Contacts of the helix formed by residues 2 - 22 (chain F) in PDB entry 1XDA
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 VAL 2 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E IPH 4.6 24.5 - - + +
1F PHE* 1.3 74.9 - - - +
3F ASN* 1.3 70.4 + - - +
5F HIS* 2.9 12.1 + - + +
6F LEU* 2.9 41.5 + - + +
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Residues in contact with ASN 3 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D MYR 3.6 35.9 - - + +
1F PHE* 3.2 37.9 - - + -
2F VAL* 1.3 81.8 - - - +
4F GLN* 1.3 55.5 + - - +
6F LEU* 3.3 10.1 + - - +
7F CYS* 3.0 23.0 + - - +
39F MYR 5.7 2.6 - - - +
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Residues in contact with GLN 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D MYR 3.8 24.7 - - + +
3E VAL* 3.6 30.8 - - + +
1F PHE* 3.2 24.7 + - + +
3F ASN* 1.3 74.6 - - - +
5F HIS* 1.3 61.9 + - - +
7F CYS* 3.2 3.5 + - - +
8F GLY* 2.8 28.2 + - - -
26F TYR* 4.8 1.8 + - - +
28F PRO* 3.7 12.5 - - - +
29F LYS* 3.3 44.2 + - - +
39F MYR 6.2 1.6 - - - +
16H TYR* 3.8 0.8 + - - +
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Residues in contact with HIS 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E IPH 3.7 47.4 - + + -
1F PHE 3.2 10.9 + - - +
2F VAL* 2.9 14.9 + - - +
4F GLN* 1.3 77.2 - - - +
6F LEU* 1.3 66.8 + - + +
9F SER* 3.2 8.7 + - - -
16H TYR* 2.6 56.4 + + - -
17H LEU* 5.0 13.3 - - + +
20H GLY* 6.3 2.5 - - - -
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Residues in contact with LEU 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D MYR 6.3 0.7 - - + -
22E IPH 4.1 25.8 - - + -
2F VAL* 2.9 32.6 + - + +
3F ASN* 3.8 9.2 - - - +
4F GLN 3.3 0.2 - - - -
5F HIS* 1.3 77.5 - - + +
7F CYS* 1.3 65.7 + - - +
9F SER* 3.2 13.6 + - - -
10F HIS* 3.1 22.9 - - - -
31F CL 3.8 25.6 - - + -
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Residues in contact with CYS 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D MYR 4.3 11.0 - - + +
6E CYS 4.2 4.5 - - - -
7E CYS* 2.0 58.3 - - + -
3F ASN 3.0 14.2 + - - +
4F GLN* 3.6 7.0 - - - +
6F LEU* 1.3 76.5 - - - +
8F GLY* 1.3 57.8 + - - +
10F HIS* 3.1 9.7 + - - +
11F LEU* 2.9 31.7 + - - +
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Residues in contact with GLY 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E VAL* 5.3 0.2 - - - -
7E CYS* 5.1 0.7 - - - -
4F GLN 2.8 12.3 + - - -
7F CYS* 1.3 76.5 - - - +
9F SER* 1.3 63.1 + - - +
11F LEU* 3.2 10.4 + - - +
12F VAL* 3.0 28.9 + - - +
26F TYR* 3.5 19.3 - - - -
16H TYR* 3.3 18.4 - - - -
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Residues in contact with SER 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F HIS* 3.2 10.8 + - - -
6F LEU* 3.2 13.6 + - - -
7F CYS 3.1 0.8 - - - -
8F GLY* 1.3 78.0 - - - +
10F HIS* 1.3 66.0 + - - +
12F VAL* 3.5 1.2 + - - +
13F GLU* 3.3 13.7 + - - +
13H GLU* 2.8 42.1 + - - +
16H TYR* 3.4 20.3 - - - -
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Residues in contact with HIS 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LEU 3.1 22.2 - - - -
7F CYS* 3.1 9.9 + - - +
9F SER* 1.3 79.4 + - - +
11F LEU* 1.4 63.2 + - - +
13F GLU* 3.4 6.7 + - - +
14F ALA* 3.0 28.4 + - - +
30F ZN 2.0 37.5 - - - -
31F CL 3.4 5.3 - - + +
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Residues in contact with LEU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E ILE* 4.0 34.3 - - + +
3E VAL* 4.4 2.7 - - + -
6E CYS* 3.7 26.5 - - + +
7E CYS* 3.6 25.8 - - - -
11E CYS* 5.8 0.2 - - + -
16E LEU* 4.1 19.0 - - + +
7F CYS* 2.9 18.7 + - - +
8F GLY* 3.2 14.1 + - - +
10F HIS* 1.4 76.9 - - - +
12F VAL* 1.3 59.3 + - - +
14F ALA* 3.2 7.1 + - + +
15F LEU* 2.8 34.0 + - - +
26F TYR* 4.4 9.6 - - + -
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Residues in contact with VAL 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F GLY 3.0 19.3 + - - +
9F SER 3.9 3.8 - - - +
10F HIS 3.2 0.2 - - - -
11F LEU* 1.3 77.9 - - - +
13F GLU* 1.3 56.9 + - - +
15F LEU* 3.4 5.7 + - + +
16F TYR* 2.9 28.1 + - - +
24F PHE* 3.8 11.3 - - + -
26F TYR* 3.6 38.4 - - + -
