Contacts of the helix formed by residues 29 - 35 (chain I) in PDB entry 5LK5
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 ASP 29 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C LEU 4.7 3.6 - - - -
61C GLU* 3.3 30.6 - - + +
27I PHE* 3.5 1.8 - - - -
28I LEU* 1.3 75.8 + - + +
30I GLY* 1.3 65.1 + - - +
31I ASP 3.2 0.3 + - - -
32I GLY* 2.9 23.0 + - - -
33I TRP 4.0 1.7 + - - -
36I ARG* 2.9 43.9 + - - -
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Residues in contact with GLY 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LEU 4.0 7.0 + - - -
29C ASP* 5.4 0.4 - - - +
30C GLY* 3.9 25.6 - - - -
61C GLU* 4.6 2.0 - - - -
64C LYS* 5.8 1.6 - - - -
27I PHE 4.8 4.2 + - - +
28I LEU 3.5 5.5 + - - -
29I ASP* 1.3 76.6 + - - +
31I ASP* 1.3 66.7 + - - -
32I GLY 3.2 0.9 + - - -
33I TRP* 3.7 6.1 - - - -
51I LEU* 3.5 22.0 - - - +
64I LYS* 6.2 0.4 - - - -
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Residues in contact with ASP 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER* 4.7 15.8 - - - -
207A GLY 5.2 5.1 - - - +
30C GLY* 4.4 11.6 - - - -
31C ASP 5.3 0.5 + - - -
51C LEU* 5.6 5.1 - - - +
61C GLU* 3.8 7.9 + - - +
64C LYS* 4.6 19.4 + - - +
29I ASP 3.2 0.4 + - - -
30I GLY* 1.3 75.6 - - - -
32I GLY* 1.3 61.4 + - - +
33I TRP* 3.1 10.9 + - - -
34I THR* 2.7 42.5 + - + +
51I LEU* 4.4 8.5 - - - +
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Residues in contact with GLY 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C GLU* 3.1 25.9 + - - -
29I ASP* 2.9 21.6 + - - -
30I GLY 3.2 0.4 - - - -
31I ASP* 1.3 76.1 - - - +
33I TRP* 1.3 62.2 + - - +
34I THR 3.0 0.9 + - - -
35I SER* 2.9 24.7 + - - -
36I ARG* 3.6 14.1 + - - -
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Residues in contact with TRP 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A PRO* 4.0 16.6 - - + -
205A GLY* 3.9 26.9 - - - -
25I GLU* 4.2 0.2 - - - +
27I PHE* 3.6 25.1 - + + -
29I ASP* 4.0 1.6 + - - -
30I GLY 3.7 18.4 - - - -
31I ASP* 3.0 8.1 + - - +
32I GLY* 1.3 74.6 - - - +
34I THR* 1.3 75.8 - - + +
35I SER 3.1 1.3 - - - -
36I ARG* 2.9 38.1 + - - +
37I TRP* 3.2 31.1 + + + -
39I GLU* 6.0 0.4 - - - -
49I PHE* 4.3 11.9 - - + -
51I LEU* 3.7 41.4 - - + +
66I LEU* 3.7 31.2 - - + -
77I LEU* 4.1 15.5 - - + -
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Residues in contact with THR 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LEU* 4.6 15.5 - - - +
204A PRO* 2.9 57.6 - - - +
205A GLY* 3.9 4.3 - - - -
206A SER 5.0 1.3 - - - +
207A GLY 5.7 2.6 + - - +
31I ASP* 2.7 29.6 + - + +
33I TRP* 1.3 103.1 - - + +
35I SER* 1.3 60.2 + - - +
37I TRP 3.7 4.1 - - - +
38I ILE* 6.0 0.2 - - - +
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Residues in contact with SER 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C GLU* 4.7 15.3 + - - -
32I GLY* 2.9 17.7 + - - -
33I TRP 3.1 0.2 - - - -
34I THR* 1.3 82.1 + - - +
36I ARG* 1.3 64.0 + - - +
37I TRP 3.7 0.9 - - - -
38I ILE* 5.8 3.5 - - - +
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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