Contacts of the helix formed by residues 17 - 23 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.6 5.2 - - - -
16A ILE* 1.3 79.2 - - - +
18A GLU* 1.3 66.2 + - - -
19A HIS* 3.1 18.8 - - - -
20A GLU* 3.0 30.7 + - - +
21A ILE* 3.9 4.0 + - - +
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Residues in contact with GLU 18 (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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9A TYR* 2.5 43.6 + - - -
10A SER* 5.9 0.5 - - - -
13A LEU* 3.8 23.1 - - + +
16A ILE 4.0 0.6 + - - -
17A GLY* 1.3 71.6 - - - -
19A HIS* 1.3 61.6 + - - +
21A ILE* 3.1 11.4 + - - +
22A THR* 3.0 25.3 + - - +
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Residues in contact with HIS 19 (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 GLY* 4.1 19.2 - - - -
18A GLU* 1.3 78.7 + - - +
20A GLU* 1.3 63.7 + - + +
22A THR* 3.7 9.6 - - - -
23A TYR* 2.9 73.8 + + + +
296D ASP* 3.1 37.7 + - - -
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Residues in contact with GLU 20 (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 PHE 4.2 0.2 - - - +
16A ILE* 3.5 18.7 - - + +
17A GLY* 3.0 28.1 + - - +
19A HIS* 1.3 95.9 + - + +
21A ILE* 1.3 61.6 + - - +
23A TYR* 4.0 1.7 + - - +
24A LEU* 3.6 21.7 - - - +
256A VAL* 4.2 4.8 - - - +
260A ALA* 3.9 6.1 - - + +
264A LYS* 2.9 34.7 + - - -
296D ASP* 3.8 16.1 - - - +
298D LYS* 2.7 33.7 + - - +
413D GLY 4.7 8.7 - - - +
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Residues in contact with ILE 21 (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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9A TYR* 3.1 52.9 - - + +
16A ILE* 4.6 7.6 - - + -
17A GLY 4.5 5.6 - - - +
18A GLU* 3.1 11.3 + - - +
20A GLU* 1.3 77.4 - - - +
22A THR* 1.3 67.5 + - - +
24A LEU* 3.0 13.3 + - - +
246A LEU* 3.2 40.9 - - + +
247A GLU* 6.4 0.9 - - - -
253A GLN* 4.9 9.2 - - + +
256A VAL* 3.9 14.8 - - + -
257A VAL* 3.6 25.4 - - + -
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Residues in contact with THR 22 (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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18A GLU* 3.0 16.4 + - - +
19A HIS* 3.7 12.1 - - - -
21A ILE* 1.3 78.0 - - - +
23A TYR* 1.3 68.8 + - + +
24A LEU 3.1 1.6 + - - -
25A ARG* 3.2 23.7 + - + +
246A LEU* 5.1 1.6 - - - -
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Residues in contact with TYR 23 (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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19A HIS* 2.9 54.2 + + + +
20A GLU* 4.3 1.3 - - - +
21A ILE 3.1 1.0 + - - -
22A THR* 1.3 83.9 - - + +
24A LEU* 1.3 71.1 + - + +
25A ARG 3.4 0.6 + - - -
26A ASP* 4.9 3.7 + - - +
27A ALA* 5.5 0.9 + - - +
41D ALA* 3.4 31.0 - - + +
410D TYR* 6.5 0.9 - - + -
413D GLY* 3.7 22.4 - - - +
414D VAL* 3.9 9.6 - - - +
415D ASN* 3.7 33.3 + - + +
418D ASP* 5.5 0.2 + - - -
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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
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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