Contacts of the helix formed by residues 23 - 32 (chain A) in PDB entry 2ICP
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 SER 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LEU* 5.4 1.6 - - - -
21A ASN 3.9 1.8 + - - -
22A VAL* 1.3 78.0 - - - +
24A LEU* 1.3 59.8 + - - +
25A ARG* 3.6 6.7 + - - +
26A GLU* 3.0 36.1 + - - +
27A PHE* 2.9 27.4 + - - +
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Residues in contact with LEU 24 (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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14A GLN* 5.9 2.4 + - - +
17A LEU* 5.6 0.9 - - - -
23A SER* 1.3 73.9 - - - +
25A ARG* 1.3 71.2 + - + +
27A PHE* 3.1 8.4 + - + +
28A ALA* 2.9 25.1 + - - +
35A PRO* 3.9 29.8 - - + +
38A ALA* 3.4 23.8 - - + -
39A SER* 3.9 17.3 - - - +
42A LEU* 3.7 27.4 - - + -
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Residues in contact with ARG 25 (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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23A SER* 3.3 7.4 + - - +
24A LEU* 1.3 89.1 - - + +
26A GLU* 1.3 59.1 + - + +
28A ALA* 3.5 5.0 + - - +
29A ARG* 3.0 43.9 + - - +
35A PRO* 5.0 15.3 - - + +
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Residues in contact with GLU 26 (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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21A ASN 4.1 4.2 - - - +
22A VAL* 3.6 18.8 - - + +
23A SER* 3.0 36.5 + - - +
25A ARG* 1.3 77.8 - - + +
27A PHE* 1.3 62.7 + - - +
29A ARG* 3.4 29.0 + - - +
30A ALA* 3.1 24.6 + - - +
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Residues in contact with PHE 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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13A ILE* 3.8 14.8 - - + -
17A LEU* 3.7 33.2 - - + -
22A VAL* 3.8 5.1 - - + +
23A SER 2.9 12.6 + - - +
24A LEU* 3.3 7.9 - - - +
26A GLU* 1.3 74.5 - - - +
28A ALA* 1.3 66.8 + - - +
30A ALA* 3.3 4.5 + - - +
31A MSE 2.9 60.1 + - + +
33A ILE* 4.7 1.1 - - + -
38A ALA* 4.1 17.3 - - + -
41A LEU* 4.3 9.0 - - + -
42A LEU* 3.4 30.3 - - + -
56A LEU* 3.8 10.5 - - + -
59A VAL* 4.8 5.4 - - + -
60A ILE* 3.7 22.7 - - + -
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Residues in contact with ALA 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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24A LEU 2.9 15.8 + - - +
25A ARG* 3.9 5.8 - - - +
27A PHE* 1.3 76.8 - - - +
29A ARG* 1.3 57.6 + - - +
31A MSE 3.3 0.5 + - - -
32A GLU* 2.9 23.9 + - - -
33A ILE* 2.9 38.8 + - + +
34A ALA 4.0 4.5 - - - +
35A PRO* 4.0 13.5 - - + -
38A ALA* 3.7 20.2 - - + -
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Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ARG* 3.0 36.3 + - - +
26A GLU* 3.5 25.6 + - - +
28A ALA* 1.3 76.7 - - - +
30A ALA* 1.3 61.9 + - - +
32A GLU* 3.2 18.2 + - - +
33A ILE 4.9 0.9 - - - -
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLU 3.1 13.3 + - - +
27A PHE* 3.8 2.9 - - - +
29A ARG* 1.3 80.1 - - - +
31A MSE 1.3 60.0 + - - +
32A GLU* 3.1 7.0 + - - +
59A VAL* 3.5 34.6 - - + +
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Residues in contact with MSE 31 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A PHE* 2.9 50.5 + - + +
30A ALA* 1.3 75.8 - - - +
32A GLU* 1.3 55.1 + - - +
33A ILE* 3.7 19.4 - - + +
41A LEU* 4.6 1.8 - - + -
52A MSE 3.8 24.9 - - - +
55A LYS* 2.7 82.8 + - + +
56A LEU* 3.9 24.5 - - + -
59A VAL* 3.8 14.6 - - + -
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Residues in contact with GLU 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 ALA 2.9 5.6 + - - -
29A ARG* 3.2 12.5 + - - +
30A ALA 3.1 8.6 - - - +
31A MSE 1.3 81.7 - - - +
33A ILE* 1.3 59.6 + - - +
55A LYS* 3.1 22.6 + - - +
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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