Contacts of the helix formed by residues 37 - 54 (chain B) in PDB entry 1UXI
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 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LEU* 3.2 37.0 - - - +
221A LYS* 4.3 3.6 - - - -
36B GLU* 1.3 71.4 - - - +
38B VAL* 1.3 53.1 + - - -
40B GLN* 3.0 24.5 + - - +
41B GLY* 2.7 32.6 + - - -
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A LEU 3.6 4.9 + - - -
220A LEU* 3.8 14.0 - - + +
10B ALA* 3.7 27.4 - - + +
33B ASP* 4.2 6.5 - - - +
35B VAL* 3.0 50.0 - - + +
36B GLU 3.2 1.6 + - - +
37B GLY* 1.3 71.3 - - - +
39B PRO* 1.3 67.3 - - + +
42B LYS* 3.1 43.0 + - - +
1310B NAD 4.7 3.8 - - - +
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Residues in contact with PRO 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ALA* 3.7 22.2 - - + -
31B LEU* 3.4 27.1 - - + +
33B ASP* 3.7 10.1 - - + -
35B VAL 3.1 17.7 - - - +
38B VAL* 1.3 94.0 - - + +
40B GLN* 1.3 75.5 + - - +
42B LYS* 3.8 2.1 - - + +
43B ALA* 2.8 33.8 + - - +
61B GLY* 3.7 3.0 - - - -
62B THR 3.5 20.6 - - - +
63B ASN* 4.1 0.9 - - - +
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Residues in contact with GLN 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A LEU* 4.1 19.0 - - + +
37B GLY* 3.0 28.3 + - - +
39B PRO* 1.3 83.7 - - - +
41B GLY* 1.3 61.9 + - - +
43B ALA* 3.7 1.3 - - - +
44B LEU* 3.0 27.0 + - - +
61B GLY* 3.7 22.0 - - - +
62B THR* 4.0 9.3 - - - +
63B ASN* 2.7 28.9 + - - +
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Residues in contact with GLY 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ILE* 4.4 5.6 - - - +
219A LEU* 3.7 23.5 - - - +
220A LEU* 4.0 13.5 - - - -
37B GLY 2.7 22.2 + - - -
38B VAL 3.9 0.7 - - - -
40B GLN* 1.3 75.9 - - - +
42B LYS* 1.3 55.7 + - - +
44B LEU* 3.4 2.1 + - - +
45B ASP* 2.9 30.2 + - - +
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Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 6.3 0.2 - - - -
220A LEU* 3.8 16.4 - - + -
226A TYR* 3.6 24.3 + - + +
227A TYR* 4.0 14.1 - - + -
10B ALA* 2.8 31.3 + - + +
11B GLY* 4.1 12.7 + - - -
12B PHE* 5.7 0.2 - - - +
15B SER* 3.9 15.4 + - - -
31B LEU* 4.8 10.3 - - + -
38B VAL* 3.1 30.1 + - + +
39B PRO* 4.1 2.5 - - + +
41B GLY* 1.3 72.8 - - - +
43B ALA* 1.3 61.1 + - - +
45B ASP* 3.7 6.3 - - - +
46B LEU* 2.8 32.2 + - - +
1310B NAD 5.4 0.2 + - - -
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 4.4 5.8 - - + +
39B PRO 2.8 19.5 + - - +
40B GLN 3.7 3.4 - - - +
42B LYS* 1.3 78.1 - - - +
44B LEU* 1.3 57.0 + - - +
46B LEU* 3.2 2.1 + - - +
47B TYR* 2.8 30.0 + - - +
59B VAL* 3.9 19.6 - - + +
60B THR* 3.4 15.7 - - - +
61B GLY* 3.3 25.4 - - - +
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A THR* 5.7 0.7 - - + -
155A PHE* 4.6 4.7 - - + -
158A MET* 5.6 8.1 - - + -
208A ARG* 3.9 16.4 - - - +
215A GLU* 3.6 40.2 - - + +
216A ILE* 4.2 10.8 - - + -
219A LEU* 4.4 8.1 - - + -
40B GLN 3.0 18.3 + - - +
41B GLY 3.8 3.1 - - - +
43B ALA* 1.3 76.4 - - - +
45B ASP* 1.3 59.5 + - - +
47B TYR* 3.1 12.3 + - + +
48B GLU* 2.8 60.4 + - + +
59B VAL 5.4 0.7 - - - -
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Residues in contact with ASP 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ILE* 3.9 17.9 - - + +
220A LEU* 5.6 0.8 - - + +
225A ALA* 3.6 10.3 - - + +
226A TYR* 2.7 31.1 + - - -
227A TYR* 2.8 22.8 + - + -
228A ALA* 2.9 32.2 + - - +
229A PRO* 3.6 4.3 - - - +
41B GLY 2.9 18.3 + - - +
42B LYS* 3.7 5.4 - - - +
44B LEU* 1.3 76.1 - - - +
46B LEU* 1.3 61.5 + - - +
48B GLU* 3.2 12.8 + - - +
49B ALA 3.3 8.1 + - - -
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TRP* 4.5 12.1 - - + -
