Contacts of the helix formed by residues 5 - 25 (chain C) in PDB entry 1DVM
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 PRO 5 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C SER* 1.3 54.6 + - - +
7C TYR* 3.3 2.5 - - + +
8C VAL* 3.3 9.1 + - + +
9C ALA* 2.7 37.4 + - - +
74C ALA* 3.1 49.4 - - + +
77C HIS* 3.3 31.6 - - + +
78C LEU* 3.5 21.7 - - + +
81C GLU* 4.5 4.1 - - - +
367C THR* 4.3 15.8 - - - -
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Residues in contact with SER 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PRO* 1.3 71.6 - - - +
7C TYR* 1.3 57.7 + - - +
9C ALA* 3.6 1.0 - - - +
10C HIS* 2.8 31.2 + - - +
366C PRO 4.8 2.8 + - - -
367C THR* 3.9 28.2 + - - +
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Residues in contact with TYR 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PRO* 3.3 1.7 - - + +
6C SER* 1.3 77.9 - - - +
8C VAL* 1.3 59.6 + - + +
10C HIS* 3.0 18.8 + + - +
11C LEU* 2.9 68.3 + - + +
63C GLY 4.5 6.2 + - - -
64C PHE* 5.1 2.4 - - + +
71C MET* 4.3 15.9 - - + -
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Residues in contact with VAL 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PRO* 3.3 13.3 + - + +
7C TYR* 1.3 78.1 - - + +
9C ALA* 1.3 64.3 + - - +
11C LEU* 3.1 10.4 + - - +
12C ALA* 2.9 23.4 + - - +
64C PHE* 5.5 2.6 - - + -
71C MET* 3.5 27.4 - - + +
74C ALA* 3.3 28.0 - - + -
75C LEU* 3.3 41.7 - - + -
78C LEU* 4.0 11.0 - - + -
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Residues in contact with ALA 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PRO 2.7 21.0 + - - +
6C SER* 3.6 2.0 - - - +
8C VAL* 1.3 71.6 - - - +
10C HIS* 1.3 54.4 + - - +
12C ALA* 3.8 1.9 - - - +
13C SER* 2.7 41.3 + - - -
78C LEU* 4.0 15.7 - - + -
367C THR 3.5 22.7 - - - +
368C GLY 4.6 0.9 - - - -
369C THR* 3.5 26.7 - - - +
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Residues in contact with HIS 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER 2.8 19.2 + - - +
7C TYR* 3.2 20.2 - + - +
9C ALA* 1.3 76.4 - - - +
11C LEU* 1.3 62.1 + - + +
13C SER* 4.4 4.3 - - - -
14C ASP* 2.8 47.1 + - + +
256C ALA* 4.2 16.4 - - + +
257C GLN* 3.6 41.6 + - + +
367C THR 5.1 0.4 + - - -
368C GLY 5.8 0.6 - - - -
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Residues in contact with LEU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TYR* 2.9 52.5 + - + +
8C VAL* 3.1 9.2 + - - +
10C HIS* 1.3 82.2 - - + +
12C ALA* 1.3 57.4 + - - +
14C ASP* 3.7 2.9 - - - +
15C PHE* 2.9 34.4 + - - +
62C MET 4.2 10.9 - - - +
63C GLY* 3.9 16.6 - - - +
64C PHE* 3.5 37.2 - - + -
71C MET* 3.6 22.2 - - + -
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Residues in contact with ALA 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL 2.9 16.4 + - - +
9C ALA* 3.8 4.5 - - - +
11C LEU* 1.3 75.3 - - - +
13C SER* 1.3 59.2 + - - +
15C PHE* 3.7 1.7 - - - +
16C GLY* 2.8 26.3 + - - -
36C PRO 3.7 2.2 - - - +
37C TYR* 4.5 19.1 - - + -
40C ALA* 3.3 31.3 - - + +
41C SER 5.5 0.4 - - - +
62C MET* 5.4 0.4 - - - -
64C PHE* 4.7 7.3 - - + -
75C LEU* 4.9 13.2 - - + -
78C LEU* 5.2 0.4 - - + -
369C THR* 5.7 0.2 - - + -
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Residues in contact with SER 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ALA 2.7 27.5 + - - -
10C HIS* 4.0 2.9 - - - -
12C ALA* 1.3 72.6 - - - +
14C ASP* 1.3 56.7 + - - +
16C GLY* 3.1 2.4 + - - -
17C VAL* 2.8 36.5 + - - +
36C PRO* 4.0 3.9 - - - +
37C TYR* 5.3 0.7 - - - +
256C ALA* 4.3 7.0 - - - -
368C GLY 3.5 6.0 + - - -
369C THR* 3.2 14.6 - - - +
370C VAL* 3.0 42.4 + - - -
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Residues in contact with ASP 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C HIS* 2.8 38.4 + - + +
11C LEU* 3.7 3.6 - - - +
13C SER* 1.3 73.3 - - - +
15C PHE* 1.3 63.2 + - - +
17C VAL* 3.5 4.3 + - - +
18C ARG* 3.2 44.9 + - - +
255C SER* 4.8 6.2 - - - -
256C ALA* 3.8 26.8 + - + +
257C GLN* 5.1 0.5 + - - +
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Residues in contact with PHE 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU 2.9 18.2 + - - +
12C ALA* 3.7 2.5 - - - +
14C ASP* 1.3 75.0 + - - +
16C GLY* 1.3 60.3 + - - +
18C ARG* 3.0 24.7 + - - +
19C VAL* 3.0 40.8 + - + +
39C VAL* 4.5 2.9 - - + -
40C ALA* 3.9 19.7 - - + -
43C LEU* 4.2 11.9 - - + -
61C ALA* 3.3 27.6 - - + -
