Contacts of the helix formed by residues 4 - 24 (chain C) in PDB entry 2RD9
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 GLN 4 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ASN 3.3 6.2 + - - +
3C PHE* 1.3 82.0 - - - +
5C MSE 1.3 67.4 + - - +
6C ASN* 3.1 23.6 + - - +
7C GLU* 3.3 27.9 + - + +
8C ALA* 2.9 22.9 + - - +
157D ARG* 6.1 0.4 - - - +
158D TYR* 3.8 2.8 + - - -
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Residues in contact with MSE 5 (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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3C PHE* 3.7 17.6 - - + -
4C GLN* 1.3 72.0 - - - +
6C ASN* 1.3 65.5 + - - +
8C ALA* 3.1 5.2 + - + +
9C ILE* 2.9 39.2 + - + +
108C LEU* 4.1 20.4 - - + -
109C ARG* 6.5 0.4 - - - -
112C VAL* 3.8 33.4 - - - +
114C SER 5.8 1.6 - - - +
115C GLU* 4.3 19.1 + - - +
118C LEU* 4.3 6.6 - - + +
136C LEU* 3.5 30.3 - - + -
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Residues in contact with ASN 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLN* 3.1 28.8 + - - +
5C MSE 1.3 77.2 + - - +
7C GLU* 1.3 71.8 + - - +
9C ILE* 3.5 7.7 + - - +
10C GLN* 3.1 35.9 + - - +
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Residues in contact with GLU 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ASN 4.5 0.9 - - - +
4C GLN* 3.3 32.4 + - + +
5C MSE 3.2 0.2 - - - -
6C ASN* 1.3 92.3 + - - +
8C ALA* 1.3 60.8 + - - +
10C GLN* 3.3 21.7 - - - +
11C LEU 3.4 3.6 + - - -
27D SER* 3.0 34.6 + - - -
29D SER* 3.4 10.8 + - - -
30D TRP* 3.2 29.5 + - + +
157D ARG* 3.3 30.2 + - - -
158D TYR* 4.5 2.5 - - - +
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Residues in contact with ALA 8 (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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3C PHE* 3.4 34.8 - - + -
4C GLN 2.9 10.9 + - - +
5C MSE 3.5 5.4 - - + +
7C GLU* 1.3 73.5 - - - +
9C ILE* 1.3 61.2 + - + +
11C LEU* 3.3 5.4 + - - +
12C LEU* 3.0 35.0 + - + +
136C LEU* 5.4 0.9 - - + +
140C VAL* 3.8 17.9 - - + +
30D TRP* 4.9 2.5 - - - -
158D TYR* 3.8 10.7 + - - +
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Residues in contact with ILE 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C MSE 2.9 36.3 + - + +
6C ASN* 3.8 7.0 - - - +
8C ALA* 1.3 73.5 - - + +
10C GLN* 1.3 56.2 + - - +
12C LEU* 4.3 6.7 - - + -
13C GLU* 2.8 45.9 + - + +
105C LEU* 4.6 9.6 - - + -
108C LEU* 4.1 28.9 - - + -
109C ARG* 3.4 55.4 - - + +
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Residues in contact with GLN 10 (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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6C ASN* 3.1 29.9 + - - +
7C GLU* 3.3 15.0 - - - +
8C ALA 3.3 0.2 - - - -
9C ILE* 1.3 73.4 - - - +
11C LEU* 1.3 61.8 + - - +
13C GLU* 3.3 22.7 - - - +
14C ARG* 3.2 30.0 + - - +
25D GLY 4.4 7.4 + - - +
26D LEU* 3.7 16.4 - - + -
27D SER* 3.0 40.8 + - - +
30D TRP* 3.7 8.7 - - - -
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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
