5 + - - +
39A ARG* 3.2 4.9 + - - +
40A VAL* 3.0 36.5 + - + +
52A VAL* 4.8 8.7 - - + -
95A GLY* 3.8 13.7 - - - -
96A ILE 3.7 28.3 - - - +
97A ASP* 3.8 20.2 - - + +
120A ILE* 3.4 42.8 - - + +
122A ALA* 4.0 12.3 - - + +
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Residues in contact with MET 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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33A SER* 3.0 22.8 + - - +
34A THR* 3.3 6.3 + - - +
36A LEU* 1.3 80.2 - - + +
38A ARG* 1.3 60.2 + - - +
40A VAL* 3.9 8.0 - - + +
41A ARG* 2.8 71.0 + - + +
52A VAL* 4.1 38.1 - - + -
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Residues in contact with ARG 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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34A THR 2.9 14.4 + - - +
35A GLU* 2.8 45.3 + - - +
36A LEU 3.3 0.2 - - - -
37A MET* 1.3 75.6 - - - +
39A ARG* 1.3 75.6 + - - +
41A ARG* 3.5 7.6 + - - +
42A ARG* 3.3 44.3 + - - +
30B SER 2.8 23.0 + - - +
31B GLY* 3.4 34.7 - - - +
34B THR* 3.8 15.0 - - + -
35B GLU* 4.1 17.9 + - - +
149B LEU* 3.8 25.4 - - - +
150B THR* 4.5 2.0 + - - +
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Residues in contact with ARG 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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22A GLN* 2.9 44.5 + - - +
23A VAL 4.8 1.6 + - - +
24A ILE* 3.7 20.0 - - - +
35A GLU* 3.0 38.9 + - - +
36A LEU 3.6 6.7 - - - +
38A ARG* 1.3 88.3 - - - +
40A VAL* 1.3 61.7 - - - +
42A ARG* 3.4 28.3 + - - +
43A PHE* 3.3 21.7 - - - -
120A ILE* 3.8 19.5 - - + +
145A SER* 4.3 9.8 + - - -
147A VAL* 3.7 30.5 - - - +
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Residues in contact with VAL 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 LEU* 3.0 37.9 + - + +
37A MET* 3.9 10.1 - - + +
39A ARG* 1.3 74.7 - - - +
41A ARG* 1.3 64.8 + - + +
43A PHE* 3.1 12.3 + - - +
44A GLN* 3.1 23.3 + - + +
50A CYS* 3.8 27.0 - - + -
51A LEU 5.5 0.9 - - - +
52A VAL* 4.1 21.1 - - + -
93A VAL* 4.7 6.3 - - + +
95A GLY* 4.3 15.7 - - - +
120A ILE* 4.5 9.9 - - + -
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Residues in contact with ARG 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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37A MET* 2.8 64.1 + - + +
38A ARG* 3.9 5.8 - - - +
40A VAL* 1.3 72.5 - - + +
42A ARG* 1.3 57.1 + - + +
44A GLN* 3.8 20.3 - - + +
45A ILE* 2.9 34.4 + - - +
34B THR* 4.0 26.3 + - - +
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Residues in contact with ARG 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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22A GLN* 5.7 1.4 + - - +
38A ARG* 3.3 40.2 + - - +
39A ARG* 3.4 29.7 + - - +
40A VAL 3.2 0.4 - - - -
41A ARG* 1.3 79.4 - - - +
43A PHE* 1.3 77.1 + - - +
45A ILE* 3.5 15.7 - - - +
46A ALA* 3.6 6.1 + - - +
29B PHE 3.8 22.7 - - - +
30B SER 3.9 6.7 - - - +
31B GLY* 5.4 0.4 - - - -
150B THR* 2.8 46.9 + - - +
151B ALA* 4.1 5.2 + - - +
152B VAL* 3.8 32.4 + - + +
159B GLU* 4.9 4.8 + - - +
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Residues in contact with PHE 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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20A GLN* 5.7 1.3 - - - -
22A GLN* 5.0 7.9 - - - -
39A ARG 3.3 24.5 - - - -
40A VAL 3.1 5.9 + - - +
42A ARG* 1.3 93.9 - - - +
44A GLN* 1.3 66.6 + - - +
46A ALA 3.0 10.2 + - - -
48A TYR* 3.1 51.0 + + + +
50A CYS* 4.3 2.0 - - - -
93A VAL* 3.8 35.2 - - + -
118A THR* 4.2 20.0 - - + -
120A ILE* 4.2 16.4 - - + -
152B VAL* 3.8 19.7 - - + -
157B PHE 5.8 1.3 - - - -
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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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40A VAL* 3.1 18.2 + - - +
41A ARG* 3.4 21.4 + - + +
43A PHE* 1.3 76.4 - - - +
45A ILE* 1.3 59.1 + - + +
47A GLN* 2.9 25.1 + - - +
48A TYR 3.8 13.2 + - - +
50A CYS* 3.8 20.3 - - - +
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Residues in contact with ILE 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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41A ARG 2.9 15.0 + - - +
42A ARG* 3.5 16.4 - - - +
44A GLN* 1.3 76.8 - - - +
46A ALA* 1.3 58.4 + - + +
47A GLN* 3.3 9.9 + - - +
29B PHE* 3.7 43.1 - - + +
152B VAL 6.0 0.7 - - - +
154B MET* 3.7 25.7 - - + +
178B ALA* 4.2 12.9 - - + +
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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