Contacts of the strand formed by residues 36 - 42 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10I LYS* 4.2 2.7 - - - -
11I ILE* 3.0 12.6 - - + +
13I PHE* 3.7 27.4 - - + -
29I ILE* 4.1 13.5 - - + +
30I ALA* 5.5 0.5 - - - -
32I HIS 2.9 8.3 + - - +
33I GLY* 3.4 26.7 + - - +
34I ASP 3.3 0.6 - - - -
35I ARG* 1.3 82.0 - - - +
37I GLU* 1.3 62.4 + - - +
309I ILE* 4.2 13.5 - - + -
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Residues in contact with GLU 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I LYS* 3.9 32.4 + - + +
11I ILE 2.8 11.2 + - - +
12I ARG* 3.0 46.1 + - + +
13I PHE 2.8 26.1 + - - -
29I ILE* 4.2 3.8 - - - -
33I GLY 5.7 0.2 - - - +
36I ALA* 1.3 75.9 - - - +
38I LEU* 1.3 62.5 + - - +
39I VAL* 3.2 11.4 + - + +
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Residues in contact with LEU 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I PHE* 3.3 21.1 - - + +
14I GLY* 4.1 6.7 - - - -
15I LEU* 4.1 9.6 - - + +
26I ILE* 3.7 36.8 - - + +
29I ILE* 3.7 26.5 - - + +
37I GLU* 1.3 72.6 - - - +
39I VAL* 1.3 59.6 + - - +
40I GLU 3.2 28.0 - - - +
41I ILE* 4.0 17.7 - - + -
56I THR* 4.2 14.1 - - + +
57I GLY 5.0 2.9 - - - +
58I ALA* 4.4 6.6 - - + +
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Residues in contact with VAL 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I ARG* 3.3 42.4 - - + +
13I PHE 2.6 16.7 + - - +
37I GLU* 3.8 24.2 - - - +
38I LEU* 1.3 70.8 - - - +
40I GLU* 1.3 83.7 + - + +
57I GLY 4.8 0.2 - - - +
58I ALA* 2.9 27.5 - - - +
59I ARG* 3.2 6.7 + - + +
72I ASN* 4.9 6.3 - - - +
73I ALA* 5.2 2.2 - - + +
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Residues in contact with GLU 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I PHE 3.6 2.0 + - - -
14I GLY* 3.4 8.2 - - - -
15I LEU 3.0 20.2 + - - -
38I LEU* 3.2 4.2 - - - +
39I VAL* 1.3 97.8 - - + +
41I ILE* 1.3 71.4 + - - +
59I ARG* 3.3 14.9 + - + +
61I PHE* 3.8 15.0 - - + -
67I MET* 3.5 29.4 - - + +
71I GLY* 3.6 5.2 - - - -
72I ASN* 2.9 46.8 + - - -
73I ALA* 4.0 12.0 + - + +
76I LEU* 5.4 0.9 - - - +
97I ARG* 5.5 0.2 + - - -
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Residues in contact with ILE 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I LEU* 3.4 13.2 - - + +
18I CYS* 3.9 16.8 - - - -
26I ILE* 6.1 0.4 - - + -
38I LEU* 4.0 21.1 - - + -
40I GLU* 1.3 84.8 - - - +
42I CYS* 1.3 61.4 + - - +
49I LEU* 4.1 13.6 - - + +
52I ALA* 3.8 5.4 - - + -
53I GLU* 3.3 42.6 - - + +
56I THR* 3.5 11.4 - - - +
58I ALA* 3.6 20.2 - - + +
59I ARG 3.0 9.7 + - - +
60I PRO* 3.5 1.6 - - + +
61I PHE* 3.1 24.9 + - - -
67I MET* 4.8 1.3 - - - -
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Residues in contact with CYS 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I LEU 3.0 9.0 + - - +
16I VAL* 4.2 5.6 - - - -
17I GLY* 2.8 25.6 + - - -
18I CYS* 3.6 4.2 - - - -
41I ILE* 1.3 76.7 - - - +
43I ASP* 1.3 68.6 + - - +
49I LEU* 4.4 1.6 - - - -
61I PHE 3.4 10.3 - - - +
62I SER 4.4 0.2 - - - -
63I SER* 3.6 35.4 - - - -
64I LEU* 3.7 11.2 - - - -
67I MET* 3.5 24.0 - - + -
500I NAI 4.2 13.9 - - - -
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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