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7C GLU 3.4 1.7 + - - +
8C ALA 3.3 8.6 + - - +
9C ILE 3.2 0.6 - - - -
10C GLN* 1.3 78.3 - - - +
12C LEU* 1.3 65.3 + - - +
14C ARG* 3.0 15.8 + - + +
15C THR* 3.3 16.3 + - - +
140C VAL* 3.6 22.9 - - + -
143C ASP* 5.2 0.2 - - - -
144C LEU* 4.0 12.8 - - + -
22D PHE* 4.6 14.3 - - + +
26D LEU* 3.6 19.7 - - + -
30D TRP* 3.3 47.8 - - + +
154D MSE 3.1 31.4 - - + -
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Residues in contact with LEU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ALA* 3.0 24.8 + - + +
9C ILE* 3.9 4.3 - - - +
11C LEU* 1.3 77.5 - - - +
13C GLU* 1.3 61.4 + - - +
14C ARG 3.3 0.7 + - - -
15C THR 3.8 0.2 + - - -
16C PRO* 3.8 3.5 - - - +
101C ARG* 2.7 32.4 + - - +
105C LEU* 3.9 25.4 - - + -
108C LEU* 4.8 6.3 - - + -
136C LEU* 5.1 2.7 - - + +
139C TRP* 3.6 56.3 - - + +
140C VAL* 3.9 26.2 - - + -
143C ASP* 3.6 16.2 - - - +
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Residues in contact with GLU 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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9C ILE* 2.8 29.6 + - - +
10C GLN* 3.3 23.3 - - - +
11C LEU 3.2 0.2 - - - -
12C LEU* 1.3 77.0 - - - +
14C ARG* 1.3 77.7 + - + +
15C THR 3.7 0.2 - - - -
16C PRO* 4.0 8.0 - - - +
17C LYS* 5.1 2.8 + - - +
98C GLN* 4.6 11.3 + - - +
101C ARG* 4.8 1.1 - - - -
105C LEU* 3.5 20.7 - - + +
109C ARG* 4.4 9.2 + - - -
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Residues in contact with ARG 14 (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 GLN* 3.2 29.7 + - - +
11C LEU* 3.0 9.8 + - - +
13C GLU* 1.3 96.7 + - + +
15C THR* 1.3 65.0 + - - +
16C PRO* 3.3 3.0 - - - -
17C LYS* 3.3 7.7 + - - +
18C THR* 2.9 33.4 + - - +
21D VAL* 3.6 15.5 + - + +
22D PHE* 3.3 26.1 + - + +
24D GLU 2.7 31.3 + - - -
25D GLY* 4.0 10.0 + - - -
26D LEU* 3.5 16.9 - - - +
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Residues in contact with THR 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* 3.3 10.9 + - - +
14C ARG* 1.3 76.6 - - - +
16C PRO* 1.4 69.6 - - - +
18C THR* 3.3 5.6 + - - -
19C LEU* 3.0 35.4 + - + +
49C LEU* 4.9 2.7 - - + -
97C PHE* 3.8 19.3 - - + -
101C ARG* 3.9 3.1 - - - -
143C ASP* 2.7 42.2 + - + +
144C LEU* 5.9 0.9 - - - +
147C ILE* 4.1 20.0 - - + +
22D PHE* 5.4 3.7 - - - -
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Residues in contact with PRO 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 LEU 3.8 10.8 - - - +
13C GLU 4.0 5.6 - - - +
14C ARG 3.5 3.8 - - - -
15C THR* 1.4 93.7 - - - +
17C LYS* 1.3 61.6 + - - +
19C LEU* 3.4 2.8 + - + +
20C GLU* 3.1 23.7 + - - +
94C PHE* 5.1 5.5 - - - +
97C PHE* 3.8 28.7 - - + +
98C GLN* 3.8 35.0 - - + +
101C ARG* 3.7 29.8 - - + +
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Residues in contact with LYS 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 GLU 5.2 2.0 - - - +
14C ARG* 3.3 10.6 + - - +
16C PRO* 1.3 76.8 - - - +
18C THR* 1.3 65.1 + - - +
20C GLU* 3.3 26.1 + - - +
21C VAL* 3.0 44.8 + - - +
98C GLN* 4.1 13.9 + - - +
17D LYS* 6.4 0.7 - - - +
21D VAL* 3.6 21.5 - - + -
