Contacts of the helix formed by residues 21 - 31 (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 ILE 21 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I GLY 2.9 0.4 + - - +
20I ARG* 1.3 76.5 - - - +
22I SER* 1.3 66.7 + - - +
23I LYS 3.3 2.7 - - - -
24I ASN* 3.0 28.2 + - + +
25I HIS* 3.2 20.6 + - + +
79I ALA* 3.7 17.9 - - + -
102I GLU* 4.0 4.0 - - - +
301I HIS* 3.7 17.3 - - + -
500I NAI 2.7 91.3 + - + +
550I HP7 5.0 5.8 - - - +
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Residues in contact with SER 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I LEU* 3.6 28.0 - - - -
17I GLY 3.8 2.9 - - - -
18I CYS* 3.0 15.3 - - - +
19I GLY 2.4 36.7 + - - -
21I ILE* 1.3 80.7 - - - +
23I LYS* 1.3 55.3 + - - +
25I HIS* 2.6 31.6 + - - +
26I ILE* 2.8 23.4 + - - +
52I ALA* 5.8 0.9 - - - +
79I ALA* 5.0 0.4 - - - -
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Residues in contact with LYS 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I GLY 3.9 11.2 - - - +
20I ARG* 3.7 37.5 + - - +
21I ILE 3.3 0.4 - - - -
22I SER* 1.3 77.9 - - - +
24I ASN* 1.3 60.0 + - - +
26I ILE* 3.9 15.0 - - + +
27I GLY* 2.9 24.8 + - - -
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Residues in contact with ASN 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I ARG* 5.0 4.9 + - - +
21I ILE* 3.0 34.2 + - + +
23I LYS* 1.3 80.1 - - - +
25I HIS* 1.3 59.3 + - - +
27I GLY* 3.9 0.8 - - - -
28I ALA* 2.9 29.1 + - - +
298I GLY 3.8 8.5 + - - +
299I PHE* 3.7 39.5 - - - +
300I GLY 4.7 0.2 + - - -
301I HIS* 3.8 26.0 + - + +
302I PRO* 5.6 0.9 - - - +
550I HP7 5.5 3.6 + - - -
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Residues in contact with HIS 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I LEU* 4.4 11.4 - - + -
21I ILE* 3.2 31.6 + - + -
22I SER* 2.6 17.1 + - - +
24I ASN* 1.3 70.2 - - - +
26I ILE* 1.3 67.0 + - - +
28I ALA* 2.9 3.3 + - - +
29I ILE* 2.9 31.7 + - + +
77I VAL* 3.3 21.2 - - + +
79I ALA* 4.4 5.8 - - + +
100I VAL* 5.3 0.4 - - + -
102I GLU* 2.7 40.2 + - + +
129I VAL* 4.3 9.9 - - + -
301I HIS* 3.3 18.4 + + - -
305I TYR* 3.1 33.7 + + - +
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Residues in contact with ILE 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I LEU* 5.2 4.5 - - + +
22I SER* 2.8 27.2 + - - +
23I LYS* 3.9 16.4 - - + +
25I HIS* 1.3 72.1 - - - +
27I GLY* 1.3 67.0 + - - +
29I ILE* 3.2 3.8 + - - +
30I ALA* 2.9 30.2 + - + +
38I LEU* 3.7 30.6 - - + +
41I ILE* 6.3 0.2 - - + -
52I ALA* 4.6 15.7 - - + -
55I ALA* 5.7 4.9 - - + +
56I THR* 3.8 26.2 - - + -
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Residues in contact with GLY 27 (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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23I LYS 2.9 17.8 + - - -
24I ASN* 3.9 1.1 - - - -
25I HIS 3.1 0.2 + - - -
26I ILE* 1.3 83.6 - - - +
28I ALA* 1.3 60.3 + - - +
30I ALA* 3.8 4.3 + - - +
31I GLN* 3.3 25.4 + - - +
302I PRO* 5.6 0.9 - - - -
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Residues in contact with ALA 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I ASN 2.9 20.2 + - - +
25I HIS 2.9 0.8 + - - +
27I GLY* 1.3 76.2 - - - +
29I ILE* 1.3 60.7 + - - +
31I GLN* 3.5 6.9 - - - +
32I HIS* 3.2 27.5 - - - -
301I HIS* 3.7 2.7 - - + -
302I PRO* 3.5 40.1 - - + +
305I TYR* 3.7 22.3 - - + +
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Residues in contact with ILE 29 (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* 3.7 40.8 - - + -
14I GLY 5.7 0.4 - - - +
15I LEU* 6.3 1.3 - - + -
25I HIS* 2.9 23.2 + - + +
26I ILE* 3.8 4.3 - - - +
28I ALA* 1.3 75.2 - - - +
30I ALA* 1.3 68.3 + - - +
31I GLN 3.1 0.2 - - - -
32I HIS* 2.9 23.4 + - - +
33I GLY* 3.6 1.2 + - - -
36I ALA* 4.1 11.1 - - + +
37I GLU* 4.2 0.9 - - - -
38I LEU* 3.7 39.0 - - + +
77I VAL* 4.9 2.9 - - + -
305I TYR* 3.7 35.7 - - + +
309I ILE* 5.7 0.9 - - - -
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Residues in contact with ALA 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I ILE* 2.9 21.7 + - + +
27I GLY* 4.0 4.9 - - - +
29I ILE* 1.3 75.2 - - - +
31I GLN* 1.3 53.6 + - - +
32I HIS 2.5 1.6 + - - -
33I GLY* 2.3 37.6 + - - +
36I ALA 5.5 0.4 - - - -
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Residues in contact with GLN 31 (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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27I GLY 3.3 17.3 + - - +
28I ALA 3.5 7.6 - - - +
29I ILE 3.1 0.4 - - - -
30I ALA* 1.3 76.4 - - - +
32I HIS* 1.3 71.4 + - + +
33I GLY 3.5 0.7 - - - -
302I PRO* 3.7 29.9 - - - +
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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