Contacts of the helix formed by residues 10 - 28 (chain C) in PDB entry 3D87
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 ALA 10 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C SER* 4.2 0.4 - - - -
9C PRO* 1.3 70.8 - - - +
11C TRP* 1.3 52.3 + - - +
12C THR* 2.4 20.8 + - - -
13C GLN* 2.9 52.6 + - + +
14C CYS* 2.9 10.2 + - - -
115C LEU* 4.9 8.9 + - + +
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Residues in contact with TRP 11 (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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8C SER* 4.2 17.9 + - - -
9C PRO* 2.3 34.7 + - + -
10C ALA* 1.3 62.8 - - - +
12C THR* 1.3 53.6 + - - +
14C CYS* 3.3 5.8 - - - +
15C GLN* 2.6 35.5 + - - +
63C LEU* 5.2 4.0 - - + -
67C SER* 4.4 19.3 - - - -
71C LEU* 4.7 13.5 - - + -
160C VAL* 3.6 19.3 - - + -
161C PHE* 3.6 34.8 - + - +
164C GLY* 3.3 36.3 - - - -
165C ALA* 3.6 15.7 - - - -
168C LEU* 3.4 34.4 - - + +
169C SER* 3.7 25.8 - - - -
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Residues in contact with THR 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ALA 2.4 13.2 + - - -
11C TRP* 1.3 69.7 - - - +
13C GLN* 1.3 53.0 + - - +
14C CYS 2.7 4.2 + - - -
15C GLN* 2.7 12.7 + - - +
16C GLN* 2.2 71.3 + - - +
165C ALA* 4.4 8.4 - - + +
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Residues in contact with GLN 13 (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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10C ALA* 2.9 33.7 + - + +
12C THR* 1.3 73.1 - - - +
14C CYS* 1.3 52.2 + - - +
16C GLN* 3.6 10.0 - - - +
17C LEU* 2.8 38.9 + - + +
115C LEU* 3.2 29.8 - - + +
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Residues in contact with CYS 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PRO* 4.3 15.3 - - - -
10C ALA 2.9 15.9 + - - +
11C TRP* 3.3 9.6 - - - +
12C THR 2.7 0.2 - - - -
13C GLN* 1.3 76.1 - - - +
15C GLN* 1.3 61.2 + - - +
16C GLN 3.0 1.1 - - - -
18C SER* 2.8 35.6 + - - -
112C LEU* 4.0 15.1 - - - +
115C LEU* 4.3 10.1 - - - +
116C LEU* 3.9 16.2 - - - -
161C PHE* 3.3 35.7 - - + -
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Residues in contact with GLN 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 TRP 2.6 22.2 + - - +
12C THR* 2.7 12.6 + - - +
14C CYS* 1.3 70.5 - - - +
16C GLN* 1.3 92.9 + - - +
18C SER* 3.3 14.2 + - - +
19C GLN* 3.5 24.7 + - - +
161C PHE* 3.1 16.1 - - - +
162C ALA* 3.5 26.5 - - + +
165C ALA* 3.6 9.6 - - + +
291D ARG* 5.9 0.8 - - - +
292D TYR* 5.1 3.1 + - + +
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Residues in contact with GLN 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 THR* 2.2 84.9 + - - +
13C GLN* 3.6 9.9 - - - -
15C GLN* 1.3 83.3 + - - +
17C LEU* 1.3 69.4 - - - +
19C GLN* 2.8 17.4 + - - +
20C LYS* 3.1 14.6 + - + +
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Residues in contact with LEU 17 (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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13C GLN* 2.8 21.7 + - + +
16C GLN* 1.3 76.9 - - - +
18C SER* 1.3 50.2 + - - +
20C LYS* 3.2 9.7 + - + +
21C LEU* 2.8 29.6 + - + +
108C SER* 3.1 35.7 - - - +
111C GLY* 4.2 9.2 - - - +
112C LEU* 4.0 32.8 - - + +
115C LEU* 4.9 10.5 - - + -
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Residues in contact with SER 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 CYS 2.8 25.8 + - - -
15C GLN* 3.3 12.6 + - - +
17C LEU* 1.3 74.1 - - - +
19C GLN* 1.3 61.4 + - - +
21C LEU* 2.9 17.8 - - - +
22C CYS* 3.2 16.1 + - - -
112C LEU* 3.3 21.3 - - - +
154C VAL* 4.7 1.2 - - - +
157C ALA* 4.9 1.8 - - - -
158C ALA* 3.6 21.3 + - - +
161C PHE* 3.7 17.2 - - - +
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Residues in contact with GLN 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 GLN* 3.5 28.0 + - - +
16C GLN 2.8 4.0 + - - +
18C SER* 1.3 76.5 + - - +
20C LYS* 1.3 69.9 + - + +
21C LEU 2.9 1.3 - - - -
22C CYS* 3.3 16.3 + - + +
23C THR* 3.1 19.0 + - - +
