Contacts of the helix formed by residues 31 - 39 (chain A) in PDB entry 1L3E
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 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLN* 1.3 78.7 - - - +
32A GLU* 1.3 65.3 + - - +
33A GLU* 3.2 2.6 - - - +
34A LEU* 3.3 18.2 - - - +
35A LEU* 3.9 6.1 - - - +
157B MET* 3.7 5.6 - - - +
158B THR* 3.7 34.6 + - - +
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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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31A GLY* 1.3 70.3 - - - +
33A GLU* 1.3 83.8 + - + +
34A LEU 3.1 0.9 - - - -
35A LEU* 3.2 11.8 + - + +
36A ARG* 3.2 28.9 + - - +
158B THR* 3.8 18.3 + - + +
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Residues in contact with GLU 33 (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 LEU* 3.3 26.1 - - - +
29A LEU* 3.6 16.8 - - + -
30A GLN* 4.1 5.6 + - - +
31A GLY 3.2 2.0 - - - +
32A GLU* 1.3 96.7 - - + +
34A LEU* 1.3 56.5 + - - +
35A LEU 3.2 0.2 - - - -
36A ARG* 3.9 5.1 - - - +
37A ALA* 2.6 39.6 + - + +
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Residues in contact with LEU 34 (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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29A LEU* 3.4 21.0 - - + +
30A GLN* 2.7 34.2 - - - +
31A GLY 3.3 12.9 + - - +
32A GLU 3.1 0.2 - - - -
33A GLU* 1.3 79.1 - - - +
35A LEU* 1.3 61.8 + - + +
38A LEU* 2.7 40.2 + - - +
154B LEU* 5.3 0.4 - - + -
157B MET* 3.0 36.6 - - + -
175B ARG* 4.8 5.4 - - + +
178B ILE* 3.0 47.1 - - + -
179B SER 4.8 0.9 - - - +
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Residues in contact with LEU 35 (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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31A GLY 3.9 8.7 - - - +
32A GLU* 3.2 12.5 + - + +
33A GLU 3.2 0.2 - - - -
34A LEU* 1.3 79.9 - - + +
36A ARG* 1.3 65.7 + - - +
37A ALA 3.2 0.2 - - - -
38A LEU* 5.4 1.3 - - + -
39A ASP* 3.4 11.8 + - - +
127B HIS* 3.1 36.9 - - + +
130B GLN* 6.0 2.0 - - - +
131B ARG* 5.8 0.7 + - - -
154B LEU* 3.9 35.4 - - + +
158B THR* 4.3 21.8 - - + +
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Residues in contact with ARG 36 (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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32A GLU* 3.2 22.7 + - - +
33A GLU* 3.9 7.9 - - - +
35A LEU* 1.3 79.2 + - - +
37A ALA* 1.3 61.4 + - - +
39A ASP* 3.8 26.8 + - - +
40A GLN* 4.7 8.3 + - - +
131B ARG* 3.8 26.0 - - - +
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Residues in contact with ALA 37 (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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29A LEU* 2.9 45.1 - - + -
33A GLU* 2.6 24.2 + - + +
36A ARG* 1.3 71.0 - - - +
38A LEU* 1.3 61.3 + - - +
39A ASP 2.7 6.0 + - - -
40A GLN* 2.8 26.1 + - - +
182B LYS* 3.9 13.3 - - - +
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Residues in contact with LEU 38 (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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29A LEU* 4.2 2.4 - - + +
34A LEU* 2.7 27.6 + - + +
35A LEU* 3.8 0.6 + - + -
37A ALA* 1.3 72.8 - - - +
39A ASP* 1.3 55.0 + - - +
40A GLN 3.2 4.5 + - - -
41A VAL* 4.5 9.7 + - - +
123B LEU* 4.6 9.2 - - + +
124B LEU* 4.4 20.0 - - + -
127B HIS* 3.3 43.8 + - + +
154B LEU* 5.3 6.7 - - + -
178B ILE* 3.0 53.6 - - + -
181B TRP* 5.5 9.4 - - + -
182B LYS* 6.0 2.2 - - + -
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Residues in contact with ASP 39 (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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35A LEU 3.4 11.3 + - - +
36A ARG* 4.1 21.5 + - - +
37A ALA 2.7 1.6 + - - -
38A LEU* 1.3 75.1 - - - +
40A GLN* 1.3 65.3 + - - +
41A VAL* 3.6 10.0 + - - +
127B HIS* 3.1 24.2 + - - +
128B LYS* 6.1 1.0 - - - +
131B ARG* 4.1 25.8 + - - +
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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