Contacts of the helix formed by residues 38 - 58 (chain F) in PDB entry 1OUQ
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 38 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LYS* 4.6 11.3 - - - +
37F PHE* 1.3 71.2 - - - +
39F GLU* 1.3 55.6 + - - +
40F HIS* 2.9 18.5 + - - +
41F THR* 2.5 35.3 + - - -
42F TRP* 3.1 6.3 + - - -
199F ARG* 5.8 1.8 - - - -
123H T 3.0 32.3 + - - +
124H A 2.5 30.0 + - - -
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Residues in contact with GLU 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LYS* 5.1 4.1 - - - +
37F PHE 3.7 2.8 + - - -
38F SER* 1.3 72.6 + - - +
40F HIS* 1.3 83.2 + - + +
42F TRP* 3.3 10.0 + - - +
43F LYS* 3.0 54.2 + - - +
124H A 5.6 0.4 - - - +
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Residues in contact with HIS 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F SER* 2.9 9.6 + - - +
39F GLU* 1.3 98.2 + - + +
41F THR* 1.3 62.1 + - - +
43F LYS* 3.8 21.6 + - + +
44F MET* 3.4 26.3 + - - +
175F ALA* 6.1 2.0 - - + -
123H T 4.6 1.2 - - + +
124H A 3.6 44.2 + - + +
125H T 3.6 41.0 - - + +
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Residues in contact with THR 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F PHE* 4.4 5.4 - - + -
38F SER* 2.5 28.1 + - - -
40F HIS* 1.3 70.9 - - - +
42F TRP* 1.3 65.5 + - + +
44F MET* 3.3 4.0 + - - +
45F LEU* 2.9 22.0 + - + +
94F GLN* 4.3 5.7 - - - +
97F MET* 4.3 30.5 - - + -
122H T 3.7 16.3 - - - +
123H T 2.8 46.3 + - + +
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Residues in contact with TRP 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F MET* 4.1 22.0 - - + -
31F PHE* 3.8 45.8 - + - -
34F ARG* 3.5 50.5 + - + -
37F PHE* 3.5 19.7 - + + +
38F SER 3.1 15.4 + - - -
39F GLU* 3.3 9.8 + - - +
41F THR* 1.3 77.9 - - - +
43F LYS* 1.3 65.9 + - - +
45F LEU* 2.8 35.8 + - + +
46F LEU* 2.9 48.7 + - + +
97F MET* 5.7 1.5 - - + +
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Residues in contact with LYS 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F GLU* 3.0 47.9 + - - +
40F HIS* 4.0 21.9 + - + +
42F TRP* 1.3 76.5 - - + +
44F MET* 1.3 64.2 + - + +
46F LEU* 3.5 6.7 + - - +
47F SER* 3.1 25.9 + - - -
50F ARG* 4.9 2.1 + - - -
111G T 4.9 10.4 - - + +
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Residues in contact with MET 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 HIS 3.4 14.0 + - - +
41F THR* 3.3 2.5 + - - +
42F TRP 3.2 0.8 - - - -
43F LYS* 1.3 77.5 - - + +
45F LEU* 1.3 64.9 + - - +
47F SER* 4.0 7.1 - - - +
48F VAL* 3.0 29.9 + - + +
90F GLN* 3.0 33.9 - - + +
91F HIS* 6.0 1.1 - - - +
94F GLN* 3.9 9.9 - - - +
111G T 4.3 15.9 - - + +
112G A 3.5 30.5 - - + +
113G T 3.1 32.8 - - + +
123H T 5.1 1.6 - - + -
124H A 3.6 16.4 - - - +
125H T 5.5 0.4 - - - +
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Residues in contact with LEU 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F MET* 5.4 5.8 - - + -
31F PHE* 6.1 1.1 - - + -
41F THR* 2.9 12.0 + - + +
42F TRP* 2.8 43.2 + - + +
44F MET* 1.3 75.4 - - - +
46F LEU* 1.3 62.1 - - + +
48F VAL* 4.0 0.9 - - - +
49F CYS* 2.8 47.2 + - - +
94F GLN* 3.3 39.7 - - + +
97F MET* 4.6 15.0 - - + -
98F LEU* 4.6 18.4 - - + -
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Residues in contact with LEU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F PHE* 5.9 2.9 - - + -
42F TRP* 2.9 48.4 + - + +
43F LYS* 4.0 4.3 - - - +
45F LEU* 1.3 81.4 - - + +
47F SER* 1.3 57.8 + - - +
49F CYS* 3.6 7.6 - - + +
50F ARG* 2.9 49.6 + - - +
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Residues in contact with SER 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F LYS 3.1 18.1 + - - -
44F MET* 4.0 11.4 - - - +
45F LEU 3.2 0.2 - - - -
46F LEU* 1.3 75.5 - - - +
48F VAL* 1.3 66.1 + - - +
49F CYS 3.0 0.9 - - - -
50F ARG* 3.4 13.1 + - - +
51F SER* 3.0 25.7 + - - -
91F HIS* 5.7 0.4 - - - -
111G T 2.8 49.7 + - - +
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Residues in contact with VAL 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F MET* 3.0 22.5 + - + +
45F LEU 4.9 0.2 - - - +
47F SER* 1.3 76.4 - - - +
49F CYS* 1.3 57.9 + - - +
51F SER* 3.7 5.5 - - - -
52F TRP* 2.9 26.4 + - + +
74F TYR* 4.4 1.3 + - + +
90F GLN* 4.2 11.0 - - + +
91F HIS* 3.3 59.0 - - + +
