Contacts of the helix formed by residues 17 - 27 (chain B) in PDB entry 2I62
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 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B HIS 3.3 7.6 + - - +
16B PHE* 1.3 73.1 - - - +
18B PRO* 1.4 63.0 - - - +
19B ARG* 3.3 9.9 + - - +
20B ASP* 2.9 35.7 + - + +
21B TYR* 3.0 27.5 + - - +
207B ILE* 4.3 8.7 - - + +
210B GLN* 6.4 0.4 - - + -
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Residues in contact with PRO 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PHE* 3.4 12.3 - - + +
17B ASN* 1.4 87.1 - - - +
19B ARG* 1.3 58.5 + - - +
21B TYR* 3.3 3.3 + - - +
22B LEU* 3.0 34.2 + - - +
67B PRO* 3.9 4.7 - - + +
90B GLN* 3.5 33.2 - - + +
91B ASN* 3.3 27.1 - - - +
94B GLU* 3.6 27.6 - - + +
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Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASN* 3.3 7.4 + - - +
18B PRO* 1.3 80.8 - - - +
20B ASP* 1.3 57.1 + - - +
22B LEU* 3.4 2.8 + - - +
23B GLU* 2.9 55.6 + - - +
94B GLU* 2.8 35.7 + - - +
97B LYS* 4.5 6.3 - - - +
104B GLY* 2.5 30.4 + - - -
105B ALA* 3.3 8.7 + - - +
106B PHE* 3.2 35.3 - - - +
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Residues in contact with ASP 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASN* 2.9 31.9 + - + +
19B ARG* 1.3 72.5 - - - +
21B TYR* 1.3 66.2 + - - +
23B GLU* 3.4 13.1 + - - +
24B LYS* 2.8 65.5 + - - +
207B ILE* 3.6 20.6 - - + +
208B GLY* 4.3 1.6 + - - -
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Residues in contact with TYR 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PHE* 3.6 25.6 - + + -
17B ASN 3.0 14.2 + - - +
18B PRO 3.4 7.9 - - - +
20B ASP* 1.3 77.8 - - - +
22B LEU* 1.3 56.2 + - - +
25B TYR* 2.9 71.8 + + - +
26B TYR* 3.5 27.0 + + - -
67B PRO* 3.8 20.2 - - + -
68B THR* 3.7 10.1 - - + -
165B LEU* 4.7 4.9 - - - +
205B TYR* 4.3 12.8 - + - -
207B ILE* 3.7 18.1 - - + +
4002B SAH 2.7 45.6 + - + +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PRO 3.0 15.4 + - - +
19B ARG* 3.5 7.9 - - - +
21B TYR* 1.3 77.8 - - + +
23B GLU* 1.3 58.0 - - - +
26B TYR* 2.9 34.4 + - + -
27B SER 3.3 6.6 + - - -
67B PRO* 3.7 22.7 - - + +
68B THR* 3.7 18.4 - - + -
94B GLU* 3.9 27.6 - - + +
106B PHE* 3.5 43.4 - - + -
108B TRP* 3.7 28.3 - - + +
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ARG* 2.9 46.8 + - - +
20B ASP* 3.8 17.9 - - - +
21B TYR 3.4 0.2 - - - -
22B LEU* 1.3 76.4 - - - +
24B LYS* 1.3 65.8 + - + +
27B SER* 2.7 29.0 + - - -
32B HIS* 3.7 9.3 - - + -
106B PHE* 4.2 11.4 - - + -
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Residues in contact with LYS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ASP* 2.8 45.8 + - - +
21B TYR 4.1 1.3 - - - +
23B GLU* 1.3 84.1 + - + +
25B TYR* 1.3 70.4 + - + +
27B SER* 5.2 0.2 - - - -
32B HIS* 3.6 39.7 + - + +
35B GLU* 3.7 12.1 - - - +
206B MET 5.6 0.2 - - - +
207B ILE* 4.2 3.8 - - + -
208B GLY* 3.5 39.7 - - - +
247B THR* 5.6 0.3 + - - -
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Residues in contact with TYR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TYR* 2.9 48.7 + + - +
24B LYS* 1.3 88.4 - - + +
26B TYR* 1.3 90.6 + + + +
27B SER 3.9 0.4 - - - -
28B PHE 5.4 0.4 - - - -
32B HIS* 6.2 0.2 - - - -
35B GLU* 4.0 25.0 - - + +
36B ASN* 5.2 2.9 - - - +
39B LEU* 4.3 6.4 - - - +
165B LEU* 6.5 0.2 - - + -
205B TYR* 3.5 17.3 - + + +
206B MET 2.7 37.7 + - - -
207B ILE* 4.4 2.5 - - + -
243B TYR* 3.9 28.7 - + - -
247B THR* 3.3 31.6 - - + +
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Residues in contact with TYR 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TYR* 3.5 19.1 + + - -
22B LEU* 2.9 17.1 + - + +
25B TYR* 1.3 101.4 - + + +
27B SER* 1.3 66.0 + - - +
28B PHE 3.2 3.7 + - - +
39B LEU* 3.8 31.9 - - + -
42B LEU* 4.8 4.2 - - + +
68B THR* 3.6 14.6 - - + -
70B TYR* 3.4 32.8 + + - -
106B PHE* 3.7 13.4 - - + -
107B ASP 5.2 0.5 - - - +
108B TRP* 3.7 21.8 - + + -
111B VAL* 3.9 16.3 - - - +
165B LEU* 3.5 12.5 - - - +
243B TYR* 5.1 1.6 + - - -
4002B SAH 2.6 29.3 + - - -
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU 3.3 2.8 + - - -
23B GLU* 2.7 30.0 + - - -
25B TYR 3.9 0.4 - - - -
26B TYR* 1.3 77.9 - - - +
28B PHE* 1.3 70.4 + - - +
29B GLY* 3.2 9.2 + - - -
31B ARG 5.4 0.2 + - - -
32B HIS* 4.0 11.8 + - - +
36B ASN* 5.4 0.2 + - - -
106B PHE* 3.7 15.7 - - - -
107B ASP 5.3 1.9 - - - +
110B PRO* 4.1 12.7 - - - +
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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