Contacts of the helix formed by residues 32 - 49 (chain H) in PDB entry 1V8O
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 LEU 32 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G TYR* 4.1 13.9 - - + +
6H LEU* 3.9 10.5 - - + +
31H ILE* 1.3 81.5 - - - +
33H HIS* 1.3 58.8 + - - +
34H LEU* 2.9 8.3 - - + +
35H THR* 2.7 33.4 + - - +
36H ILE 3.9 1.0 + - - -
70H VAL* 4.1 3.6 - - - -
71H LEU* 4.2 11.0 - - + -
72H GLU 4.8 4.7 - - - +
94H SER* 4.0 28.3 - - - +
95H TYR* 3.6 39.7 - - + +
98H VAL* 3.7 37.9 - - + -
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Residues in contact with HIS 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G HIS* 3.5 52.3 - + + -
37G TYR* 4.6 1.3 - - + -
72G GLU* 6.2 0.4 - - - -
73G ASP* 2.8 24.6 + - - +
32H LEU* 1.3 72.1 - - - +
34H LEU* 1.3 63.0 + - - +
35H THR 3.3 0.3 + - - -
36H ILE* 3.3 15.1 + - + +
37H TYR* 3.1 21.0 - - - -
70H VAL* 3.5 25.5 + - + +
71H LEU 3.7 15.0 + - - -
72H GLU* 5.2 1.4 - - - -
73H ASP* 3.3 26.7 + - - +
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Residues in contact with LEU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G LEU* 5.6 3.8 - - + -
37G TYR* 3.6 53.9 - - + -
91G TYR* 5.0 1.6 - - + +
32H LEU* 2.9 6.0 + - + +
33H HIS* 1.3 79.3 - - - +
35H THR* 1.3 62.8 - - - +
37H TYR* 2.9 14.7 + - + -
38H GLU* 2.9 58.6 + - + +
91H TYR* 3.9 29.6 - - + +
94H SER* 4.6 1.3 - - - -
95H TYR* 3.8 18.4 - - + +
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Residues in contact with THR 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL 3.9 6.3 - - - +
8H ASP 3.9 7.4 - - - +
9H ALA* 3.8 27.1 - - - +
12H LEU* 4.4 12.6 - - + -
31H ILE* 3.4 19.8 - - + +
32H LEU 2.7 34.7 + - - -
34H LEU* 1.3 72.9 - - - +
36H ILE* 1.3 53.0 + - - -
38H GLU* 4.2 3.1 - - - -
39H ALA* 2.8 38.0 + - - +
65H MSE 4.6 1.1 - - + -
95H TYR* 3.0 17.9 + - - -
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Residues in contact with ILE 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G ASP* 3.2 33.4 - - + +
74G PRO 5.0 11.0 - - - +
76G LEU* 4.7 17.3 - - + +
90G PHE* 4.1 6.7 - - + -
31H ILE* 4.0 21.1 - - + -
33H HIS* 3.7 15.5 - - - +
34H LEU 3.2 0.6 - - - -
35H THR* 1.3 73.7 - - - +
37H TYR* 1.3 66.0 + - + +
39H ALA* 3.9 1.2 - - - +
40H GLY* 2.9 25.3 + - - -
65H MSE 3.9 21.1 - - + -
70H VAL* 4.9 8.1 - - + -
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Residues in contact with TYR 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G LEU* 4.1 13.1 - - + +
33G HIS* 4.5 0.4 - - + -
34G LEU* 3.4 52.5 - - + -
73G ASP* 2.9 32.0 + - + -
74G PRO* 3.3 21.2 - - + +
90G PHE* 3.8 11.8 - + - -
91G TYR* 3.5 18.7 - + + -
94G SER* 3.6 27.8 - - - -
33H HIS 3.1 28.3 - - - -
34H LEU* 2.9 10.3 + - + +
36H ILE* 1.3 79.1 - - + +
38H GLU* 1.3 61.5 + - - +
40H GLY* 3.7 0.2 - - - -
41H ASN* 2.8 33.6 + - - +
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Residues in contact with GLU 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G TYR* 3.7 15.7 - - - +
9H ALA* 3.5 23.6 - - + +
34H LEU* 2.9 32.9 + - + +
35H THR 3.9 1.1 - - - +
37H TYR* 1.3 73.0 - - - +
39H ALA* 1.3 62.4 + - - +
41H ASN* 3.4 1.4 + - - +
42H ALA* 3.0 24.6 + - - +
91H TYR* 3.5 32.3 - - + +
92H ASP* 5.6 1.0 - - - +
95H TYR* 2.7 35.8 + - - -
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Residues in contact with ALA 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ALA* 4.2 8.7 - - + +
12H LEU* 4.9 8.5 - - + -
13H TYR* 3.9 10.5 - - + -
35H THR* 2.8 23.1 + - + +
36H ILE 3.9 2.2 - - - +
38H GLU* 1.3 74.8 - - - +
40H GLY* 1.3 63.0 + - - +
42H ALA* 3.2 8.3 + - - +
43H LEU 3.1 17.7 + - - -
61H LEU* 3.7 22.4 - - + +
65H MSE 4.0 21.1 - - + -
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Residues in contact with GLY 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G LEU* 4.3 12.1 - - - -
80G MSE 4.4 1.2 - - - +