94F GLN* 3.9 11.7 - - + -
95F LEU* 3.3 28.5 - - + -
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Residues in contact with CYS 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F LEU* 2.8 44.1 + - - +
46F LEU* 3.6 11.2 - - + +
48F VAL* 1.3 79.5 - - - +
50F ARG* 1.3 59.1 + - - +
52F TRP* 3.2 8.3 + - - +
53F ALA* 2.9 29.2 + - - +
63F TRP* 4.2 18.3 - - + -
95F LEU* 5.2 6.7 - - - -
98F LEU* 3.7 24.0 - - - -
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Residues in contact with ARG 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F LYS 4.9 2.0 + - - -
46F LEU* 2.9 41.9 + - - +
47F SER* 3.6 12.8 - - - +
49F CYS* 1.3 76.7 - - - +
51F SER* 1.3 60.6 + - - +
53F ALA* 3.6 7.7 - - - +
54F ALA* 3.0 27.5 + - - +
110G G 4.0 16.7 + - - +
111G T 2.4 45.3 + - - +
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Residues in contact with SER 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F SER* 3.0 19.0 + - - -
48F VAL* 3.8 4.5 - - - -
50F ARG* 1.3 79.5 - - - +
52F TRP* 1.3 61.3 + - - +
53F ALA 3.2 0.4 - - - -
54F ALA* 4.1 5.9 - - - +
55F TRP* 3.7 15.1 + - - +
74F TYR* 2.8 28.0 + - - -
77F TYR* 5.8 1.2 - - - -
78F LEU* 5.2 1.7 - - - +
91F HIS* 3.8 12.6 - - - -
111G T 6.0 1.1 - - - -
112G A 5.6 1.4 + - - -
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Residues in contact with TRP 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F VAL 2.9 18.7 + - - +
49F CYS* 3.2 3.1 + - - +
51F SER* 1.3 77.8 - - - +
53F ALA* 1.3 57.4 + - - +
55F TRP* 3.9 11.2 - + - -
56F CYS* 2.8 51.9 + - - +
62F LYS 4.4 2.5 - - - -
63F TRP* 2.7 50.5 + + + +
66F ALA* 3.9 19.7 - - + -
70F ASP* 4.1 9.4 - - + -
71F VAL* 3.7 25.8 - - + -
74F TYR* 3.4 52.7 - + + +
95F LEU* 3.6 33.5 - - + +
98F LEU* 6.1 0.9 - - + -
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Residues in contact with ALA 53 (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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49F CYS 2.9 15.8 + - - +
50F ARG* 3.6 9.4 - - - +
52F TRP* 1.3 78.5 - - - +
54F ALA* 1.3 70.1 + - - +
56F CYS* 3.3 6.6 + - - +
57F LYS* 3.0 21.1 + - - +
63F TRP* 4.6 26.8 - - + +
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Residues in contact with ALA 54 (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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50F ARG 3.0 17.4 + - - +
51F SER* 4.1 7.0 - - - +
53F ALA* 1.3 74.3 - - - +
55F TRP* 1.3 69.6 + - - +
57F LYS* 2.7 18.7 + - - +
58F LEU* 3.2 12.7 + - - +
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Residues in contact with TRP 55 (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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51F SER 3.7 15.8 + - - +
52F TRP* 3.9 14.2 - + - -
54F ALA* 1.3 77.9 - - - +
56F CYS* 1.3 77.8 + - - +
57F LYS 2.7 12.6 + - - -
58F LEU* 3.1 14.2 + - - +
59F ASN* 3.3 53.9 + - - +
61F ARG* 4.4 12.2 - - - +
70F ASP* 4.4 4.8 + - - +
73F ASP* 4.1 12.8 - - + -
74F TYR* 3.7 44.6 - + + +
77F TYR* 3.2 57.0 - + + -
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Residues in contact with CYS 56 (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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52F TRP* 2.8 54.2 + - - +
53F ALA 3.4 5.6 - - - +
54F ALA 3.0 0.4 + - - -
55F TRP* 1.3 87.3 - - - +
57F LYS* 1.3 57.2 + - - +
59F ASN* 4.5 1.3 - - - -
60F ASN 3.8 0.7 + - - -
61F ARG* 2.9 45.3 + - - +
62F LYS 3.5 21.8 - - - -
63F TRP* 3.6 15.7 - - + -
70F ASP* 5.6 0.2 - - - -
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Residues in contact with LYS 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F ALA 3.0 9.8 + - - +
54F ALA* 2.7 17.7 + - - +
56F CYS* 1.3 70.5 - - - +
58F LEU* 1.3 55.1 + - + +
59F ASN 2.7 16.9 + - - -
60F ASN* 2.8 16.5 + - - +
61F ARG 4.8 2.2 - - - +
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Residues in contact with LEU 58 (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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54F ALA 3.2 9.3 + - - +
55F TRP* 3.1 5.4 + - - +
57F LYS* 1.3 75.5 - - + +
59F ASN* 1.3 77.6 + - - +
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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
------------------------------------------------------------
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