270D ASP* 3.5 13.6 + - - +
291D ARG* 2.8 53.3 + - - +
292D TYR* 4.0 15.8 + - + -
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Residues in contact with LYS 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 GLN* 3.1 14.0 + - + +
17C LEU* 3.5 15.9 - - + +
19C GLN* 1.3 79.3 - - + +
21C LEU* 1.3 63.4 - - - +
23C THR* 3.3 8.9 + - - -
24C LEU* 3.0 28.4 + - + +
108C SER* 4.6 2.9 - - - +
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Residues in contact with LEU 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 LEU 2.8 12.8 + - - +
18C SER* 2.9 15.7 - - - +
20C LYS* 1.3 78.1 - - - +
22C CYS* 1.3 54.2 + - - +
24C LEU* 3.1 6.7 - - - +
25C ALA 2.9 22.5 + - - -
78C LEU* 5.1 3.6 - - + -
105C LEU* 4.1 5.6 - - + +
108C SER* 3.7 35.0 + - - +
109C LEU* 3.9 17.7 - - + -
112C LEU* 3.8 34.8 - - + -
154C VAL* 3.3 38.8 - - + -
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Residues in contact with CYS 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 SER 3.2 12.9 + - - -
19C GLN* 3.3 8.4 + - + +
21C LEU* 1.3 74.6 - - - +
23C THR* 1.3 67.2 + - - +
24C LEU 3.0 1.3 - - - -
25C ALA* 3.2 7.4 + - - +
26C TRP* 2.8 30.8 + - + -
154C VAL* 3.4 36.3 - - + -
155C ALA* 4.2 0.2 - - - -
158C ALA* 3.7 14.4 - - - -
291D ARG 5.2 2.7 - - - +
292D TYR* 3.6 32.3 - - + +
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Residues in contact with THR 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 GLN* 3.1 15.3 + - - +
20C LYS* 3.3 10.7 + - - -
22C CYS* 1.3 77.1 - - - +
24C LEU* 1.3 63.2 + - - +
26C TRP* 3.1 8.0 + - + +
27C SER* 2.9 33.0 + - - +
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Residues in contact with LEU 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 LYS* 3.0 19.8 + - + +
21C LEU* 3.1 11.4 - - - +
22C CYS 3.0 0.2 - - - -
23C THR* 1.3 77.3 - - - +
25C ALA* 1.3 63.6 + - - +
26C TRP 3.0 0.3 + - - -
27C SER* 3.1 8.4 + - - -
28C ALA* 2.9 26.3 + - - +
101C PRO* 3.5 14.4 - - + +
104C GLN* 3.2 23.3 - - + +
105C LEU* 3.0 46.4 - - + +
108C SER* 4.0 17.3 - - - +
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Residues in contact with ALA 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 LEU 2.9 11.4 + - - +
22C CYS 3.4 10.8 - - - +
24C LEU* 1.3 76.5 - - - +
26C TRP* 1.3 61.9 + - + +
29C HIS 3.4 3.5 + - - -
105C LEU* 3.5 14.0 - - + +
147C LEU* 3.0 26.0 - - - +
150C LEU* 3.9 22.0 - - + -
151C GLN* 3.1 28.8 + - + -
154C VAL* 4.2 4.9 - - + -
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Residues in contact with TRP 26 (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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22C CYS* 2.8 25.9 + - - +
23C THR* 3.1 8.9 + - + +
24C LEU 3.0 1.0 - - - -
25C ALA* 1.3 74.9 - - + +
27C SER* 1.3 57.2 + - - +
29C HIS 2.7 12.2 + - - -
30C PRO* 2.6 36.2 - - + +
31C LEU* 4.1 33.2 - - + -
148C ARG* 4.9 5.4 - - + -
151C GLN* 3.5 39.9 + - + +
154C VAL* 5.8 0.2 - - - +
292D TYR 3.9 14.3 + - - -
293D TYR* 3.5 31.5 - + - +
294D SER* 3.5 59.4 - - - +
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Residues in contact with SER 27 (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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30A PRO* 3.8 7.8 - - - +
23C THR* 2.9 23.6 + - - +
24C LEU* 3.1 11.3 + - - -
26C TRP* 1.3 74.1 - - - +
28C ALA* 1.3 58.7 + - - +
29C HIS 3.1 5.2 + - - -
30C PRO* 3.2 17.1 - - - +
101C PRO* 4.4 12.0 - - - +
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Residues in contact with ALA 28 (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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30A PRO* 3.2 8.6 - - - +
31A LEU* 3.0 21.7 - - - +
24C LEU 2.9 6.9 + - - +
25C ALA 3.7 2.7 - - - +
27C SER* 1.3 75.4 - - - +
29C HIS* 1.3 64.3 + - - +
101C PRO* 3.5 28.7 - - + +
102C VAL* 3.9 7.6 - - + +
105C LEU* 2.9 37.0 - - + -
147C LEU* 3.9 2.8 - - + +
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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