12H VAL* 3.7 41.1 - - + +
13H GLU* 4.5 4.5 - - - +
16H TYR* 3.9 15.3 - - + -
24H PHE* 4.1 5.6 - - + -
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Residues in contact with GLU 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F SER 3.3 13.7 + - - +
10F HIS* 3.8 9.4 - - - +
11F LEU 3.3 0.6 - - - -
12F VAL* 1.3 73.4 - - - +
14F ALA* 1.3 66.7 + - - +
16F TYR* 3.3 19.7 + - - +
17F LEU* 3.3 20.2 + - + +
9H SER* 2.6 35.1 + - - +
12H VAL* 4.9 3.4 - - - +
13H GLU* 4.6 8.1 + - - +
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Residues in contact with ALA 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E LEU* 5.9 1.3 - - + -
16E LEU* 3.8 24.2 - - + -
10F HIS 3.0 14.6 + - - +
11F LEU* 3.2 11.0 + - + +
13F GLU* 1.3 78.7 - - - +
15F LEU* 1.3 56.5 + - - +
17F LEU* 3.3 5.7 + - - +
18F VAL* 2.9 34.0 + - + +
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Residues in contact with LEU 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E ILE* 3.7 26.5 - - + -
16E LEU* 3.3 37.7 - - + +
19E TYR* 3.9 11.4 - - + -
11F LEU 2.8 25.8 + - - +
12F VAL* 3.8 3.4 - - - +
14F ALA* 1.3 70.0 - - - +
16F TYR* 1.3 68.8 + - - +
18F VAL* 4.5 1.8 - - - +
19F CYS* 2.9 38.8 + - - +
24F PHE* 3.6 36.8 - - + -
25F PHE 4.1 11.9 - - - +
26F TYR* 4.5 9.4 - - + -
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Residues in contact with TYR 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F VAL 2.9 18.1 + - - +
13F GLU* 3.5 22.0 - - - +
14F ALA 3.2 0.2 - - - -
15F LEU* 1.3 80.3 - - - +
17F LEU* 1.3 64.0 + - + +
20F GLY* 3.5 19.1 + - - +
24F PHE* 3.6 11.6 - - + -
4H GLN 3.9 1.2 + - - -
5H HIS* 2.5 59.4 + + - -
8H GLY* 3.1 20.0 - - - -
9H SER* 3.3 18.2 - - - -
12H VAL* 3.9 19.5 - - + -
26H TYR* 3.7 34.2 + + - -
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Residues in contact with LEU 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E LEU* 6.6 0.4 - - + -
13F GLU* 3.3 13.1 + - + +
14F ALA* 3.3 9.5 + - - +
15F LEU 3.2 0.4 - - - -
16F TYR* 1.3 81.7 - - + +
18F VAL* 1.3 69.7 + - + +
19F CYS 3.5 0.3 + - - -
20F GLY* 3.7 6.8 + - - -
22G IPH 4.4 15.0 - - + -
5H HIS* 4.1 25.7 - - + +
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Residues in contact with VAL 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E LEU* 3.8 47.3 - - + +
16E LEU* 4.1 12.8 - - + -
17E GLU* 3.7 35.0 - - + +
20E CYS* 4.3 2.7 - - - -
14F ALA* 2.9 20.4 + - - +
15F LEU* 4.1 5.4 - - - +
17F LEU* 1.3 81.4 - - + +
19F CYS* 1.3 59.7 + - - +
20F GLY* 4.7 0.3 - - - -
22F ARG* 3.3 12.0 + - - -
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Residues in contact with CYS 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E CYS* 2.0 57.0 - - + -
15F LEU* 2.9 34.4 + - - +
16F TYR 4.7 0.2 - - - +
18F VAL* 1.3 74.1 - - - +
20F GLY* 1.3 65.4 + - - +
21F GLU 3.4 0.5 + - - -
22F ARG* 3.2 27.3 + - - +
23F GLY* 3.4 22.2 - - - +
24F PHE* 3.8 11.9 - - + -
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Residues in contact with GLY 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F TYR* 3.5 16.3 + - - +
17F LEU 3.7 5.2 + - - -
18F VAL 3.4 3.4 + - - -
19F CYS* 1.3 77.5 - - - +
21F GLU* 1.4 63.0 + - - -
23F GLY* 3.1 14.7 + - - -
5H HIS* 6.5 1.3 - - - -
26H TYR* 5.2 2.9 - - - -
28H PRO* 4.0 6.5 - - - +
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Residues in contact with GLU 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F CYS 3.4 0.6 + - - -
20F GLY* 1.4 71.1 - - - -
22F ARG* 1.3 61.2 + - + +
23F GLY 3.4 0.2 + - - -
28H PRO* 3.5 20.7 - - + +
29H LYS* 4.5 31.2 + - + +
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Residues in contact with ARG 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E GLU* 2.9 39.5 + - - +
20E CYS* 3.8 18.9 - - + +
21E ASN* 3.2 44.3 + - - +
18F VAL 3.3 24.2 + - - -
19F CYS* 3.2 12.5 + - - +
20F GLY 3.2 1.0 - - - -
21F GLU* 1.3 77.4 - - + +
23F GLY* 1.3 69.3 + - - +
26H TYR 4.3 0.2 - - - +
27H THR* 5.0 1.6 - - - -
28H PRO* 4.5 2.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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