Contacts of the helix formed by residues 21 - 34 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C SER* 3.9 24.9 - - - -
14C ILE 3.5 16.4 - - - +
15C PHE* 3.7 22.9 - - + -
19C GLY 4.2 0.2 + - - -
20C HIS* 1.3 70.9 - - - +
22C PHE* 1.3 65.7 + - - +
23C GLN 4.3 0.4 - - - +
24C VAL* 3.0 39.6 + - + +
25C GLU* 3.1 17.1 + - - +
81D LEU* 3.6 26.1 - - + +
130D ARG* 3.5 38.6 - - - +
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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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14C ILE 3.8 7.5 + - - +
16C SER* 3.4 35.4 - - - -
17C PRO* 5.5 2.5 - - + -
18C ASP* 4.6 12.8 - - - -
20C HIS* 3.6 10.4 + - + -
21C ILE* 1.3 72.0 - - - +
23C GLN* 1.3 58.1 + - + +
25C GLU* 3.1 8.5 + - + +
26C TYR* 2.8 71.9 + + + -
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Residues in contact with GLN 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 3.8 19.9 - - - +
15B PHE* 3.1 69.6 + - - +
12C LEU* 3.3 27.9 - - + +
13C SER* 3.7 23.7 - - - +
14C ILE 5.7 0.2 - - - +
21C ILE* 3.3 1.4 - - - +
22C PHE* 1.3 78.9 - - + +
24C VAL* 1.3 57.5 + - - +
26C TYR* 3.6 9.4 + - - +
27C ALA* 3.0 26.0 + - - +
130C ARG* 4.3 4.2 - - - +
131C PRO* 4.0 12.3 - - + +
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Residues in contact with VAL 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ILE* 3.0 32.0 + - + +
23C GLN* 1.3 73.0 - - - +
25C GLU* 1.3 70.1 + - - +
27C ALA* 3.0 8.8 + - - +
28C LEU* 3.0 28.3 + - + +
124C THR* 3.8 30.5 - - + -
131C PRO* 4.1 8.1 - - + -
153C PRO* 4.2 4.6 - - + +
154C SER* 3.8 36.8 - - - +
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Residues in contact with GLU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C HIS* 3.6 35.7 + - + +
21C ILE 3.1 15.0 + - - +
22C PHE* 3.1 16.1 + - + +
24C VAL* 1.3 80.0 - - - +
26C TYR* 1.3 67.8 + - + +
28C LEU* 3.3 30.8 + - + +
29C GLU* 3.3 17.4 + - - +
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Residues in contact with TYR 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.7 24.0 - - + -
16B SER 3.3 27.1 - - - +
17B PRO* 3.7 43.7 - - + +
19B GLY* 3.2 21.6 - - - -
22C PHE* 2.8 59.5 + + + +
23C GLN* 4.0 11.0 - - - +
24C VAL 3.2 0.2 - - - -
25C GLU* 1.3 80.8 - - + +
27C ALA* 1.3 65.3 + - - +
29C GLU* 3.2 15.6 + - + +
30C ALA* 3.3 1.6 + - - +
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Residues in contact with ALA 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.8 21.0 - - + -
23C GLN 3.0 15.4 + - - +
24C VAL* 3.2 15.0 - - - +
26C TYR* 1.3 77.7 - - - +
28C LEU* 1.3 58.6 + - - +
30C ALA* 3.1 15.6 + - - +
31C VAL* 3.3 13.5 + - - +
131C PRO* 4.2 5.4 - - + -
132C PHE 3.7 21.5 - - - +
133C GLY* 4.0 2.5 - - - -
153C PRO* 3.8 11.7 - - + -
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Residues in contact with LEU 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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24C VAL* 3.0 18.8 + - + +
25C GLU* 3.4 27.4 - - + +
26C TYR 3.2 0.4 - - - -
27C ALA* 1.3 76.2 - - - +
29C GLU* 1.3 56.0 + - - +
31C VAL* 3.2 14.1 + - + +
32C LYS* 3.0 45.0 + - + +
135C SER* 4.6 7.9 - - - +
152C GLU* 4.2 24.2 - - + +
153C PRO* 4.3 21.5 - - + +
154C SER 6.3 0.2 - - - +
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Residues in contact with GLU 29 (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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17B PRO 3.5 19.2 - - - +
18B GLU* 3.6 21.2 - - - +
25C GLU* 3.3 14.6 + - - +
26C TYR* 3.2 14.2 + - + +
28C LEU* 1.3 77.5 - - - +
30C ALA* 1.3 62.4 + - - +
32C LYS* 3.2 39.7 + - - +
33C ARG* 3.1 23.9 + - - +
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Residues in contact with ALA 30 (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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15B PHE* 4.0 17.5 - - + -
19B GLY* 3.4 23.5 - - - +
26C TYR 3.3 3.1 + - - +
27C ALA 3.1 11.5 + - - +
29C GLU* 1.3 75.5 - - - +
31C VAL* 1.3 64.1 + - - +
33C ARG* 3.3 11.4 + - - +
34C GLY 3.2 14.9 + - - -
80C GLY* 3.8 9.9 - - - -
81C LEU* 4.5 11.6 - - + +
133C GLY* 4.1 12.1 - - - +
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Residues in contact with VAL 31 (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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27C ALA 3.3 12.1 + - - +
28C LEU* 3.2 14.9 + - + +
30C ALA* 1.3 76.3 - - - +
32C LYS* 1.3 56.2 + - + +
34C GLY* 2.8 23.6 + - - -
79C SER* 3.6 22.2 - - - +
80C GLY* 4.0 6.3 - - - -
133C GLY 3.8 5.6 - - - +
134C VAL* 3.6 8.3 - - - +
135C SER* 3.5 45.1 - - - +
153C PRO* 4.2 6.5 - - + -
165C ILE* 4.8 2.0 - - + -
166C GLY* 3.4 20.3 - - - +
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Residues in contact with LYS 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.0 30.6 + - + +
29C GLU* 3.2 45.1 - - - +
31C VAL* 1.3 75.9 - - + +
33C ARG* 1.3 57.0 - - - +
166C GLY* 4.3 9.2 - - - +
167C ARG* 3.1 29.5 - - - +
170C LYS* 4.9 12.1 - - - +
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Residues in contact with ARG 33 (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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18B GLU* 2.5 45.3 + - - +
19B GLY 3.4 18.1 + - - -
20B ARG* 3.7 36.5 - - - +
29C GLU 3.1 11.1 + - - +
30C ALA* 3.6 8.9 - - - +
31C VAL 3.1 0.8 - - - -
32C LYS* 1.3 74.2 - - - +
34C GLY* 1.3 67.7 + - - +
35C THR 3.9 0.3 + - - -
167C ARG* 4.3 13.0 + - - -
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Residues in contact with GLY 34 (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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30C ALA 3.2 6.3 + - - -
31C VAL 2.8 13.4 + - - +
33C ARG* 1.3 80.7 - - - +
35C THR* 1.3 64.3 + - - +
80C GLY* 4.0 23.1 - - - -
166C GLY* 3.7 0.2 - - - -
167C ARG* 2.9 29.4 + - - +
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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
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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