Contacts of the helix formed by residues 21 - 33 (chain Q) in PDB entry 3SDI
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 ILE 21 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13Q SER* 3.9 26.0 - - - -
14Q ILE 3.4 17.0 - - - +
15Q PHE* 3.7 22.9 - - + -
20Q HIS* 1.3 69.8 - - - +
22Q PHE* 1.3 59.3 + - - +
23Q GLN 4.5 1.1 - - - +
24Q VAL* 3.1 31.6 + - + +
25Q GLU* 2.9 31.8 + - - +
81R LEU* 3.5 30.5 - - + -
130R ARG* 3.6 31.0 - - - +
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Residues in contact with PHE 22 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Q ILE 4.0 5.3 + - - +
16Q SER* 3.5 36.8 - - - -
18Q ASP* 4.4 14.8 - - - -
20Q HIS* 3.5 11.0 + + + -
21Q ILE* 1.3 73.6 - - - +
23Q GLN* 1.3 52.5 + - + +
25Q GLU* 3.1 12.4 + - + +
26Q TYR* 2.6 80.2 + + + -
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Residues in contact with GLN 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P ILE* 3.8 19.9 - - + +
15P PHE* 3.2 63.3 + - - +
12Q LEU* 3.7 26.6 - - + +
13Q SER* 3.8 20.4 - - - +
21Q ILE* 3.4 1.4 - - + +
22Q PHE* 1.3 74.5 - - + +
24Q VAL* 1.3 61.4 + - - +
26Q TYR* 3.6 8.5 + - - +
27Q ALA* 3.0 27.2 + - - +
130Q ARG* 4.2 14.1 - - - +
131Q PRO* 4.0 7.2 - - + +
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Residues in contact with VAL 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Q ILE* 3.1 34.8 + - + +
23Q GLN* 1.3 75.7 - - - +
25Q GLU* 1.3 68.4 + - - +
27Q ALA* 3.2 19.3 + - - +
28Q LEU* 3.3 17.0 + - + +
124Q THR* 3.8 32.3 - - + -
131Q PRO* 4.1 11.9 - - + -
153Q PRO* 4.5 3.0 - - + +
154Q SER* 3.8 33.4 - - - +
81R LEU* 6.5 0.9 - - + -
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Residues in contact with GLU 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Q HIS* 3.3 33.5 + - - +
21Q ILE 2.9 18.5 + - - +
22Q PHE* 3.2 22.4 - - + +
24Q VAL* 1.3 81.6 - - - +
26Q TYR* 1.3 67.5 + - + +
28Q LEU* 3.2 37.2 + - - +
29Q GLU* 3.5 8.7 + - - +
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Residues in contact with TYR 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P PHE* 3.7 24.0 - - + -
16P SER 3.2 26.2 - - - +
17P PRO* 3.6 43.5 - - + +
19P GLY* 3.4 8.0 - - - -
22Q PHE* 2.6 62.8 + + + +
23Q GLN* 3.9 9.9 - - - +
25Q GLU* 1.3 74.1 - - + +
27Q ALA* 1.3 65.5 + - - +
29Q GLU* 3.0 22.9 + - + +
30Q ALA 3.3 5.0 + - - -
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Residues in contact with ALA 27 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P PHE* 3.6 26.1 - - + -
23Q GLN 3.0 15.2 + - - +
24Q VAL* 3.2 12.8 + - - +
26Q TYR* 1.3 76.5 - - - +
28Q LEU* 1.3 62.4 + - - +
30Q ALA* 3.0 16.0 + - - +
31Q VAL* 3.2 16.4 + - - +
131Q PRO* 4.5 4.0 - - + -
132Q PHE 3.7 19.7 - - - +
133Q GLY* 4.2 1.8 - - - -
153Q PRO* 3.8 8.7 - - + -
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Residues in contact with LEU 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Q VAL* 3.3 15.8 + - + +
25Q GLU* 3.2 32.4 + - - +
27Q ALA* 1.3 77.5 - - - +
29Q GLU* 1.3 56.9 + - + +
31Q VAL* 3.2 13.1 + - + +
32Q LYS* 2.9 41.5 + - + +
135Q SER* 4.9 4.0 - - - +
152Q GLU* 4.8 18.6 - - + +
153Q PRO* 4.2 23.5 - - + +
154Q SER* 6.4 1.1 - - - -
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Residues in contact with GLU 29 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17P PRO 3.7 16.6 - - - +
18P GLU* 3.3 21.5 - - - +
19P GLY 4.0 0.2 - - - +
25Q GLU 3.5 11.0 + - - +
26Q TYR* 3.0 16.2 + - + +
28Q LEU* 1.3 78.3 - - - +
30Q ALA* 1.3 55.3 + - - +
32Q LYS* 3.1 38.3 - - - +
33Q ARG* 3.0 29.8 + - - +
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Residues in contact with ALA 30 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P PHE* 4.4 12.1 - - + -
19P GLY* 3.4 27.9 - - - +
26Q TYR 3.3 3.0 + - - +
27Q ALA 3.0 10.8 + - - +
29Q GLU* 1.3 75.4 - - - +
31Q VAL* 1.3 61.6 + - - +
33Q ARG* 3.4 11.0 + - - +
34Q GLY* 3.1 19.1 + - - -
80Q GLY* 3.7 11.0 - - - -
81Q LEU* 4.5 17.7 - - + +
133Q GLY* 4.5 4.7 - - - +
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Residues in contact with VAL 31 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27Q ALA 3.2 14.1 + - - +
28Q LEU* 3.2 14.6 + - + +
30Q ALA* 1.3 73.9 - - - +
32Q LYS* 1.3 57.7 + - - +
34Q GLY* 2.8 23.9 + - - -
79Q SER* 3.5 24.9 - - - +
80Q GLY* 3.9 7.0 - - - -
133Q GLY 3.9 0.9 - - - +
134Q VAL 3.9 13.7 - - - +
135Q SER* 3.7 37.9 - - - +
153Q PRO* 4.1 10.1 - - + -
165Q ILE* 4.8 2.0 - - + -
166Q GLY* 3.3 22.1 - - - +
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Residues in contact with LYS 32 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q LEU* 2.9 24.3 + - + +
29Q GLU* 3.1 44.2 - - - +
31Q VAL* 1.3 76.5 - - - +
33Q ARG* 1.3 56.4 + - - +
166Q GLY 4.2 10.8 - - - +
167Q ARG* 2.9 32.2 + - - +
169Q SER* 6.0 1.3 - - - +
170Q LYS* 4.8 19.8 - - - +
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Residues in contact with ARG 33 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P GLU* 2.7 39.4 + - - +
19P GLY 3.9 13.2 + - - -
20P ARG* 3.3 45.8 - - - +
29Q GLU 3.0 13.8 + - - +
30Q ALA* 3.6 7.6 - - - +
31Q VAL 3.1 0.6 - - - -
32Q LYS* 1.3 75.2 - - - +
34Q GLY* 1.3 63.8 + - - +
35Q THR* 5.6 0.3 - - - +
81Q LEU* 6.4 2.2 - - - -
167Q ARG* 4.1 15.1 + - - +
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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