Contacts of the helix formed by residues 31 - 44 (chain N) in PDB entry 5U0A
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 SER 31 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K G 4.0 10.6 + - - -
15N TRP* 4.0 14.4 - - - +
16N GLY 4.6 4.7 + - - -
17N GLU* 5.4 0.4 - - - -
27N LEU* 3.6 24.0 - - - -
29N TYR 3.6 0.4 + - - -
30N PRO* 1.3 74.2 - - - +
32N ARG* 1.3 66.5 + - - +
33N SER* 3.9 1.4 + - - -
34N GLY* 2.8 21.8 + - - -
35N LEU* 3.2 13.0 + - - +
202N ASP* 3.4 20.6 - - - -
217N ARG* 3.6 1.1 - - - +
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Residues in contact with ARG 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31N SER* 1.3 70.8 - - - +
33N SER* 1.3 66.0 + - - +
35N LEU* 3.2 7.0 + - - +
36N ILE* 2.9 47.2 + - + +
54N TYR 3.6 12.9 + - - -
55N LYS* 4.0 9.1 - - - +
56N GLU 3.9 6.7 - - - +
57N LEU* 3.0 43.4 + - - +
59N PHE* 4.0 19.4 - - + -
187N GLU* 2.6 38.9 + - - -
202N ASP* 3.1 13.0 + - + -
203N VAL* 4.3 26.3 - - - +
204N PRO* 4.7 1.8 - - + +
217N ARG* 3.4 23.4 - - - +
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Residues in contact with SER 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K U 4.0 0.3 - - - +
3K G 2.6 43.0 + - - -
31N SER* 3.0 3.0 + - - -
32N ARG* 1.3 78.9 - - - +
34N GLY* 1.3 57.8 + - - +
36N ILE* 3.8 0.5 - - - +
37N GLY* 2.9 24.6 + - - -
202N ASP* 3.0 29.7 + - - +
204N PRO* 4.3 8.1 - - - -
207N PHE* 3.6 10.0 - - - -
214N TYR* 3.0 16.1 - - - -
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Residues in contact with GLY 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K U 3.5 29.4 - - - +
3K G 3.9 0.6 + - - -
15N TRP* 3.9 19.3 - - - -
31N SER* 2.8 15.6 + - - -
33N SER* 1.3 80.8 + - - +
35N LEU* 1.3 55.3 + - - -
37N GLY 3.2 1.4 + - - -
38N MET* 2.8 26.5 + - - +
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Residues in contact with LEU 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N LEU* 4.6 9.9 - - + -
8N LEU* 4.3 7.4 - - + -
15N TRP* 4.0 15.0 - - + -
30N PRO* 3.3 34.1 - - + -
31N SER 3.2 15.8 + - - +
32N ARG* 3.2 8.5 + - - +
34N GLY* 1.3 74.9 - - - +
36N ILE* 1.3 63.2 + - - +
38N MET* 3.0 11.7 + - - +
39N PHE* 3.0 30.6 + - + -
59N PHE* 3.5 38.8 - - + -
61N VAL* 5.6 0.7 - - + -
115N VAL* 3.8 26.7 - - + -
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Residues in contact with ILE 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N ARG* 2.9 60.7 + - + +
33N SER 3.8 2.2 - - - +
35N LEU* 1.3 75.9 - - - +
37N GLY* 1.3 57.9 + - - +
39N PHE* 3.1 11.2 + - + +
40N ALA* 2.9 26.0 + - - +
51N LEU* 4.6 2.7 - - + -
54N TYR* 3.6 40.0 - - + +
55N LYS* 5.2 0.4 - - - +
57N LEU* 5.8 0.9 - - + -
59N PHE* 4.3 13.0 - - + -
203N VAL* 5.9 0.2 - - + -
204N PRO* 3.8 28.5 - - + -
207N PHE* 4.3 7.2 - - + -
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Residues in contact with GLY 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K A 3.7 2.9 + - - -
2K U 3.5 22.1 - - - -
33N SER 2.9 12.1 + - - -
34N GLY 3.6 0.2 - - - -
36N ILE* 1.3 77.4 - - - +
38N MET* 1.3 56.4 + - - +
40N ALA* 3.7 1.9 - - - +
41N ALA* 2.8 30.0 + - - +
207N PHE* 3.3 27.3 - - - -
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Residues in contact with MET 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K U 3.7 21.2 - - + +