227A TYR* 3.8 30.2 - - + -
15B SER 5.0 1.1 - - - +
18B ALA* 3.6 42.4 - - + +
19B HIS* 3.8 12.3 - - + +
22B ALA* 4.0 20.2 - - + -
29B ILE* 5.5 0.2 - - + -
31B LEU* 5.5 1.3 - - + -
42B LYS 2.8 18.4 + - - +
43B ALA* 3.7 4.0 - - - +
45B ASP* 1.3 76.3 - - - +
47B TYR* 1.3 64.9 + - - +
49B ALA* 3.1 13.3 + - - +
50B SER 3.7 3.3 + - - -
55B PHE* 4.2 14.1 - - + -
59B VAL* 4.3 16.2 - - + -
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Residues in contact with TYR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A THR* 3.6 22.8 + - + -
158A MET* 4.1 28.3 - - + +
164A VAL* 5.0 8.0 - - + +
43B ALA 2.8 12.6 + - - +
44B LEU* 3.3 18.4 - - + +
46B LEU* 1.3 77.8 - - - +
48B GLU* 1.3 56.9 + - + +
50B SER* 2.7 45.2 + - - -
51B PRO* 3.8 0.3 - - - +
57B VAL* 3.6 23.5 + - - -
58B ARG* 4.1 11.4 - - + +
59B VAL* 3.5 35.9 - - + +
60B THR* 5.7 2.9 - - + -
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ALA* 3.6 17.8 - - - +
151A ARG* 2.7 47.2 + - + +
154A THR* 3.5 20.4 + - + +
155A PHE* 3.5 21.1 - - + -
212A GLY 5.2 0.3 - - - +
215A GLU* 4.5 1.4 - - - +
216A ILE* 3.4 12.7 - - - +
228A ALA* 4.0 10.2 - - + +
44B LEU* 2.8 51.6 + - + +
45B ASP* 3.2 6.2 + - - +
47B TYR* 1.3 71.3 - - - +
49B ALA* 1.3 57.9 + - - +
50B SER 3.3 0.2 - - - -
51B PRO* 3.2 14.3 - - - +
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TRP* 4.3 13.7 - - + -
227A TYR 3.9 3.6 - - - +
228A ALA* 3.6 29.4 - - - +
231A ALA* 3.8 14.1 - - + -
45B ASP 3.3 3.2 + - - +
46B LEU* 3.1 12.2 + - - +
47B TYR 3.0 1.6 + - - -
48B GLU* 1.3 77.6 - - - +
50B SER* 1.3 64.8 + - - +
51B PRO* 3.3 0.7 - - - -
52B ILE* 3.0 20.4 + - - +
53B GLU* 3.1 12.3 + - - +
55B PHE* 4.4 2.5 - - + -
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Residues in contact with SER 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A VAL* 3.7 17.5 - - - +
46B LEU 3.7 2.6 + - - -
47B TYR* 2.7 29.6 + - - -
49B ALA* 1.3 77.9 - - - +
51B PRO* 1.4 61.5 - - - +
54B GLY* 2.6 35.3 + - - -
55B PHE* 3.0 47.2 + - - -
57B VAL* 4.7 5.2 - - - -
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Residues in contact with PRO 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ALA* 3.7 11.4 - - - +
153A ARG* 3.3 46.7 + - + +
154A THR* 3.1 26.7 - - - +
164A VAL* 3.8 27.6 - - + +
165A LYS* 5.9 0.7 - - - -
48B GLU 3.2 15.7 - - - +
49B ALA 3.4 0.7 - - - -
50B SER* 1.4 97.6 - - - +
52B ILE* 1.3 59.9 + - - +
54B GLY* 3.9 5.7 + - - -
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Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A VAL* 4.1 10.5 - - + +
147A LEU* 4.7 0.4 - - - -
150A ALA* 3.5 31.6 - - + -
153A ARG* 4.7 5.6 - - - +
228A ALA 3.8 12.1 - - - +
231A ALA* 3.6 29.6 - - + +
232A ALA* 3.7 27.1 - - + +
235A GLN* 3.6 36.8 - - + +
49B ALA* 3.0 12.3 + - - +
51B PRO* 1.3 78.6 - - - +
53B GLU* 1.3 68.8 + - - +
54B GLY* 3.4 0.5 + - - -
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TRP* 3.2 50.8 - - + +
24A LYS* 3.2 34.2 + - - -
231A ALA* 4.1 17.4 - - + +
235A GLN* 5.6 0.5 + - - +
49B ALA 3.1 7.5 + - - +
52B ILE* 1.3 83.0 - - - +
54B GLY* 1.3 62.2 + - - +
55B PHE* 3.3 27.7 - - + +
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Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A VAL* 4.9 0.9 - - - -
165A LYS* 3.0 37.3 + - - +
25B GLU* 5.1 0.2 - - - -
50B SER 2.6 18.5 + - - -
51B PRO* 4.3 7.4 - - - -
52B ILE 3.2 3.0 - - - -
53B GLU* 1.3 77.1 - - - +
55B PHE* 1.3 56.4 + - - +
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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
------------------------------------------------------------
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