Contacts of the helix formed by residues 2 - 22 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G IPH 4.4 23.3 - - + +
1H PHE* 1.3 71.5 - - - +
3H ASN* 1.3 64.3 - - - +
5H HIS* 2.8 20.9 + - + +
6H LEU* 2.9 34.1 + - + +
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Residues in contact with ASN 3 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H PHE* 3.3 22.5 - - + -
2H VAL* 1.3 77.1 - - - +
4H GLN* 1.3 56.3 + - - +
6H LEU* 3.3 19.6 + - - +
7H CYS* 2.9 29.5 + - - +
39H MYR 3.1 42.2 - - + +
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Residues in contact with GLN 4 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F TYR* 3.9 2.1 + - - -
3G VAL* 3.8 28.2 - - + +
7G CYS* 4.8 0.9 - - - -
1H PHE* 3.0 44.0 + - + +
3H ASN* 1.3 77.7 - - - +
5H HIS* 1.3 62.4 + - - +
7H CYS* 3.4 3.9 + - - +
8H GLY* 3.0 19.8 + - - -
29H LYS* 4.2 9.4 - - - -
39H MYR 3.7 52.1 - - + +
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Residues in contact with HIS 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F TYR* 2.5 56.0 + + - -
17F LEU* 4.1 20.1 - - + +
20F GLY* 6.5 0.9 - - - -
22G IPH 3.5 50.2 - + - -
1H PHE 3.2 8.1 + - - +
2H VAL* 2.8 14.2 + - + +
4H GLN* 1.3 80.2 - - - +
6H LEU* 1.3 63.9 + - + +
9H SER* 3.3 7.4 + - - -
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Residues in contact with LEU 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G IPH 3.9 29.6 - - + -
2H VAL* 2.9 30.7 + - + +
3H ASN* 3.8 18.2 - - - +
5H HIS* 1.3 77.4 - - + +
7H CYS* 1.3 63.7 + - - +
9H SER* 3.1 16.4 + - - -
10H HIS* 3.2 19.7 - - + -
31H CL 3.8 25.1 - - + -
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Residues in contact with CYS 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G CYS 4.1 4.7 - - - -
7G CYS* 2.0 56.3 - - + -
3H ASN* 2.9 18.3 + - - +
4H GLN* 3.6 4.3 - - - +
6H LEU* 1.3 76.7 - - - +
8H GLY* 1.3 62.9 + - - +
10H HIS* 3.0 12.8 + - - +
11H LEU* 2.9 21.6 + - - +
39H MYR 4.3 13.9 - - + -
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Residues in contact with GLY 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F TYR* 3.1 24.2 - - - -
3G VAL* 5.5 1.6 - - - -
7G CYS* 4.3 1.5 - - - -
4H GLN 3.0 12.7 + - - -
5H HIS 3.4 0.6 + - - -
6H LEU 3.3 0.2 - - - -
7H CYS* 1.3 75.6 - - - +
9H SER* 1.3 61.7 + - - +
11H LEU* 3.1 11.7 + - - +
12H VAL* 3.0 28.9 + - - +
26H TYR* 3.9 11.2 - - - -
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Residues in contact with SER 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F GLU* 2.6 32.4 + - - +
16F TYR* 3.3 22.5 - - - -
5H HIS 3.3 6.8 + - - -
6H LEU* 3.1 15.8 + - - -
8H GLY* 1.3 74.5 - - - +
10H HIS* 1.3 67.4 + - - +
12H VAL* 3.3 18.8 - - - +
13H GLU* 3.4 10.0 + - - +
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Residues in contact with HIS 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LEU 3.2 22.7 - - - -
7H CYS* 3.0 9.7 + - - +
9H SER* 1.3 80.9 + - - +
11H LEU* 1.3 64.3 + - - +
13H GLU* 3.3 7.6 + - - +
14H ALA* 3.1 22.6 + - - +
30H ZN 2.0 36.2 - - - -
31H CL 3.5 4.9 - - + +
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Residues in contact with LEU 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G ILE* 3.9 37.0 - - + +
3G VAL* 4.2 8.7 - - + -
6G CYS* 3.4 30.3 - - + +
7G CYS* 3.8 23.3 - - - -
11G CYS* 5.6 0.2 - - + -
16G LEU* 4.1 17.7 - - + +
7H CYS* 2.9 15.9 + - - +
8H GLY* 3.1 13.4 + - - +
10H HIS* 1.3 77.1 - - - +
12H VAL* 1.3 61.2 + - - +
14H ALA* 3.3 5.9 + - + +
15H LEU* 2.9 30.1 + - - +
26H TYR* 4.7 5.6 - - + -
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Residues in contact with VAL 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F VAL* 3.7 29.4 - - + +
13F GLU* 4.9 4.0 - - - +
16F TYR* 3.9 24.9 - - + -
24F PHE* 3.8 11.2 - - + -
8H GLY 3.0 14.4 + - - +
9H SER* 3.3 16.4 - - - +
11H LEU* 1.3 75.2 - - - +
13H GLU* 1.3 59.2 + - + +
15H LEU* 3.4 8.0 + - - +
16H TYR* 2.8 30.3 + - - +
24H PHE* 4.0 3.2 - - + -
26H TYR* 3.6 38.1 - - + -
