Contacts of the strand formed by residues 36 - 42 (chain L) in PDB entry 3Q2K
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 ALA 36 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10L LYS* 4.3 1.6 - - - -
11L ILE* 3.3 20.9 - - + +
13L PHE* 3.9 12.3 - - + -
29L ILE* 4.2 7.7 - - + +
30L ALA* 5.9 0.5 - - - -
32L HIS* 2.8 19.0 + - + +
33L GLY* 3.2 16.2 - - - +
34L ASP 3.5 1.0 - - - -
35L ARG* 1.3 81.5 - - - +
37L GLU* 1.3 64.5 + - - +
309L ILE* 3.7 26.9 - - + -
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Residues in contact with GLU 37 (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 ARG* 5.7 0.9 - - - -
10L LYS* 3.6 29.3 + - + +
11L ILE 3.0 10.2 + - - +
12L ARG* 3.4 33.1 - - + +
13L PHE* 3.4 16.6 + - - -
29L ILE* 4.1 4.3 - - - +
30L ALA* 6.6 0.2 - - - +
33L GLY 5.1 1.3 - - - +
36L ALA* 1.3 78.1 - - - +
38L LEU* 1.3 65.4 + - - +
39L VAL* 3.4 11.4 + - + +
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Residues in contact with LEU 38 (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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13L PHE* 3.1 31.6 - - + +
15L LEU* 4.0 19.1 - - + -
26L ILE* 4.1 31.2 - - + +
29L ILE* 3.8 32.6 - - + +
30L ALA 5.8 0.7 - - - +
37L GLU* 1.3 70.0 - - - +
39L VAL* 1.3 61.1 + - - +
40L GLU 3.3 20.2 - - - +
41L ILE* 4.1 11.7 - - + -
56L THR* 4.8 12.3 - - + +
57L GLY 4.8 3.5 - - - +
58L ALA* 4.4 8.9 - - + +
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Residues in contact with VAL 39 (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 ARG* 3.5 46.2 - - + +
13L PHE 2.6 14.5 + - - +
37L GLU* 3.4 25.8 - - + +
38L LEU* 1.3 75.3 - - - +
40L GLU* 1.3 84.1 + - + +
58L ALA* 3.3 7.3 - - - +
59L ARG* 3.3 20.3 + - + +
72L ASN* 4.7 1.3 - - - +
73L ALA 4.9 1.3 - - - +
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Residues in contact with GLU 40 (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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13L PHE 3.4 4.6 + - - -
14L GLY* 4.1 0.2 - - - -
15L LEU 3.0 17.3 + - - -
38L LEU* 3.3 6.4 - - - +
39L VAL* 1.3 94.8 - - + +
41L ILE* 1.3 76.0 + - - +
58L ALA* 4.3 0.4 - - - -
59L ARG* 3.7 13.0 - - + +
61L PHE* 3.5 18.7 - - + -
67L MET* 3.2 37.3 - - + +
71L GLY* 3.0 25.5 - - - -
72L ASN* 2.7 23.1 + - - +
73L ALA* 2.9 14.8 + - - +
76L LEU* 6.0 0.2 - - - +
97L ARG* 5.1 0.7 + - - -
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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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15L LEU* 3.5 21.5 - - + +
18L CYS* 4.7 7.0 - - - -
38L LEU* 4.1 12.3 - - + -
40L GLU* 1.3 87.6 - - - +
42L CYS* 1.3 56.5 + - - +
49L LEU* 4.2 12.8 - - + +
52L ALA* 3.5 18.8 - - + +
53L GLU* 3.4 37.0 - - + +
56L THR* 3.9 8.5 - - - +
58L ALA* 3.8 25.8 - - + +
59L ARG 3.2 10.6 + - - +
60L PRO* 3.4 2.2 - - + +
61L PHE* 2.8 31.5 + - - -
67L MET* 4.3 1.6 - - - -
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Residues in contact with CYS 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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15L LEU 2.7 17.0 + - - +
16L VAL* 4.2 16.2 - - + -
17L GLY 3.4 13.9 + - - -
18L CYS* 3.2 12.5 - - - -
41L ILE* 1.3 76.9 - - - +
43L ASP* 1.3 70.0 + - - +
49L LEU* 4.5 1.1 - - - -
61L PHE* 3.2 7.9 - - + +
62L SER 4.7 0.2 - - - -
63L SER* 3.3 38.4 - - - -
64L LEU* 3.9 8.3 - - - -
67L MET* 3.5 17.0 - - - -
500L NAI 4.2 7.9 - - - -
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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