Contacts of the helix formed by residues 24 - 32 (chain A) in PDB entry 1IEQ
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 THR 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ARG 4.7 1.3 - - - +
23A MET* 1.3 77.1 - - - +
25A LEU* 1.3 65.5 + - - +
26A ALA* 3.5 8.8 + - - +
27A GLU* 2.9 36.6 + - - +
28A LYS* 3.1 22.2 + - - +
49A PHE* 5.1 0.7 - - - -
85A ARG* 4.1 12.6 - - - +
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Residues in contact with LEU 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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24A THR* 1.3 74.2 - - - +
26A ALA* 1.3 63.7 + - - +
28A LYS* 3.2 6.0 + - + +
29A ILE* 3.0 45.0 + - + +
329A THR* 4.3 15.5 - - + -
332A VAL* 4.0 31.9 - - + -
333A ASN* 3.6 24.9 - - - +
339A MET* 4.1 17.0 - - - -
342A ILE* 4.7 7.2 - - + -
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Residues in contact with ALA 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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24A THR* 3.2 8.3 + - - +
25A LEU* 1.3 79.4 - - - +
27A GLU* 1.3 58.5 + - - +
29A ILE* 3.6 5.4 + - - +
30A GLY* 3.0 24.8 + - - -
48A ASN 4.4 1.4 - - - +
49A PHE* 3.9 24.0 - - + -
325A ILE* 5.8 5.5 - - + +
329A THR* 5.9 1.8 - - - -
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Residues in contact with GLU 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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23A MET* 3.3 21.3 - - + +
24A THR* 2.9 32.9 + - - +
26A ALA* 1.3 74.3 - - - +
28A LYS* 1.3 63.3 + - - +
30A GLY* 3.5 1.0 + - - -
31A GLN* 3.3 18.4 + - - +
49A PHE* 3.7 46.6 - - + +
84A THR* 5.9 0.2 - - - -
85A ARG* 2.9 46.2 + - - +
86A LEU* 3.5 19.6 + - + +
88A ILE* 5.5 1.5 - - + +
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Residues in contact with LYS 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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20A LEU* 3.7 26.1 + - + +
23A MET* 3.5 38.4 + - + -
24A THR 3.1 12.6 + - - +
25A LEU* 3.2 7.8 + - - +
27A GLU* 1.3 75.3 - - - +
29A ILE* 1.3 65.4 + - - +
30A GLY 3.0 2.0 + - - -
31A GLN* 3.2 10.2 + - - +
32A MET* 3.4 16.4 + - - +
339A MET* 3.1 22.9 - - + +
342A ILE* 3.7 12.1 - - + -
343A ASP* 2.6 32.6 + - - +
346A VAL* 3.5 18.6 - - + +
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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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25A LEU* 3.0 40.1 + - + +
26A ALA* 4.2 4.3 - - - +
28A LYS* 1.3 75.7 - - - +
30A GLY* 1.3 60.2 + - - +
32A MET* 3.3 15.4 + - - +
33A THR* 2.9 21.8 + - - +
324A PHE* 4.7 1.3 - - + -
325A ILE* 3.9 33.2 - - + -
328A LEU* 3.9 29.2 - - + +
329A THR* 3.4 41.5 - - - +
332A VAL* 4.6 2.0 - - + -
342A ILE* 4.8 7.9 - - + -
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Residues in contact with GLY 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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26A ALA 3.0 17.0 + - - -
27A GLU 3.5 1.5 + - - -
28A LYS 3.0 1.6 - - - -
29A ILE* 1.3 76.6 - - - +
31A GLN* 1.3 62.8 + - - +
33A THR* 3.0 18.1 + - - -
48A ASN 3.7 11.9 - - - -
49A PHE 3.3 19.7 - - - +
50A ILE* 3.7 0.5 - - - -
51A GLY 2.9 17.8 + - - -
325A ILE* 5.2 2.5 - - - -
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Residues in contact with GLN 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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23A MET* 3.7 16.8 - - + -
27A GLU 3.3 13.3 + - - +
28A LYS 3.2 9.7 + - - +
30A GLY* 1.3 75.4 - - - +
32A MET* 1.3 58.3 + - - +
33A THR 3.1 3.9 + - - +
49A PHE* 3.8 9.3 + - - +
50A ILE 4.6 1.4 + - - -
51A GLY* 3.8 19.7 - - - -
88A ILE* 3.2 38.6 + - + +
314A MET* 3.8 12.0 - - - +
346A VAL* 4.3 14.1 - - + -
349A ILE* 3.3 29.3 - - + +
350A LEU* 4.1 5.5 - - + +
353A LYS* 2.9 28.1 + - - +
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Residues in contact with MET 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 LYS 3.4 15.3 - - - +
29A ILE* 3.3 13.4 + - - +
30A GLY 3.1 0.6 - - - -
31A GLN* 1.3 75.7 - - - +
33A THR* 1.3 59.2 + - - +
308A ILE* 3.7 32.3 - - + -
312A LEU 4.7 0.2 - - - +
313A ASP 3.4 21.3 - - - +
314A MET* 4.1 2.5 - - - -
315A ILE* 2.9 32.5 + - + +
324A PHE* 4.1 7.6 - - + -
328A LEU* 4.2 6.1 - - + -
341A ARG* 5.3 0.2 - - - +
342A ILE* 3.8 38.1 - - + -
345A ALA* 3.7 20.9 - - + -
346A VAL* 4.1 9.0 - - + -
349A ILE* 3.8 10.3 - - + -
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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