Contacts of the helix formed by residues 40 - 49 (chain L) in PDB entry 6PSU
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 GLN 40 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133J ARG* 2.6 37.6 + - - +
31L LEU* 5.8 0.7 - - - -
39L ASP* 1.3 81.2 + - - +
41L ILE* 1.3 58.2 + - - +
43L ASP* 3.6 6.4 - - - +
44L ILE* 2.8 33.6 + - - +
94L THR* 3.1 36.1 + - - +
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Residues in contact with ILE 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L VAL 5.6 3.4 - - - +
28L ASN* 4.5 26.9 - - - +
31L LEU* 4.7 15.0 - - + -
39L ASP* 3.1 12.1 + - + +
40L GLN* 1.3 77.3 - - - +
42L GLU* 1.3 74.5 + - + +
44L ILE* 3.0 22.0 - - - +
45L ILE* 3.0 31.0 + - + +
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Residues in contact with GLU 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313J GLY* 6.4 2.2 - - - -
314J ARG* 5.9 7.4 + - - -
24L TYR* 4.8 12.2 + - - -
39L ASP* 3.2 23.9 + - + +
41L ILE* 1.3 86.2 - - + +
43L ASP* 1.3 65.4 + - - +
45L ILE* 3.3 8.1 + - - +
46L GLN* 3.0 24.8 + - - +
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Residues in contact with ASP 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J LYS* 4.6 8.4 + - - -
133J ARG* 2.7 33.7 + - - +
136J GLU* 5.3 0.2 - - - +
39L ASP 3.0 16.6 + - - +
40L GLN* 3.6 9.5 - - - +
42L GLU* 1.3 77.5 - - - +
44L ILE* 1.3 58.2 + - - +
46L GLN* 3.3 6.9 + - - +
47L MET* 2.9 49.5 + - - +
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Residues in contact with ILE 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L LEU* 3.9 20.4 - - + -
12L LEU* 5.2 4.9 - - + -
27L VAL* 4.7 6.7 - - + -
31L LEU* 3.3 46.0 - - + -
40L GLN 2.8 21.5 + - - +
41L ILE* 3.0 24.2 - - - +
43L ASP* 1.3 72.2 - - - +
45L ILE* 1.3 64.9 + - + +
47L MET* 3.6 8.5 - - + +
48L ILE* 2.9 30.4 + - + +
84L LEU* 5.8 8.3 - - + -
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Residues in contact with ILE 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L LEU 6.1 0.2 - - - +
24L TYR* 3.9 38.1 - - + -
27L VAL* 3.5 31.2 - - + -
28L ASN 5.6 0.4 - - - +
41L ILE* 3.0 33.9 + - + +
42L GLU* 3.8 8.7 - - - +
44L ILE* 1.3 76.0 - - + +
46L GLN* 1.3 62.8 + - - +
48L ILE* 2.9 26.7 - - + +
49L ASN 3.1 6.1 + - - -
55L VAL* 3.8 22.6 - - + +
56L MET 5.5 2.0 - - - +
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Residues in contact with GLN 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J LYS 5.5 2.1 + - - +
120J LEU* 4.7 14.9 - - - +
310J GLY 5.0 11.9 - - - +
311J ARG* 4.4 24.8 - - - +
42L GLU 3.0 17.4 + - - +
43L ASP* 3.7 6.0 - - - +
45L ILE* 1.3 76.1 - - - +
47L MET* 1.3 89.9 + - - +
49L ASN* 3.2 24.2 - - + +
50L ASP 4.6 0.3 + - - -
55L VAL* 5.7 0.2 - - - -
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Residues in contact with MET 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J LYS* 4.3 32.1 - - + +
120J LEU* 5.6 9.1 - - - +
132J LEU* 6.0 6.3 - - + -
43L ASP* 2.9 36.1 + - - +
44L ILE* 3.6 9.4 - - + +
45L ILE 3.1 0.2 - - - -
46L GLN* 1.3 102.0 - - - +
48L ILE* 1.3 61.2 + - - +
49L ASN 3.1 5.6 + - - -
50L ASP* 3.6 9.4 + - - +
80L ALA* 4.1 19.0 - - + +
83L VAL* 5.1 29.8 - - + -
84L LEU* 5.9 7.0 - - + -
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Residues in contact with ILE 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L LEU* 3.2 34.1 - - + -
13L VAL* 4.6 1.6 - - + -
22L LEU* 4.1 17.5 - - + -
27L VAL* 4.9 15.9 - - + -
44L ILE* 2.9 19.3 + - + +
45L ILE* 2.9 26.7 - - + +
47L MET* 1.3 74.7 - - - +
49L ASN* 1.3 65.5 + - - +
50L ASP 3.2 1.0 + - - -
51L MET* 3.9 11.9 + - + -
53L ILE* 3.3 38.5 - - + +
55L VAL* 3.3 18.6 - - + -
84L LEU* 5.6 3.1 - - + -
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Residues in contact with ASN 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L ILE 3.1 7.1 + - - +
46L GLN* 3.2 22.4 + - - +
47L MET 3.1 0.8 - - - -
48L ILE* 1.3 77.7 - - - +
50L ASP* 1.3 67.3 + - + +
52L GLY* 3.9 0.9 - - - -
53L ILE 3.0 19.9 + - - -
54L GLN* 3.3 9.7 + - - -
55L VAL* 3.7 29.6 + - + +
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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