Contacts of the helix formed by residues 26 - 36 (chain A) in PDB entry 1X6E
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 ARG 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A TYR* 4.4 2.0 - - - +
24A PHE* 3.4 24.3 - - - +
25A SER* 1.3 93.0 + - - +
27A SER* 1.3 64.6 + - - +
28A SER* 4.1 10.5 - - - +
29A ILE* 3.6 32.1 + - + +
30A LEU* 3.4 5.5 + - - +
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 2.7 53.5 + - - -
26A ARG* 1.3 68.7 - - - +
28A SER* 1.3 60.4 + - - +
29A ILE 3.0 2.0 - - - -
30A LEU* 2.8 22.5 + - - +
31A VAL* 2.9 22.0 + - - +
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ARG* 4.1 13.3 - - - +
27A SER* 1.3 76.7 - - - +
29A ILE* 1.3 63.8 + - - +
31A VAL* 4.2 6.7 - - - +
32A GLN* 3.2 32.5 + - - +
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Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.3 28.3 - - + -
25A SER* 4.9 3.8 - - - +
26A ARG* 3.6 46.4 + - + +
27A SER 3.0 0.8 - - - -
28A SER* 1.3 79.7 + - - +
30A LEU* 1.3 62.9 + - - +
32A GLN* 3.7 6.2 + - - +
33A HIS* 3.2 21.1 + - - +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.5 28.3 - - + -
16A GLY 3.4 22.0 - - - +
17A CYS* 3.4 41.1 - - + +
24A PHE* 3.4 26.7 - - + -
26A ARG 3.4 8.9 + - - +
27A SER* 2.8 14.3 + - - +
29A ILE* 1.3 71.5 - - - +
31A VAL* 1.3 65.0 + - + +
33A HIS* 2.8 18.9 + - - +
34A GLN* 2.8 31.0 + - + +
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 6.3 0.9 - - + -
27A SER* 2.9 24.4 + - - +
28A SER* 4.2 6.7 - - - +
30A LEU* 1.3 80.7 - - + +
32A GLN* 1.3 69.4 + - + +
34A GLN* 3.1 23.4 + - + +
35A ARG* 3.2 17.2 + - + +
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Residues in contact with GLN 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A SER* 3.2 19.6 + - - +
29A ILE* 3.9 5.8 - - - +
30A LEU 3.2 0.4 - - - -
31A VAL* 1.3 81.9 - - + +
33A HIS* 1.3 56.4 + - - +
35A ARG* 3.0 53.9 + - - +
36A VAL* 3.2 15.8 - - - +
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Residues in contact with HIS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A CYS* 3.8 6.7 - - + -
20A CYS* 3.8 2.9 - - - -
22A LYS* 3.2 31.9 - - + +
24A PHE* 3.1 37.4 - + + -
29A ILE 3.2 9.5 + - - +
30A LEU 2.8 7.7 + - - +
32A GLN* 1.3 77.1 - - - +
34A GLN* 1.3 59.2 + - - +
35A ARG 3.4 0.4 - - - -
36A VAL* 3.1 28.8 - - + +
37A HIS* 3.3 7.8 - - - -
201A ZN 2.4 31.5 - - - -
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Residues in contact with GLN 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY 4.5 0.9 - - - +
17A CYS* 3.2 31.9 - - - -
18A VAL* 3.2 24.1 + - - +
19A GLU* 4.5 8.4 - - + +
30A LEU* 2.8 38.2 + - + +
31A VAL* 3.1 14.5 + - + +
33A HIS* 1.3 79.3 - - - +
35A ARG* 1.3 60.4 + - - +
36A VAL 3.4 0.9 - - - -
37A HIS* 3.7 21.4 - - - +
38A THR 4.7 0.5 + - - -
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Residues in contact with ARG 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.2 10.7 + - + +
32A GLN* 3.0 61.9 + - - +
34A GLN* 1.3 77.3 - - - +
36A VAL* 1.3 61.1 + - + +
37A HIS 3.1 2.5 - - - -
38A THR* 3.0 32.9 + - - +
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLN 3.2 18.8 - - - +
33A HIS* 3.1 31.4 - - + +
35A ARG* 1.3 80.4 - - + +
37A HIS* 1.3 70.4 + - + +
38A THR* 3.1 0.9 - - - -
39A GLY* 3.1 18.5 + - - +
40A GLU* 5.3 8.0 - - - +
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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