Contacts of the helix formed by residues 35 - 43 (chain B) in PDB entry 3AA6
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 LEU 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B GLN* 3.8 14.1 - - + +
6B LEU* 3.7 47.3 - - + +
9B ALA* 4.5 7.6 - - + -
32B VAL* 2.9 36.2 + - + +
34B SER* 1.3 81.7 + - - +
36B CYS* 1.3 64.8 + - - +
37B GLU 3.3 2.7 - - - -
38B ASP* 3.0 27.1 + - + +
39B LEU* 2.8 33.4 + - + +
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Residues in contact with CYS 36 (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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7A ARG* 5.7 0.2 - - - +
29B ILE* 3.8 24.5 - - + -
32B VAL 4.0 1.0 + - - -
33B PRO 3.2 17.8 + - - +
34B SER 3.3 2.2 + - - -
35B LEU* 1.3 75.4 - - - +
37B GLU* 1.3 64.5 + - - +
39B LEU* 3.2 1.9 + - - +
40B LEU* 2.9 43.5 + - - +
501C LEU* 3.9 18.8 - - + -
505C PHE* 3.5 39.7 - - + -
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Residues in contact with GLU 37 (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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34B SER 5.1 1.2 + - - -
35B LEU 3.3 0.6 - - - -
36B CYS* 1.3 78.4 - - - +
38B ASP* 1.3 68.0 + - - +
40B LEU* 3.3 4.7 + - - +
41B SER* 3.0 34.2 + - - +
496C MET 4.7 3.5 - - - +
497C PRO* 4.7 15.9 - - - +
498C GLY 5.0 2.6 + - - -
499C ARG* 4.5 23.4 + - + +
501C LEU* 3.8 24.2 - - + +
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Residues in contact with ASP 38 (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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6B LEU* 4.0 28.9 - - + +
34B SER 5.3 1.0 - - - +
35B LEU* 3.0 26.0 + - + +
37B GLU* 1.3 81.3 - - - +
39B LEU* 1.3 52.8 + - - +
41B SER* 3.4 6.5 + - - -
42B SER* 2.4 38.9 + - - -
245B BA 3.0 27.6 - - - -
495C LYS* 4.6 11.2 + - - +
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Residues in contact with LEU 39 (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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6B LEU* 3.7 22.2 - - + -
9B ALA* 3.8 19.7 - - + -
10B LEU* 4.6 2.0 - - + -
25B LEU* 4.0 13.6 - - + +
28B LEU* 3.7 33.7 - - + +
29B ILE* 4.0 25.6 - - + +
32B VAL* 4.6 1.3 - - + +
35B LEU* 2.8 36.7 + - + +
36B CYS 3.8 3.1 - - - +
38B ASP* 1.3 73.8 - - - +
40B LEU* 1.3 59.8 + - - +
41B SER 3.1 1.6 - - - -
42B SER* 3.6 1.3 - - - +
43B VAL* 2.9 48.3 + - + +
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Residues in contact with LEU 40 (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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25B LEU* 4.1 16.6 - - + -
29B ILE* 3.7 22.0 - - + -
36B CYS* 2.9 33.7 + - - +
37B GLU* 3.8 4.0 - - - +
39B LEU* 1.3 75.3 - - - +
41B SER* 1.3 59.2 + - - +
42B SER 3.8 0.2 + - - -
43B VAL 4.1 9.2 - - - +
63B ASP* 3.4 36.1 - - + +
66B ARG* 3.7 14.6 - - - +
501C LEU* 4.7 3.8 - - + -
502C PRO* 3.7 34.3 - - + -
504C ARG* 6.2 1.3 - - - +
505C PHE* 4.8 3.6 - - + -
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Residues in contact with SER 41 (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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37B GLU* 3.0 24.0 + - - +
38B ASP* 3.6 6.3 - - - -
39B LEU 3.1 0.2 - - - -
40B LEU* 1.3 79.1 - - - +
42B SER* 1.3 57.1 + - - +
43B VAL 3.7 0.2 - - - -
63B ASP* 4.0 12.3 + - - -
64B TYR* 3.8 15.2 + - - -
490C THR 4.3 1.6 - - - +
493C ARG* 3.0 20.9 + - - +
495C LYS* 3.6 31.6 + - - +
499C ARG* 4.1 11.8 + - - -
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Residues in contact with SER 42 (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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6B LEU* 4.2 8.1 - - - +
10B LEU* 3.6 24.4 - - - +
38B ASP 2.4 27.8 + - - -
39B LEU* 3.6 4.0 - - - -
41B SER* 1.3 77.4 - - - +
43B VAL* 1.3 63.6 + - - +
44B ASP 3.8 1.0 + - - -
490C THR* 2.6 44.0 + - - +
491C ALA* 4.2 12.1 - - - -
493C ARG* 3.9 3.1 - - - -
495C LYS* 4.8 4.9 - - - -
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Residues in contact with VAL 43 (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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10B LEU* 3.7 25.4 - - + -
13B MET* 3.7 42.0 - - + -
25B LEU* 3.9 18.1 - - + +
39B LEU* 2.9 35.3 + - + +
40B LEU 4.1 8.5 - - - +
41B SER 3.7 0.4 - - - -
42B SER* 1.3 76.4 - - - +
44B ASP* 1.3 73.9 + - - +
45B GLN* 3.7 16.1 + - - +
493C ARG* 4.8 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