Contacts of the helix formed by residues 52 - 60 (chain B) in PDB entry 2L29
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 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1599A PRO 4.9 0.2 - - - -
1600A SER* 3.4 9.7 - - - +
1601A LYS* 5.2 8.1 - - - +
1632A GLN* 5.6 3.1 + - - -
51B CYS* 1.3 79.4 - - - +
53B LEU* 1.3 69.0 + - - +
54B ALA* 2.8 38.5 + - + +
55B LEU* 3.2 21.4 + - + +
56B LEU* 3.9 5.8 + - - +
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Residues in contact with LEU 53 (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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1600A SER* 2.8 43.6 + - - +
1631A LYS* 3.5 49.8 - - + +
1632A GLN* 5.5 4.7 - - - +
16B THR* 5.9 2.7 - - + -
20B VAL* 5.3 6.3 - - + -
52B ASP* 1.3 73.1 + - - +
54B ALA* 1.3 59.8 + - - +
56B LEU* 3.2 33.7 - - + +
57B GLU* 2.9 44.8 + - + +
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Residues in contact with ALA 54 (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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52B ASP* 2.8 19.7 + - + +
53B LEU* 1.3 77.0 - - - +
55B LEU* 1.3 54.2 + - - +
57B GLU* 3.2 6.5 + - - +
58B THR* 2.8 42.3 + - + +
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Residues in contact with LEU 55 (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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42B ILE* 3.6 21.5 - - + -
45B GLU* 4.8 15.9 - - + +
46B CYS* 3.6 31.6 - - - -
51B CYS* 3.8 8.7 - - + -
52B ASP* 3.2 14.1 + - + +
54B ALA* 1.3 78.3 - - - +
56B LEU* 1.3 58.7 + - - +
58B THR* 3.7 7.4 + - + +
59B TYR* 3.0 36.8 + - + +
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Residues in contact with LEU 56 (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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1599A PRO* 5.1 9.0 - - + +
1600A SER* 5.3 1.1 - - - -
13B LEU* 6.3 1.1 - - + -
16B THR* 4.2 43.3 - - + +
17B LEU* 4.3 21.0 - - + +
20B VAL* 4.7 6.7 - - + -
21B CYS* 4.9 0.9 - - - -
42B ILE* 4.5 11.0 - - + -
46B CYS* 5.9 4.5 - - - -
51B CYS* 5.7 5.2 - - + -
52B ASP 4.2 4.7 - - - +
53B LEU* 3.2 44.9 - - + +
55B LEU* 1.3 79.5 - - + +
57B GLU* 1.3 64.8 + - + +
59B TYR* 3.6 4.0 - - - +
60B CYS* 2.8 30.1 + - - -
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Residues in contact with GLU 57 (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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1631A LYS* 2.6 47.0 + - - +
20B VAL* 5.0 17.2 - - + +
21B CYS* 5.0 0.6 - - - -
53B LEU* 2.9 28.7 + - + +
54B ALA* 3.7 6.0 - - - +
56B LEU* 1.3 81.1 - - - +
58B THR* 1.3 62.3 + - - +
59B TYR 3.3 0.7 + - - -
60B CYS* 3.3 18.8 - - - +
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Residues in contact with THR 58 (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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54B ALA* 2.8 33.3 + - + +
55B LEU* 3.7 9.4 - - + +
57B GLU* 1.3 71.9 - - - +
59B TYR* 1.3 67.4 + - - +
63B PRO* 3.9 26.0 + - - +
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Residues in contact with TYR 59 (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 LEU* 5.7 0.2 - - + -
28B PHE* 3.6 34.4 + - + -
30B ARG* 3.7 24.5 + - - -
39B SER* 3.0 26.9 + - - -
40B ARG 3.4 0.9 + - - -
41B GLY* 3.1 29.7 + - - -
42B ILE* 4.2 15.9 - - + -
55B LEU* 3.0 25.6 + - + +
56B LEU* 3.6 6.3 - - - +
57B GLU 3.1 0.2 - - - -
58B THR* 1.3 81.7 - - - +
60B CYS* 1.3 62.8 + - - +
61B ALA 2.7 25.3 + - - -
62B THR* 3.7 7.3 + - - -
63B PRO* 4.3 2.2 - - - +
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Residues in contact with CYS 60 (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 LEU* 3.6 11.4 - - - +
21B CYS* 2.0 52.0 - - - -
24B ARG* 3.5 23.3 - - + -
25B GLY 3.5 7.0 - - - -
26B PHE* 3.5 5.0 - - - -
27B TYR 3.1 24.8 + - - +
56B LEU 2.8 12.3 + - - -
57B GLU 3.3 16.6 - - - +
59B TYR* 1.3 79.1 - - - +
61B ALA* 1.3 59.1 + - - +
62B THR 5.8 0.9 - - - +
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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