62C MET* 3.7 40.8 - - + +
290C LEU* 4.1 4.9 - - + -
293C LEU* 3.6 21.3 - - + -
295C MET* 3.7 24.9 - - + -
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Residues in contact with GLY 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ALA 2.8 11.3 + - - -
13C SER 3.6 1.8 - - - -
15C PHE* 1.3 75.1 - - - +
17C VAL* 1.3 58.9 + - - +
19C VAL* 3.1 3.1 + - - +
20C PHE* 2.8 29.8 + - - +
34C PHE* 3.7 4.7 - - - -
36C PRO* 3.5 32.3 - - - -
39C VAL* 3.8 11.7 - - - -
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Residues in contact with VAL 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C SER 2.8 32.9 + - - +
14C ASP* 3.8 6.3 - - - +
15C PHE 3.3 0.2 - - - -
16C GLY* 1.3 72.8 - - - +
18C ARG* 1.3 57.3 + - + +
20C PHE* 3.7 4.5 - - - +
21C GLN* 3.0 35.8 + - - +
36C PRO* 4.2 5.2 - - - -
254C LEU* 4.4 1.6 - - + -
255C SER* 4.1 26.9 - - - +
256C ALA* 4.4 12.1 - - - +
259C ILE* 5.9 1.8 - - + -
370C VAL* 3.6 27.6 - - + -
373C MET* 3.9 25.1 - - + -
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Residues in contact with ARG 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ASP* 3.2 31.9 + - - +
15C PHE* 3.0 29.3 + - - +
17C VAL* 1.3 77.9 - - + +
19C VAL* 1.3 61.5 + - - +
21C GLN* 3.7 12.6 + - - +
22C GLN* 3.4 23.1 + - - +
61C ALA* 2.6 43.8 + - - +
62C MET 4.9 1.6 - - - -
293C LEU* 3.6 32.6 + - + +
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Residues in contact with VAL 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PHE* 3.0 45.6 + - + +
16C GLY 3.1 6.0 + - - +
18C ARG* 1.3 72.8 - - - +
20C PHE* 1.3 66.9 + - - +
22C GLN* 2.9 24.7 + - - +
23C VAL* 3.1 6.6 + - + +
34C PHE* 3.5 25.1 - - + -
39C VAL* 4.2 11.2 - - + -
286C LEU* 4.6 2.0 - - + -
289C PRO* 4.1 22.0 - - + +
290C LEU* 3.9 14.8 - - + -
293C LEU* 3.9 10.5 - - + -
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Residues in contact with PHE 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLY 2.8 16.7 + - - +
17C VAL* 3.7 7.4 - - - +
19C VAL* 1.3 76.7 - - - +
21C GLN* 1.3 69.0 + - + +
22C GLN 2.8 0.3 + - - -
23C VAL* 2.9 12.6 + - + +
24C ALA* 2.8 43.3 + - + +
32C VAL* 4.1 16.2 - - + -
34C PHE* 3.3 35.6 - - + -
36C PRO* 4.6 0.2 - - + -
251C THR* 4.0 10.3 - - - -
359C LEU* 4.7 9.4 - - + -
373C MET* 3.0 38.1 - - + -
374C GLY* 3.5 39.3 - - - -
375C GLN* 4.3 4.7 - - - -
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Residues in contact with GLN 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C VAL* 3.0 28.4 + - + +
18C ARG* 3.8 12.8 - - - +
20C PHE* 1.3 86.2 - - + +
22C GLN* 1.3 53.3 + - + +
24C ALA* 3.7 3.8 - - - +
25C GLN* 2.8 40.7 + - - +
251C THR* 2.9 31.8 + - - +
252C ASN* 3.3 25.8 + - - +
254C LEU* 2.7 36.2 + - + +
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Residues in contact with GLN 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ARG 3.4 16.4 + - - +
19C VAL* 2.9 12.7 + - - +
20C PHE 2.8 1.4 + - - -
21C GLN* 1.3 78.2 - - - +
23C VAL* 1.3 56.8 + - - +
25C GLN* 3.2 34.3 + - - +
26C ALA* 3.0 30.9 + - - +
289C PRO* 3.8 28.7 - - + +
292C ASN* 2.9 42.5 + - - +
293C LEU* 4.2 13.4 - - + +
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Residues in contact with VAL 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C VAL 3.2 17.0 - - - +
20C PHE* 2.9 15.2 + - + +
22C GLN* 1.3 72.7 - - - +
24C ALA* 1.3 59.2 + - - +
26C ALA* 3.4 7.1 + - - +
27C SER* 3.0 27.4 + - - -
32C VAL* 3.6 30.5 - - + -
34C PHE* 3.9 26.0 - - + -
284C VAL* 4.7 18.2 - - + -
289C PRO* 4.4 21.5 - - + -
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PHE* 2.8 42.8 + - + +
21C GLN 3.7 4.7 - - - +
23C VAL* 1.3 77.2 - - - +
25C GLN* 1.3 55.4 + - - +
26C ALA 3.1 4.7 - - - -
27C SER* 3.3 28.1 + - - +
32C VAL* 5.1 1.3 - - - -
251C THR* 3.9 14.6 - - + +
375C GLN* 4.0 20.0 + - - +
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Residues in contact with GLN 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLN* 2.8 22.8 + - - +
22C GLN* 3.2 43.9 + - - +
24C ALA* 1.3 74.6 - - - +
26C ALA* 1.3 58.1 + - + +
27C SER 3.5 2.8 - - - +
251C THR* 5.5 0.8 + - - +
252C ASN* 4.1 21.3 - - - +
292C ASN* 5.0 1.4 + - - -
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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
------------------------------------------------------------
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