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Residues in contact with THR 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 ARG 2.9 21.1 + - - -
15C THR* 3.3 6.9 + - - -
17C LYS* 1.3 76.8 - - - +
19C LEU* 1.3 66.1 + - + +
21C VAL* 3.9 3.3 - - - +
22C PHE* 3.1 26.7 + - + +
147C ILE* 5.1 11.0 - - + -
18D THR* 4.1 17.4 - - + +
21D VAL* 3.8 9.8 - - - +
22D PHE* 3.4 56.7 + - + -
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Residues in contact with LEU 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 THR* 3.0 29.4 + - + +
16C PRO* 4.0 4.0 - - + +
18C THR* 1.3 78.3 - - + +
20C GLU* 1.3 57.8 + - - +
22C PHE* 4.3 12.3 - - + -
23C LEU* 2.9 47.7 + - + +
46C VAL* 4.9 7.9 - - + -
49C LEU* 3.7 29.4 - - + -
94C PHE* 4.3 9.6 - - + -
97C PHE* 4.1 9.4 - - + -
147C ILE* 4.0 26.7 - - + -
150C ILE* 3.9 26.0 - - + -
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Residues in contact with GLU 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 PRO 3.1 18.1 + - - +
17C LYS* 3.6 28.3 + - + +
18C THR 3.2 0.2 - - - -
19C LEU* 1.3 75.2 - - - +
21C VAL* 1.3 59.7 + - - +
24C GLU* 2.9 55.6 + - - +
94C PHE* 3.6 41.0 - - + +
98C GLN* 5.7 4.9 - - - +
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Residues in contact with VAL 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 LYS* 3.0 41.0 + - - +
18C THR* 3.9 3.6 - - - +
20C GLU* 1.3 77.0 - - - +
22C PHE* 1.3 61.9 + - - +
24C GLU* 4.5 1.8 - - - +
14D ARG* 3.8 21.1 + - + +
17D LYS* 3.8 23.3 - - + +
18D THR* 3.5 35.2 - - - +
21D VAL* 3.8 20.6 - - + -
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Residues in contact with PHE 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 THR* 3.1 20.6 + - + +
19C LEU* 3.8 12.1 - - + +
21C VAL* 1.3 78.8 - - - +
23C LEU* 1.3 73.9 + - + +
26C LEU* 3.4 16.3 - - - +
147C ILE* 6.1 1.6 - - + -
150C ILE* 4.4 6.3 - - + -
151C VAL* 3.7 25.8 - - + -
154C MSE 3.9 17.5 - - + -
11D LEU* 3.6 23.1 - - + -
14D ARG* 3.4 19.2 - - + +
15D THR* 5.2 4.3 - - - -
18D THR* 3.6 30.1 - - + -
144D LEU* 3.9 22.9 - - + -
147D ILE* 4.2 17.7 - - + -
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Residues in contact with LEU 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 LEU* 2.9 25.0 + - + +
22C PHE* 1.3 91.6 - - + +
24C GLU* 1.3 66.2 + - - +
25C GLY 3.3 0.2 + - - -
26C LEU* 3.1 29.4 + - + +
30C TRP* 5.8 0.2 - - + -
31C HIS* 2.7 31.5 + - + +
42C VAL* 3.5 29.4 - - + -
46C VAL* 4.2 19.3 - - + -
90C ILE* 5.0 0.7 - - + -
94C PHE* 3.6 14.8 - - + -
150C ILE* 4.3 10.5 - - + -
154C MSE 3.8 23.6 - - - -
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Residues in contact with GLU 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 GLU* 2.9 43.4 + - + +
21C VAL* 4.5 1.8 - - - +
23C LEU* 1.3 74.9 - - - +
25C GLY* 1.3 62.8 + - - +
26C LEU 3.3 0.2 - - - -
31C HIS* 5.0 0.9 - - - -
90C ILE* 4.6 3.6 - - - +
91C SER* 3.3 33.2 + - - +
94C PHE* 3.7 24.2 - - + +
14D ARG* 3.1 25.1 + - - -
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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