Contacts of the helix formed by residues 21 - 32 (chain B) 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 LEU 21 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B THR* 4.9 2.2 - - - +
14B ILE 3.4 20.2 - - - +
15B PHE* 3.8 17.9 - - + -
20B ARG* 1.3 72.3 - - - +
22B TYR* 1.3 67.7 + - - +
23B GLN 3.4 1.6 - - - -
24B VAL* 3.0 24.4 + - + +
25B GLU* 2.9 32.0 + - - +
124B THR* 3.7 28.9 - - + +
154B SER* 5.8 4.0 - - - -
81C LEU* 3.9 25.6 - - + -
130C ARG* 3.5 28.0 - - - +
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Residues in contact with TYR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 4.0 37.4 + - + +
15B PHE 4.2 0.2 - - - -
16B SER* 3.6 27.8 - - - -
17B PRO* 3.7 20.1 - - - +
20B ARG* 3.6 4.6 + - + -
21B LEU* 1.3 72.0 - - - +
23B GLN* 1.3 65.2 + - + +
25B GLU* 3.0 6.8 + - - +
26B TYR* 2.9 64.4 + + + -
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Residues in contact with GLN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A THR* 3.7 17.0 + - + +
15A PHE* 2.9 63.5 + - - +
13B THR 4.5 21.4 - - - +
21B LEU 3.4 0.6 - - - -
22B TYR* 1.3 83.4 - - + +
24B VAL* 1.3 58.3 + - + +
26B TYR* 3.6 11.6 + - - +
27B ALA* 3.1 27.7 + - - +
130B ARG* 4.4 3.7 - - - +
131B PRO* 3.9 24.8 - - + +
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Residues in contact with VAL 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B THR 6.4 0.2 - - - +
21B LEU* 3.0 32.8 + - + +
23B GLN* 1.3 75.4 - - + +
25B GLU* 1.3 72.9 + - - +
27B ALA* 3.2 7.8 + - - +
28B LEU* 3.0 31.1 + - + +
124B THR* 3.5 25.6 - - - +
131B PRO* 4.4 12.3 - - + -
153B PRO* 4.2 5.1 - - + +
154B SER* 3.7 37.2 - - - +
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Residues in contact with GLU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ARG* 4.3 29.7 + - + +
21B LEU* 2.9 31.0 + - - +
22B TYR* 3.4 8.5 - - - +
24B VAL* 1.3 81.8 - - - +
26B TYR* 1.3 66.1 + - + +
28B LEU* 3.2 24.3 + - - +
29B GLU* 3.0 26.0 + - - +
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Residues in contact with TYR 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 3.5 32.0 - - + -
16A SER 3.4 17.5 - - - +
17A PRO* 3.6 44.2 - - + +
19A GLY* 3.4 9.7 - - - -
22B TYR* 2.9 53.5 + + + +
23B GLN* 3.9 10.1 - - - +
25B GLU* 1.3 85.9 - - + +
27B ALA* 1.3 57.9 + - - +
29B GLU* 3.4 9.0 + - + +
30B SER* 3.1 21.7 + - - -
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 3.9 30.7 - - + -
23B GLN 3.1 18.6 + - - +
24B VAL* 3.2 6.2 + - - +
26B TYR* 1.3 74.7 - - - +
28B LEU* 1.3 64.1 + - - +
30B SER* 3.2 6.4 + - - -
31B ILE* 3.1 24.6 + - - +
131B PRO* 4.9 2.5 - - + -
132B PHE 4.5 3.4 - - - +
133B GLY* 4.6 1.4 - - - -
153B PRO* 3.9 24.7 - - + -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 3.0 28.0 + - + +
25B GLU* 3.4 29.8 - - - +
27B ALA* 1.3 72.3 - - - +
29B GLU* 1.3 65.1 + - - +
31B ILE* 3.2 18.6 + - + +
32B SER* 3.3 13.0 + - - -
135B SER* 4.8 2.9 - - - +
152B ASN* 4.0 21.5 - - + +
153B PRO* 3.9 23.6 - - + -
154B SER* 5.8 1.3 - - - -
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PRO 3.7 19.7 - - - +
18A SER* 3.8 14.8 - - - +
19A GLY* 4.3 0.9 - - - -
25B GLU 3.0 11.7 + - - +
26B TYR* 3.4 15.5 - - + +
28B LEU* 1.3 74.2 - - - +
30B SER* 1.3 63.0 + - - +
32B SER* 2.7 36.4 + - - -
33B HIS* 3.6 20.5 + - - -
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Residues in contact with SER 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 4.0 17.0 - - - -
19A GLY* 3.2 28.3 + - - -
21A LEU* 5.9 0.2 - - - +
26B TYR 3.1 10.5 + - - -
27B ALA 3.2 10.5 - - - -
29B GLU* 1.3 76.4 - - - +
31B ILE* 1.3 63.5 + - - +
33B HIS* 3.4 21.2 + - - +
34B ALA* 4.0 4.0 + - - +
80B GLY* 5.6 1.9 - - - -
81B LEU* 4.3 14.2 - - - +
133B GLY* 5.1 0.7 + - - -
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Residues in contact with ILE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ALA 3.1 11.5 + - - +
28B LEU* 3.5 12.1 - - + +
29B GLU 3.2 0.6 - - - -
30B SER* 1.3 73.4 - - - +
32B SER* 1.3 57.7 + - - +
33B HIS 3.0 4.7 - - - -
34B ALA* 2.9 28.1 + - - +
79B ALA* 3.7 19.1 - - + +
80B GLY* 4.5 2.7 - - - -
133B GLY* 4.0 11.0 - - - +
134B VAL 3.5 22.4 - - - +
135B SER* 3.2 31.6 - - - +
153B PRO* 3.5 22.7 - - + -
165B VAL* 5.3 0.4 - - + -
166B GLY* 3.3 22.8 - - - +
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Residues in contact with SER 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU 3.3 10.6 + - - -
29B GLU* 2.7 34.5 + - - -
31B ILE* 1.3 74.8 - - - +
33B HIS* 1.3 64.4 + - - +
34B ALA 3.4 0.4 - - - -
166B GLY 3.8 14.4 - - - -
167B ALA* 3.1 25.0 - - - +
168B ASN 5.9 0.7 - - - -
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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