Contacts of the helix formed by residues 17 - 23 (chain B) in PDB entry 3IFS
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 GLY 17 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 4.8 2.0 - - - -
15B PHE 4.4 0.2 - - - -
16B ILE* 1.3 75.7 - - - +
18B GLU* 1.3 67.3 + - - -
19B HIS* 3.1 20.0 - - - -
20B GLU* 2.9 32.6 + - - +
21B ILE* 4.0 4.7 + - - +
451B CL 4.5 3.1 - - - -
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Residues in contact with GLU 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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9B TYR* 2.9 40.5 + - - -
13B LEU* 4.1 23.9 - - + +
16B ILE 3.9 1.4 + - - -
17B GLY* 1.3 70.4 - - - -
19B HIS* 1.3 62.5 + - - +
21B ILE* 3.0 21.6 + - - +
22B THR* 3.3 21.9 + - + +
451B CL 3.8 14.1 - - + +
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Residues in contact with HIS 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 GLY* 4.0 17.6 - - - -
18B GLU* 1.3 78.0 - - - +
20B GLU* 1.3 60.8 + - + +
22B THR* 3.4 9.4 - - - +
23B TYR* 2.8 74.4 + + + +
451B CL 3.3 22.6 - - + +
296C ASP* 2.9 39.3 + - - -
415C ASN* 5.9 0.4 - - + -
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Residues in contact with GLU 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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15B PHE 4.0 0.2 - - - +
16B ILE* 3.4 4.8 - - + +
17B GLY 2.9 33.6 + - - +
19B HIS* 1.3 95.6 - - + +
21B ILE* 1.3 62.9 + - + +
23B TYR* 4.4 0.2 - - - +
24B LEU* 3.5 24.4 - - - +
256B VAL* 4.2 3.4 - - - +
260B ALA* 3.9 15.4 - - + +
264B LYS* 2.9 36.9 + - - -
296C ASP* 3.8 14.0 - - - +
298C LYS* 2.8 33.1 + - - +
413C GLY 4.7 7.5 - - - +
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Residues in contact with ILE 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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9B TYR* 3.0 58.8 - - + +
16B ILE* 5.3 6.3 - - + -
17B GLY 4.4 5.6 - - - +
18B GLU* 3.0 15.8 + - - +
20B GLU* 1.3 78.6 - - + +
22B THR* 1.3 68.0 + - + +
24B LEU* 3.1 15.1 + - - +
246B LEU* 3.2 36.9 - - + +
253B GLN* 5.1 7.6 - - + -
256B VAL* 3.8 16.6 - - + +
257B VAL* 3.9 20.0 - - + -
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Residues in contact with THR 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 GLU* 3.3 15.6 + - + +
19B HIS* 3.4 17.8 + - - +
21B ILE* 1.3 80.5 - - + +
23B TYR* 1.3 70.1 + - - +
24B LEU 3.1 1.0 + - - -
25B ARG* 3.2 38.4 + - + +
246B LEU* 4.6 1.3 - - + -
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Residues in contact with TYR 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 HIS* 2.8 58.1 + + + +
20B GLU 4.4 0.2 - - - +
21B ILE 3.2 0.6 - - - -
22B THR* 1.3 81.1 + - - +
24B LEU* 1.3 66.6 + - + +
25B ARG 3.4 0.9 + - - -
26B ASP* 4.7 4.9 + - - +
41C ALA* 3.5 30.2 - - + +
410C TYR 5.6 2.3 - - - +
413C GLY* 3.5 28.6 - - - +
414C VAL 4.0 7.4 - - - +
415C ASN* 3.7 31.4 + - + +
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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