Contacts of the strand formed by residues 31 - 39 (chain I) in PDB entry 1KQ2
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 31 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23I THR* 3.8 19.1 - - + +
24I VAL 3.2 10.5 - - - +
25I PHE* 3.5 32.9 - - + -
26I PHE* 4.5 0.4 - - - -
29I GLY 4.9 3.2 + - - +
30I PHE* 1.3 99.7 - - + +
32I MET* 1.3 60.9 + - - +
33I LYS* 4.4 10.4 + - - -
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Residues in contact with MET 32 (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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22I VAL 3.8 0.9 - - - +
23I THR* 3.5 2.9 - - - -
24I VAL* 2.8 34.5 + - + +
26I PHE* 3.8 33.6 - - + -
30I PHE* 4.2 15.9 - - + -
31I GLN* 1.3 74.9 - - - +
33I LYS* 1.3 60.6 + - - +
46I LEU* 4.4 14.4 - - + -
48I SER* 3.8 17.9 - - - +
49I GLN* 6.1 0.9 - - - +
53I HIS* 3.7 42.0 - - + +
55I ILE* 4.9 0.7 - - - -
62K THR* 5.4 5.2 - - + +
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Residues in contact with LYS 33 (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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21I GLU* 3.9 31.0 - - + +
22I VAL 3.3 7.0 - - - +
23I THR* 3.5 23.6 + - - +
31I GLN* 4.4 13.3 + - - -
32I MET* 1.3 73.6 - - - +
34I GLY* 1.3 57.5 + - - +
46I LEU* 4.8 0.2 - - - -
48I SER* 2.5 29.1 + - - -
49I GLN 4.7 0.9 + - - -
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Residues in contact with GLY 34 (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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21I GLU* 3.3 12.5 - - - +
22I VAL* 2.7 42.7 + - - +
32I MET 4.1 0.6 + - - -
33I LYS* 1.3 77.0 - - - +
35I VAL* 1.3 58.1 + - - -
46I LEU* 3.9 9.8 - - - +
47I ASN 3.2 13.9 - - - -
48I SER* 3.9 3.4 - - - -
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Residues in contact with VAL 35 (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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19I GLN* 3.4 49.8 - - + +
20I THR 3.4 11.7 - - - +
21I GLU* 4.8 2.7 - - - +
34I GLY* 1.3 73.0 - - - -
36I ILE* 1.3 67.9 + - - +
37I GLU* 3.0 26.2 + - - +
46I LEU* 3.6 3.3 - - - +
47I ASN* 3.0 31.4 + - + +
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Residues in contact with ILE 36 (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 LEU* 3.7 31.4 - - + +
15I PHE* 4.1 27.6 + - + -
16I LYS* 3.4 19.7 - - + +
19I GLN* 5.6 0.7 - - - +
20I THR 4.6 1.4 + - - -
22I VAL* 4.3 13.5 - - + +
34I GLY 4.3 0.2 + - - -
35I VAL* 1.3 75.0 - - - +
37I GLU* 1.3 64.6 + - - +
38I GLU 3.7 22.7 - - - +
39I TYR* 4.6 12.6 - - + -
44I VAL* 3.9 13.7 - - + -
45I SER 3.7 3.6 - - - -
46I LEU* 3.8 16.6 - - + -
63I TYR* 4.1 19.5 - - + -
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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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16I LYS* 3.4 20.7 - - - +
19I GLN* 4.5 14.2 - - - +
35I VAL* 3.0 20.7 + - - +
36I ILE* 1.3 74.2 - - - +
38I GLU* 1.3 69.0 + - + +
45I SER* 2.9 24.6 + - - +
47I ASN* 3.0 42.8 - - - +
52I GLN* 5.3 4.0 - - - +
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Residues in contact with GLU 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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16I LYS* 4.3 12.6 - - - +
36I ILE* 3.7 7.8 - - - +
37I GLU* 1.3 85.6 - - + +
39I TYR* 1.3 74.6 + - - +
45I SER* 2.9 40.3 + - - -
7K ILE* 3.1 38.0 - - + +
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Residues in contact with TYR 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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9I ASP* 3.8 22.6 + - - +
12I LEU* 3.7 47.8 - - + -
13I GLU* 2.9 30.7 + - - +
16I LYS* 3.6 33.5 + - + +
36I ILE* 4.6 4.9 - - + -
38I GLU* 1.3 79.8 - - - +
40I ASP* 1.3 72.4 + - - +
41I LYS* 5.6 2.0 - - - -
43I VAL 3.6 12.8 - - - +
44I VAL* 4.1 15.0 - - + +
57I LYS* 5.2 0.2 - - - -
7K ILE* 2.8 20.8 - - - +
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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