Contacts of the helix formed by residues 16 - 26 (chain C) in PDB entry 3RHT
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 16 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C TYR* 3.4 18.1 - - + +
8C GLY 3.7 7.6 - - - +
9C ASP* 3.0 6.5 + - - +
11C SER 3.2 12.0 + - - +
12C LEU* 3.9 3.6 - - + +
15C ALA* 1.3 75.3 - - - +
17C GLY* 1.3 57.1 + - - +
18C TYR 3.1 0.6 + - - -
19C LEU 3.6 1.4 + - - -
20C ALA* 3.0 30.6 + - - +
32C TYR* 3.3 44.4 - - + +
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Residues in contact with GLY 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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12C LEU 3.4 20.1 + - - -
14C THR 3.1 5.2 + - - -
15C ALA 3.0 2.2 - - - -
16C ALA* 1.3 78.6 - - - +
18C TYR* 1.3 56.5 + - - +
20C ALA* 4.3 2.5 - - - -
21C GLY* 2.9 25.8 + - - -
231C ALA* 3.9 12.1 - - - +
232C GLY 4.6 1.7 - - - +
234C ILE* 3.6 14.8 - - - +
261C GOL 3.5 11.0 - - - -
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Residues in contact with TYR 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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211B HIS* 4.6 13.0 + - + +
260B GOL 5.0 2.8 + - - -
15C ALA* 3.2 27.3 + - - +
16C ALA 3.1 0.8 - - - -
17C GLY* 1.3 78.0 - - - +
19C LEU* 1.3 62.3 + - - +
22C LEU* 2.9 29.7 + - - +
208C VAL 4.3 4.9 - - - +
209C ALA* 4.1 5.4 - - + -
210C PRO* 3.5 34.6 - - + +
217C VAL* 3.8 25.8 - - + -
234C ILE* 3.3 17.4 - - + +
235C GLU 5.4 0.9 - - - -
236C VAL* 3.9 24.9 - - + -
240C TYR* 3.6 14.4 - + - +
261C GOL 3.9 33.0 + - - -
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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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6C TYR* 3.8 38.1 + - + +
15C ALA 4.5 0.4 + - - -
16C ALA 3.6 2.4 + - - -
18C TYR* 1.3 78.7 - - - +
20C ALA* 1.3 56.6 + - - +
22C LEU* 3.2 21.7 + - + +
23C MSE 2.9 37.6 + - + +
26C TRP* 4.3 8.7 - - + -
52C ILE* 3.9 28.5 - - + -
82C LEU* 4.2 12.1 - - + -
208C VAL* 4.2 18.1 - - + +
240C TYR* 4.7 0.8 + - - -
244C PHE* 4.9 4.9 - - + -
248C LEU* 3.9 22.0 - - + -
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Residues in contact with ALA 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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6C TYR* 4.1 4.8 - - + -
12C LEU* 3.6 26.2 - - + -
16C ALA 3.0 21.2 + - - +
17C GLY* 4.3 1.6 - - - -
19C LEU* 1.3 77.0 - - - +
21C GLY* 1.3 56.5 + - - +
23C MSE 3.4 4.7 + - - -
24C THR* 2.9 30.8 + - - -
30C PHE* 3.6 21.4 - - + -
228C ALA* 3.6 14.3 - - + +
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Residues in contact with GLY 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 GLY 2.9 20.5 + - - -
18C TYR 3.6 0.7 - - - -
20C ALA* 1.3 74.1 - - - +
22C LEU* 1.3 64.9 + - - +
24C THR 3.2 1.6 + - - -
25C SER* 2.9 10.0 + - - -
226C SER* 2.9 33.2 + - - -
227C GLN* 4.9 0.4 - - - -
228C ALA* 3.8 14.9 - - - +
234C ILE* 3.8 9.6 - - - -
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Residues in contact with LEU 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 TYR 2.9 19.0 + - - +
19C LEU* 3.2 17.9 + - + +
21C GLY* 1.3 70.9 - - - +
23C MSE 1.3 64.4 + - - +
25C SER* 2.7 23.8 + - - +
26C TRP* 3.0 34.2 + - + -
208C VAL* 4.8 0.4 - - + -
224C VAL* 5.1 3.4 - - + -
226C SER* 5.4 0.2 - - - -
234C ILE* 3.9 3.7 - - + +
236C VAL* 4.1 11.7 - - + -
240C TYR* 3.6 38.6 - - + +
241C SER* 3.5 33.4 - - - +
244C PHE* 4.1 17.7 - - + -
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Residues in contact with MSE 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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4C VAL* 4.0 23.6 - - - -
6C TYR* 3.7 35.9 - - + -
19C LEU* 2.9 29.5 + - + +
20C ALA* 3.8 3.6 - - - +
22C LEU* 1.3 70.8 - - - +
24C THR* 1.3 64.1 + - - +
26C TRP* 3.1 28.0 + - + -
27C GLN 3.1 4.2 + - - -
28C TRP* 2.9 43.8 + - + +
30C PHE* 3.5 41.7 - - + -
52C ILE* 4.1 9.0 - - - -
248C LEU* 4.5 2.5 - - - -
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Residues in contact with THR 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 ALA 2.9 16.3 + - - -
21C GLY 3.2 8.3 + - - -
23C MSE 1.3 75.0 - - - +
25C SER* 1.3 57.5 + - - +
27C GLN* 2.8 24.0 + - - +
28C TRP 4.5 7.4 - - - -
30C PHE* 4.0 8.2 - - - -
226C SER* 3.9 7.9 - - - +
227C GLN 4.0 15.3 - - - +
228C ALA* 3.5 17.7 - - - +
229C PRO* 4.0 10.1 - - + +
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Residues in contact with SER 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 GLY 2.9 13.6 + - - -
22C LEU* 2.7 22.1 + - - -
24C THR* 1.3 75.7 - - - +
26C TRP* 1.3 72.1 + - - +
27C GLN* 3.1 8.2 + - - +
224C VAL* 4.4 15.7 - - - +
225C THR 4.9 2.2 - - - -
226C SER* 3.7 16.9 + - - -
241C SER* 4.3 4.0 + - - -
245C ARG* 5.0 1.6 + - - -
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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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19C LEU* 4.3 7.6 - - + -
22C LEU* 3.0 36.9 + - + -
23C MSE 3.1 25.9 + - + +
25C SER* 1.3 82.7 + - - +
27C GLN* 1.3 70.0 + - - +
28C TRP* 3.3 49.7 - + + -
241C SER* 3.0 30.3 + - - -
244C PHE* 3.7 9.9 - - + -
245C ARG* 3.4 85.4 + - + +
248C LEU* 4.0 6.1 - - + -
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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