Contacts of the helix formed by residues 21 - 32 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P THR* 4.7 5.8 - - - +
14P ILE 3.6 16.2 - - - +
15P PHE* 3.6 24.5 - - + -
20P ARG* 1.3 73.9 - - - +
22P TYR* 1.3 68.8 + - - +
23P GLN 3.3 2.0 - - - -
24P VAL* 2.8 36.9 + - + +
25P GLU* 3.0 17.7 + - - +
124P THR* 3.7 27.6 - - + +
154P SER* 5.9 3.6 - - - +
81Q LEU* 4.0 26.9 - - + -
130Q ARG* 3.6 22.9 - - - +
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Residues in contact with TYR 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P THR 6.1 0.7 - - - +
14P ILE* 3.8 36.0 + - + +
15P PHE 3.9 7.1 + - - -
16P SER* 3.5 28.3 - - - -
17P PRO* 3.4 24.1 - - - +
20P ARG* 3.5 4.0 + - - -
21P LEU* 1.3 72.8 - - - +
23P GLN* 1.3 66.9 + - + +
25P GLU* 3.1 5.2 + - - +
26P TYR* 3.0 60.6 + + + -
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Residues in contact with GLN 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O THR* 3.5 21.9 - - + +
15O PHE* 2.9 67.9 + - - +
13P THR 4.4 22.9 - - - +
21P LEU 3.3 0.8 - - - -
22P TYR* 1.3 82.4 - - + +
24P VAL* 1.3 58.4 + - + +
26P TYR* 3.8 8.9 - - - +
27P ALA* 3.0 28.1 + - - +
130P ARG* 4.2 3.1 - - - +
131P PRO* 3.9 26.3 - - + +
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Residues in contact with VAL 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21P LEU* 2.8 31.7 + - + +
23P GLN* 1.3 75.1 - - + +
25P GLU* 1.3 71.5 + - - +
27P ALA* 3.0 16.9 + - - +
28P LEU* 3.0 26.4 + - + +
124P THR* 3.8 25.1 - - + +
131P PRO* 4.6 11.0 - - + -
153P PRO* 4.2 9.6 - - + +
154P SER* 3.7 31.2 - - - +
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Residues in contact with GLU 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20P ARG* 2.9 46.7 + - + +
21P LEU 3.0 24.2 + - - +
22P TYR* 3.4 8.1 - - - +
24P VAL* 1.3 82.9 - - - +
26P TYR* 1.3 72.8 + - + +
28P LEU* 3.4 15.5 + - - +
29P GLU* 3.1 20.8 + - - +
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Residues in contact with TYR 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15O PHE* 3.4 33.7 - - + -
16O SER 3.4 17.3 - - - +
17O PRO* 3.7 42.0 - - + +
19O GLY* 3.3 9.2 - - - -
22P TYR* 3.0 56.2 + + + +
23P GLN* 3.9 7.4 - - - +
25P GLU* 1.3 85.5 - - + +
27P ALA* 1.3 57.1 + - - +
29P GLU* 3.2 10.7 - - + +
30P SER* 3.0 21.0 + - - -
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Residues in contact with ALA 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15O PHE* 3.9 29.1 - - + -
23P GLN 3.0 14.7 + - - +
24P VAL* 3.0 10.1 + - - +
26P TYR* 1.3 73.6 - - - +
28P LEU* 1.3 65.9 + - - +
29P GLU 3.1 1.6 - - - -
30P SER* 3.0 13.5 + - - -
31P ILE* 3.0 19.0 + - - +
131P PRO* 4.8 2.5 - - + -
132P PHE 4.6 3.1 - - - +
133P GLY* 4.7 1.3 - - - -
153P PRO* 3.9 23.3 - - + -
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Residues in contact with LEU 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24P VAL* 3.0 29.9 + - + +
25P GLU* 3.6 21.5 - - - +
27P ALA* 1.3 75.2 - - - +
29P GLU* 1.3 56.2 + - - +
31P ILE* 3.2 10.5 + - + +
32P SER* 3.0 28.1 + - - -
135P SER* 4.7 4.9 - - - +
152P ASN* 4.0 35.2 - - + +
153P PRO* 4.2 8.5 - - + -
154P SER* 5.6 1.3 - - - -
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Residues in contact with GLU 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O PRO 3.6 16.4 - - - +
18O SER* 3.4 21.1 - - - +
25P GLU 3.1 13.7 + - - +
26P TYR* 3.2 15.5 - - - +
28P LEU* 1.3 73.7 - - - +
30P SER* 1.3 63.9 + - - +
32P SER* 2.9 27.3 + - - -
33P HIS* 3.6 31.8 + - - -
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Residues in contact with SER 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15O PHE* 3.9 20.7 - - - -
19O GLY* 3.2 26.9 + - - -
21O LEU* 5.6 0.3 - - - +
26P TYR 3.0 7.1 + - - -
27P ALA 3.0 10.7 + - - -
29P GLU* 1.3 75.3 - - - +
31P ILE* 1.3 63.3 + - - +
33P HIS* 3.3 22.5 + - - +
34P ALA* 4.0 3.6 + - - +
80P GLY* 5.7 1.9 - - - -
81P LEU* 4.0 14.9 - - - +
133P GLY* 5.5 0.4 - - - -
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Residues in contact with ILE 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P ALA 3.0 21.6 + - - +
28P LEU* 3.5 11.4 - - + +
29P GLU 3.2 0.2 - - - -
30P SER* 1.3 71.6 - - - +
32P SER* 1.3 55.0 + - - +
33P HIS 2.8 6.5 + - - -
34P ALA* 2.7 33.1 + - - +
79P ALA* 3.9 25.8 - - + +
80P GLY* 4.2 3.6 - - - -
133P GLY* 4.0 11.4 - - - +
134P VAL 3.7 10.5 - - - +
135P SER* 3.6 22.9 - - - +
153P PRO* 3.6 29.6 - - + -
166P GLY* 3.4 25.3 - - - +
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Residues in contact with SER 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P LEU 3.0 12.5 + - - -
29P GLU* 2.9 25.2 + - - -
31P ILE* 1.3 76.0 - - - +
33P HIS* 1.3 71.1 + - - +
166P GLY 3.8 12.6 - - - -
167P ALA* 3.3 21.5 - - - +
168P ASN 4.5 1.8 + - - -
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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