6N LEU* 4.4 13.7 - - + -
8N LEU* 4.3 20.9 - - + -
15N TRP* 4.9 4.3 - - - -
34N GLY 2.8 13.2 + - - +
35N LEU* 3.0 15.7 + - - +
37N GLY* 1.3 78.0 - - - +
39N PHE* 1.3 60.5 + - + +
41N ALA* 3.4 4.2 + - - +
42N ALA* 3.0 25.8 + - - +
129N LEU* 4.6 7.8 - - + +
136N PRO* 3.7 23.3 - - + +
137N TYR 4.5 7.0 - - - +
138N LEU* 4.5 10.3 - - + -
145N PRO* 4.9 0.2 - - + -
149N LEU* 3.6 42.8 - - + -
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Residues in contact with PHE 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N PHE* 4.1 10.5 - + - -
6N LEU* 3.6 33.2 - - + -
35N LEU* 3.0 18.4 + - + -
36N ILE* 3.1 6.3 + - + +
38N MET* 1.3 79.5 - - - +
40N ALA* 1.3 59.7 + - - +
42N ALA* 2.9 6.6 + - - +
43N GLN* 2.9 28.1 + - - +
54N TYR* 3.0 28.9 + + + -
57N LEU* 5.5 1.3 - - + -
59N PHE* 3.8 33.2 - + - -
117N VAL* 4.5 9.0 - - + -
125N ILE* 3.4 33.4 - - + -
129N LEU* 3.7 23.1 - - + -
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Residues in contact with ALA 40 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K A 4.0 11.9 - - - +
36N ILE 2.9 17.5 + - - +
37N GLY* 3.7 7.2 - - - +
39N PHE* 1.3 75.4 - - - +
41N ALA* 1.3 61.9 + - - +
43N GLN 3.2 0.5 + - - -
44N GLY 3.0 5.0 + - - -
45N VAL* 2.8 51.3 + - + -
51N LEU* 4.6 0.9 - - + -
54N TYR* 3.2 21.4 + - + -
207N PHE* 4.3 6.7 - - + -
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Residues in contact with ALA 41 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K A 3.0 33.1 + - - +
2K U 3.9 15.5 - - + +
37N GLY 2.8 16.0 + - - +
38N MET 3.6 4.5 - - - +
40N ALA* 1.3 75.9 - - - +
42N ALA* 1.3 62.7 + - - +
43N GLN 3.4 0.3 + - - -
44N GLY 3.5 1.0 + - - -
133N TYR* 3.5 5.9 - - - +
134N TRP* 3.1 40.7 + - + +
135N GLN 5.0 1.8 - - - +
136N PRO* 5.5 0.4 - - + -
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Residues in contact with ALA 42 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N MET 3.0 13.4 + - - +
39N PHE* 2.9 11.0 + - - +
41N ALA* 1.3 76.9 - - - +
43N GLN* 1.3 60.1 + - + +
44N GLY 3.5 0.2 - - - -
125N ILE 5.3 0.4 - - - +
128N ALA* 3.8 24.2 - - + +
129N LEU* 3.7 26.5 - - + -
131N ALA 4.3 1.9 - - - +
132N PRO* 3.7 12.1 - - + +
133N TYR* 3.1 23.6 + - - +
134N TRP 4.4 1.1 - - - +
136N PRO* 5.6 1.6 - - + -
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Residues in contact with GLN 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39N PHE* 2.9 8.3 + - - +
40N ALA 3.2 1.8 + - - +
41N ALA 3.2 0.2 - - - -
42N ALA* 1.3 76.1 - - + +
44N GLY* 1.3 61.0 + - - +
45N VAL* 3.4 6.2 + - + +
53N ARG* 3.0 31.7 + - - +
54N TYR* 2.5 31.7 + - - +
121N GLU* 5.0 1.9 + - - +
124N THR* 4.3 6.1 + - - -
125N ILE* 3.0 45.8 - - + +
128N ALA* 3.7 18.6 - - + +
133N TYR* 4.1 4.8 - - - -
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Residues in contact with GLY 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40N ALA 3.0 4.0 + - - -
41N ALA 3.5 0.6 + - - -
42N ALA 3.5 3.0 - - - -
43N GLN* 1.3 77.5 - - - +
45N VAL* 1.3 64.6 + - - +
46N ARG* 3.1 11.6 + - - +
49N ASP* 4.7 0.3 - - - +
133N TYR* 3.5 38.1 - - - +
134N TRP* 4.2 7.1 - - - -
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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