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Residues in contact with GLU 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F SER* 2.8 50.2 + - - +
12F VAL* 4.5 7.8 - - - +
13F GLU* 4.6 9.2 + - - +
9H SER 3.4 8.9 + - - +
10H HIS* 3.3 12.2 + - - +
11H LEU 3.2 0.4 - - - -
12H VAL* 1.3 81.0 - - - +
14H ALA* 1.4 61.3 + - - +
16H TYR* 3.4 10.7 + - - +
17H LEU* 3.1 22.2 + - - +
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Residues in contact with ALA 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G LEU* 6.0 0.9 - - + +
16G LEU* 3.4 28.7 - - + +
10H HIS 3.1 12.6 + - - +
11H LEU* 3.5 9.6 - - + +
13H GLU* 1.4 78.3 - - - +
15H LEU* 1.4 57.8 + - - +
17H LEU* 3.2 11.1 + - - +
18H VAL* 2.9 30.8 + - - +
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Residues in contact with LEU 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G ILE* 3.6 25.6 - - + -
16G LEU* 3.4 34.5 - - + +
19G TYR* 3.8 15.3 - - + -
11H LEU 2.9 20.6 + - - +
12H VAL* 3.7 5.4 - - - +
14H ALA* 1.4 74.3 - - - +
16H TYR* 1.3 67.2 + - - +
18H VAL* 4.4 2.2 - - + -
19H CYS* 2.9 41.6 + - - +
24H PHE* 3.8 34.1 - - + -
25H PHE 4.7 5.4 - - - +
26H TYR* 4.4 14.6 - - + -
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Residues in contact with TYR 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F GLN* 3.8 1.0 + - - +
5F HIS* 2.6 60.8 + + - -
8F GLY* 3.3 16.4 - - - -
9F SER* 3.4 26.7 - - - -
12F VAL* 3.9 17.7 - - + -
26F TYR* 3.5 36.6 + + - -
28F PRO* 5.8 2.0 - - + -
12H VAL 2.8 22.2 + - - +
13H GLU* 3.4 17.0 - - - +
15H LEU* 1.3 74.5 - - - +
17H LEU* 1.3 64.2 + - + +
19H CYS* 4.7 0.2 - - - +
20H GLY* 3.4 19.9 + - - +
24H PHE* 3.7 10.6 - + + -
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Residues in contact with LEU 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E IPH 4.6 20.6 - - + -
5F HIS* 5.0 12.0 - - + +
13G LEU* 4.3 22.9 - - + -
13H GLU 3.1 13.3 + - - +
14H ALA* 3.2 10.5 + - - +
16H TYR* 1.3 83.8 - - + +
18H VAL* 1.4 63.0 + - - +
20H GLY* 3.7 7.1 + - - -
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Residues in contact with VAL 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G LEU* 3.7 41.1 - - + +
16G LEU* 4.2 9.6 - - + -
17G GLU* 3.9 25.8 - - + +
20G CYS* 3.7 19.5 - - - -
14H ALA 2.9 18.1 + - - +
15H LEU* 4.0 3.6 - - - +
17H LEU* 1.4 76.1 - - - +
19H CYS* 1.3 67.4 + - - +
20H GLY* 3.4 0.7 + - - -
22H ARG* 2.9 20.0 + - - +
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Residues in contact with CYS 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G CYS* 2.0 55.6 - - + -
15H LEU* 2.9 28.9 + - - +
16H TYR 4.7 0.4 - - - +
18H VAL* 1.3 81.0 - - - +
20H GLY* 1.3 66.3 + - - +
21H GLU 3.4 0.5 + - - -
22H ARG* 2.8 29.8 + - - +
23H GLY 3.5 20.6 - - - +
24H PHE* 3.8 16.4 - - + -
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Residues in contact with GLY 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F HIS* 6.3 3.1 - - - -
26F TYR* 5.5 1.4 - - - -
28F PRO* 3.4 11.0 - - - +
16H TYR* 3.4 17.4 + - - +
17H LEU 3.7 5.6 + - - -
18H VAL 3.3 4.9 - - - -
19H CYS* 1.3 79.0 - - - +
21H GLU* 1.4 61.1 + - - -
22H ARG 2.9 5.7 + - - -
23H GLY* 3.3 8.7 + - - -
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Residues in contact with GLU 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F THR* 5.0 2.8 - - - +
28F PRO* 3.5 26.1 - - + +
29F LYS 5.4 8.0 - - - +
19H CYS 3.4 0.6 + - - -
20H GLY* 1.4 71.9 - - - -
22H ARG* 1.3 60.8 + - - +
23H GLY 3.3 0.4 + - - -
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Residues in contact with ARG 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F THR* 4.5 5.8 + - - +
28F PRO* 4.6 0.2 - - - -
17G GLU* 3.1 42.5 + - - +
20G CYS* 4.4 6.9 - - - +
21G ASN* 3.3 42.3 + - - +
18H VAL* 2.9 27.5 + - - +
19H CYS* 2.8 20.0 + - + +
21H GLU* 1.3 80.7 - - - +
23H GLY* 1.3 65.2 + - - +
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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