Contacts of the helix formed by residues 21 - 33 (chain T) 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 ASN 21 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12T ASN* 3.0 38.5 + - - +
14T VAL 3.8 8.0 + - - +
15T PHE* 5.3 6.0 - - + -
20T ARG* 1.3 73.6 - - - +
22T PHE* 1.3 65.4 + - - +
23T GLN* 3.1 17.3 + - - +
24T VAL* 3.2 28.1 + - + +
25T GLU* 3.1 23.9 + - - +
124T THR* 3.7 13.7 + - - -
130U ARG* 4.0 13.9 - - - +
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Residues in contact with PHE 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8T TYR* 3.3 39.0 - + + +
9T ASP* 3.9 11.4 - - + -
14T VAL 4.0 5.7 + - - -
16T SER* 3.7 24.0 - - - +
17T PRO* 5.4 1.8 - - + -
18T ASP* 4.7 2.7 - - - -
20T ARG* 3.4 38.6 + - + -
21T ASN* 1.3 76.5 + - - +
23T GLN* 1.3 62.5 + - - +
25T GLU* 3.4 8.3 + - + +
26T TYR* 3.2 54.4 + + - -
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Residues in contact with GLN 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S VAL 3.7 14.1 + - - -
14S THR* 3.7 6.8 - - - +
15S PHE* 3.0 68.8 + - - +
9T ASP 3.1 16.4 - - - +
11T SER* 3.7 15.0 + - - +
12T ASN* 3.7 31.0 - - + +
21T ASN* 3.1 8.9 + - - +
22T PHE* 1.3 74.6 - - - +
24T VAL* 1.3 65.2 + - - +
26T TYR* 3.5 6.3 + - - +
27T ALA* 3.1 20.4 + - - +
130T ARG* 4.3 0.2 - - - +
131T PRO* 4.1 12.8 - - + +
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Residues in contact with VAL 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21T ASN* 3.2 34.0 + - + +
23T GLN* 1.3 76.4 - - - +
25T GLU* 1.3 64.6 + - + +
27T ALA* 3.0 19.1 + - - +
28T VAL* 3.1 17.8 + - + +
124T THR* 3.6 32.1 - - + -
131T PRO* 3.9 12.3 - - + -
153T PRO* 4.2 4.9 - - + +
154T SER* 3.8 33.7 - - - +
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Residues in contact with GLU 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20T ARG* 2.7 57.9 + - + +
21T ASN 3.1 17.8 + - - +
22T PHE* 3.4 11.6 + - + +
23T GLN 3.2 0.2 - - - -
24T VAL* 1.3 83.0 - - + +
26T TYR* 1.3 67.9 + - + +
28T VAL* 3.5 22.2 - - + +
29T LYS* 3.5 14.2 + - - +
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Residues in contact with TYR 26 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S TYR* 4.6 0.4 - + - -
15S PHE* 3.7 21.8 - - + -
16S SER 3.1 28.7 - - - +
17S PRO* 3.6 34.8 - - + +
19S GLY* 3.4 7.7 - - - -
9T ASP* 3.0 47.8 + - + +
22T PHE* 3.2 40.2 + + + +
23T GLN* 3.9 7.6 - - - +
25T GLU* 1.3 79.9 - - + +
27T ALA* 1.3 64.5 + - - +
29T LYS* 2.9 25.5 + - + +
30T ALA 3.3 4.3 + - - -
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Residues in contact with ALA 27 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S PHE* 3.7 27.3 - - + -
23T GLN 3.1 13.6 + - - +
24T VAL 3.0 11.8 + - - +
26T TYR* 1.3 76.1 - - - +
28T VAL* 1.3 61.5 + - - +
30T ALA* 3.0 15.6 + - - +
31T VAL* 3.2 16.2 + - - +
131T PRO* 4.2 5.8 - - + -
132T PHE 3.6 22.2 - - - +
133T GLY* 4.3 1.6 - - - -
153T PRO* 3.9 7.6 - - + -
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Residues in contact with VAL 28 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24T VAL* 3.1 17.8 + - + +
25T GLU* 3.5 17.9 - - + +
27T ALA* 1.3 75.5 - - - +
29T LYS* 1.3 64.0 + - + +
31T VAL* 3.0 12.2 + - + +
32T GLU* 3.0 46.2 + - + +
152T GLU* 5.7 4.5 - - + +
153T PRO* 4.3 19.0 - - + +
154T SER 6.0 0.4 - - - +
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Residues in contact with LYS 29 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S PRO 3.6 21.3 - - - +
18S THR* 3.7 23.4 - - - +
25T GLU 3.5 13.7 + - - +
26T TYR* 2.9 12.5 + - + +
28T VAL* 1.3 77.2 - - + +
30T ALA* 1.3 58.0 + - - +
32T GLU* 3.3 23.1 + - - +
33T ASN* 3.0 28.1 + - - +
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Residues in contact with ALA 30 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S PHE* 4.3 12.1 - - + -
18S THR 5.0 0.4 - - - -
19S GLY* 3.3 29.1 - - - +
26T TYR 3.3 1.6 + - - -
27T ALA 3.0 12.6 + - - +
29T LYS* 1.3 78.8 - - - +
31T VAL* 1.3 61.3 + - - +
33T ASN* 3.3 18.0 - - - +
34T GLY* 3.7 3.8 + - - -
80T GLY* 3.8 12.1 - - - -
81T LEU* 4.5 18.5 - - + +
133T GLY* 4.7 4.0 - - - +
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Residues in contact with VAL 31 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27T ALA 3.5 13.7 - - - +
28T VAL* 3.0 9.8 + - + +
30T ALA* 1.3 73.8 - - - +
32T GLU* 1.3 56.2 + - + +
33T ASN 2.9 4.0 - - - -
34T GLY* 2.7 27.9 + - - -
79T SER* 3.6 13.0 - - - +
80T GLY* 4.0 6.3 - - - -
133T GLY 3.9 0.9 - - - -
134T VAL* 3.7 32.3 - - - +
135T SER* 3.4 26.5 - - - -
152T GLU* 5.7 0.4 - - - +
153T PRO* 3.7 15.7 - - + -
165T THR* 3.6 12.3 - - - +
166T GLY* 3.8 8.2 - - - +
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Residues in contact with GLU 32 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28T VAL* 3.0 35.8 + - + +
29T LYS* 3.6 34.8 + - - +
31T VAL* 1.3 77.3 - - + +
33T ASN* 1.3 59.0 + - - +
34T GLY 3.3 1.2 + - - -
166T GLY* 4.5 4.9 - - - +
167T LYS* 3.5 27.1 + - - +
169T ARG* 3.4 42.7 + - - +
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Residues in contact with ASN 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S THR 5.5 5.1 + - - +
29T LYS 3.0 13.4 + - - +
30T ALA* 3.3 17.7 - - - +
31T VAL 2.9 0.6 - - - -
32T GLU* 1.3 76.9 - - - +
34T GLY* 1.3 55.9 + - - +
167T LYS* 4.1 26.6 + - - +
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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