90G PHE* 3.6 27.9 - - - -
36H ILE 2.9 18.5 + - - -
39H ALA* 1.3 77.1 - - - +
41H ASN* 1.3 56.1 + - - +
43H LEU* 3.1 6.6 + - - +
44H TRP* 2.9 26.7 + - - +
61H LEU* 4.3 1.9 - - - +
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Residues in contact with ASN 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G THR* 4.0 4.8 - - - -
90G PHE* 3.3 37.4 - - + +
91G TYR* 3.6 41.1 + - + +
37H TYR 2.8 20.0 + - - +
38H GLU 3.9 2.0 - - - +
40H GLY* 1.3 72.9 - - - +
42H ALA* 1.3 61.4 + - - +
44H TRP* 3.3 12.1 - - - +
45H LYS* 3.2 45.2 + - - +
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Residues in contact with ALA 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ALA* 6.3 0.9 - - + -
13H TYR* 3.6 22.9 - - + -
38H GLU 3.0 14.6 + - - +
39H ALA* 3.3 11.9 - - - +
41H ASN* 1.3 75.4 - - - +
43H LEU* 1.3 63.5 + - - +
45H LYS* 3.2 22.8 + - - +
46H GLU* 3.5 15.9 + - - +
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Residues in contact with LEU 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G LEU* 5.0 1.3 - - + -
80G MSE 3.3 31.9 - - + -
13H TYR* 3.2 18.3 + - - +
39H ALA 3.1 8.5 + - - +
40H GLY* 3.1 7.3 + - - +
42H ALA* 1.3 78.0 - - - +
44H TRP* 1.3 62.9 + - - +
46H GLU* 3.3 11.6 + - + +
47H ALA* 3.1 17.5 + - - +
54H TRP* 4.0 9.6 - - - +
57H ALA* 3.7 26.0 - - + +
58H SER* 3.8 25.8 - - - -
61H LEU* 3.9 19.5 - - + -
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Residues in contact with TRP 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G MSE 3.3 29.8 - - + -
83G ALA* 3.7 19.2 + - + +
84G VAL* 4.6 4.2 - - + +
87G GLY 5.6 1.1 - - - -
88G LEU 2.9 28.9 + - - -
89G THR* 3.4 26.7 - - + -
90G PHE* 3.9 12.1 - - + -
40H GLY 2.9 12.4 + - - +
41H ASN* 3.3 30.5 - - - +
43H LEU* 1.3 78.7 - - - +
45H LYS* 1.3 76.2 + - + +
47H ALA* 3.1 5.0 + - + +
48H ARG* 2.8 76.3 + - + +
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Residues in contact with LYS 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F LYS* 5.7 5.7 - - - +
41H ASN* 3.2 29.9 + - - +
42H ALA* 3.2 12.9 + - - +
44H TRP* 1.3 91.9 - - + +
46H GLU* 1.3 61.9 + - + +
48H ARG* 3.0 10.5 + - + +
49H LEU* 2.8 38.0 + - + +
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Residues in contact with GLU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H TYR* 2.6 38.7 + - - -
42H ALA 3.6 10.8 - - - +
43H LEU* 3.3 14.1 + - + +
44H TRP 3.3 0.6 - - - -
45H LYS* 1.3 78.1 - - + +
47H ALA* 1.3 62.1 + - - +
49H LEU* 3.3 10.3 + - + +
50H GLY 3.3 4.7 + - - +
51H ARG* 2.8 50.7 + - - +
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Residues in contact with ALA 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F ARG* 3.8 8.1 - - - +
80G MSE 3.6 24.9 - - + -
84G VAL* 4.6 4.7 - - + -
43H LEU 3.1 8.8 + - - +
44H TRP* 3.1 10.4 + - + +
46H GLU* 1.3 76.0 - - - +
48H ARG* 1.3 64.6 + - - +
50H GLY* 3.0 14.2 + - - -
51H ARG* 4.6 7.7 + - - -
54H TRP* 3.7 27.0 - - + +
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Residues in contact with ARG 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F LEU* 5.8 1.0 - - - +
92F ASP* 4.3 11.3 + - - -
110F ASP* 3.0 34.8 + - - -
111F ARG* 2.9 39.4 + - - +
112F GLU* 3.0 49.3 + - - +
87G GLY 5.4 2.6 + - - -
1003G CL 4.1 20.6 - - - +
44H TRP* 2.8 50.7 + - + +
45H LYS* 3.2 13.7 - - - +
47H ALA* 1.3 73.9 - - - +
49H LEU* 1.3 61.0 + - + +
50H GLY 2.9 4.7 - - - -
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Residues in contact with LEU 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F SER* 3.5 33.7 - - - +
109F GLN* 3.3 36.0 + - + +
110F ASP* 4.4 9.6 - - + +
45H LYS* 2.8 24.6 + - + +
46H GLU* 3.3 6.5 + - - +
47H ALA 3.3 0.6 - - - -
48H ARG* 1.3 77.0 - - + +
50H GLY* 1.3 65.5 + - - +
51H ARG* 3.6 11.7 + - - +
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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