Contacts of the helix formed by residues 58 - 66 (chain B) in PDB entry 3L6D
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 SER 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B TRP* 3.4 16.7 - - - +
56B CYS* 3.3 3.3 + - - +
57B GLU* 1.3 86.8 + - - +
59B VAL* 1.3 63.7 + - - +
60B LYS* 3.3 25.4 + - - +
61B ALA* 3.1 23.9 + - - +
62B ALA* 3.2 21.5 + - - +
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 4.1 13.2 - - + -
38B TRP* 3.7 33.1 - - + +
58B SER* 1.3 71.3 - - - +
60B LYS* 1.3 63.6 + - - +
62B ALA* 3.1 4.3 + - - +
63B LEU* 3.0 35.0 + - + +
82B VAL* 3.6 27.8 - - + -
85B MSE 3.5 30.7 - - + -
88B VAL* 3.8 22.9 - - + -
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Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 5.2 6.9 + - - -
58B SER* 3.3 19.4 + - - +
59B VAL* 1.3 78.2 - - - +
61B ALA* 1.3 62.1 + - - +
63B LEU* 3.4 5.8 + - - +
64B SER* 3.0 28.8 + - - +
86B PRO* 3.1 36.8 - - - +
87B GLY* 3.9 25.6 - - - +
88B VAL* 4.2 4.1 - - + +
91B ALA* 3.8 11.6 - - + +
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Residues in contact with ALA 61 (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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56B CYS* 4.1 15.4 - - + -
57B GLU* 4.3 13.5 - - + +
58B SER* 3.1 25.5 + - - +
60B LYS* 1.3 80.0 - - + +
62B ALA* 1.3 56.8 + - - +
64B SER* 3.3 6.7 + - - -
65B ALA* 3.0 30.1 + - - +
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Residues in contact with ALA 62 (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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13B SER* 2.6 34.0 + - - -
15B ILE* 4.0 22.0 - - + -
37B ILE 4.8 3.1 - - - -
38B TRP* 4.2 10.8 - - + -
56B CYS* 3.6 21.0 - - - -
58B SER 3.2 12.2 + - - +
59B VAL 3.1 8.1 + - - +
61B ALA* 1.3 72.7 - - - +
63B LEU* 1.3 66.9 + - - +
65B ALA* 3.3 6.4 + - - +
66B SER 3.8 0.7 + - - -
69B THR* 3.7 0.6 + - - -
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Residues in contact with LEU 63 (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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15B ILE* 4.8 1.1 - - + -
59B VAL* 3.0 27.5 + - + +
60B LYS* 3.7 7.6 - - - +
62B ALA* 1.3 75.1 - - - +
64B SER* 1.3 58.9 - - - +
66B SER 3.2 10.0 - - - +
69B THR* 3.3 27.5 + - + +
71B PHE* 4.2 8.1 - - + -
88B VAL* 3.7 35.2 - - + +
91B ALA* 3.8 18.4 - - + +
92B LEU* 3.8 15.3 - - + -
95B ARG* 3.0 27.0 + - + +
97B ILE* 3.5 27.1 - - + -
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Residues in contact with SER 64 (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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8B PHE* 3.4 6.1 - - - -
60B LYS* 3.0 18.0 + - - +
61B ALA* 3.3 6.9 + - - -
63B LEU* 1.3 75.9 - - - +
65B ALA* 1.3 64.2 + - - +
66B SER 3.3 1.2 + - - -
91B ALA* 3.8 15.1 - - - +
95B ARG* 3.1 29.2 + - - +
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Residues in contact with ALA 65 (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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8B PHE* 3.4 11.7 - - - -
9B GLU 4.2 2.6 + - - -
10B PHE* 3.5 39.1 + - + +
13B SER* 4.1 6.3 - - - +
36B ALA* 4.2 8.3 - - + -
54B HIS* 5.8 0.4 - - + -
56B CYS* 4.6 4.0 - - - -
61B ALA 3.0 17.4 + - - +
62B ALA* 3.8 7.2 - - - +
63B LEU 3.3 1.2 - - - -
64B SER* 1.3 78.0 - - - +
66B SER* 1.3 59.1 + - - +
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Residues in contact with SER 66 (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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8B PHE* 3.3 7.0 - - - -
10B PHE* 3.2 17.8 - - - +
12B VAL 3.1 20.2 - - - -
13B SER* 2.8 25.1 + - - -
62B ALA 3.8 2.2 + - - -
63B LEU 3.2 16.1 - - - +
64B SER 3.3 0.6 - - - -
65B ALA* 1.3 76.0 - - - +
67B PRO* 1.3 75.9 - - - +
68B ALA* 3.3 18.4 + - - +
95B ARG* 3.3 6.6 + - - -
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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