Contacts of the helix formed by residues 21 - 31 (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 ILE 21 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20L ARG* 1.3 76.1 - - - +
22L SER* 1.3 67.4 + - - +
23L LYS 3.1 0.4 - - - -
24L ASN* 2.9 37.1 + - - +
25L HIS* 3.5 5.6 + - + -
79L ALA* 4.3 12.6 - - + -
102L GLU* 4.1 7.6 - - + +
301L HIS* 3.7 27.6 - - + +
500L NAI 3.2 82.4 + - + +
550L HP7 5.4 3.6 - - - +
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Residues in contact with SER 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L LEU* 4.1 10.8 - - - +
17L GLY 3.2 26.9 - - - -
18L CYS* 3.4 14.4 + - - +
19L GLY 2.9 20.0 + - - -
21L ILE* 1.3 82.3 - - - +
23L LYS* 1.3 59.8 + - - +
25L HIS* 2.9 27.1 + - - +
26L ILE* 3.1 24.8 + - - +
52L ALA* 5.9 0.3 - - - +
79L ALA* 4.7 3.6 - - - -
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Residues in contact with LYS 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L GLY 5.0 2.0 - - - +
20L ARG* 3.2 16.8 + - - +
21L ILE 3.1 1.0 - - - -
22L SER* 1.3 84.0 + - - +
24L ASN* 1.3 58.9 + - - +
26L ILE* 3.5 16.7 - - + +
27L GLY* 3.0 25.5 + - - -
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Residues in contact with ASN 24 (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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20L ARG 4.5 2.8 + - - -
21L ILE* 2.9 37.3 + - - +
23L LYS* 1.3 78.0 - - - +
25L HIS* 1.3 55.3 + - - +
27L GLY* 4.7 1.1 - - - +
28L ALA* 2.7 36.3 + - - +
301L HIS* 3.6 31.7 + - + +
302L PRO* 4.8 1.6 - - - +
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Residues in contact with HIS 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L LEU* 4.6 11.4 - - + -
21L ILE* 3.5 24.0 + - + -
22L SER* 2.9 9.1 + - - +
24L ASN* 1.3 75.8 - - - +
26L ILE* 1.3 69.9 + - - +
28L ALA* 3.1 2.5 + - - +
29L ILE* 2.8 32.9 + - + +
77L VAL* 3.7 20.1 - - + +
79L ALA* 4.3 11.4 - - + -
102L GLU* 2.6 34.9 + - - +
129L VAL* 4.2 11.9 - - + -
301L HIS* 3.6 17.9 - + - -
305L TYR* 2.9 39.1 + + - +
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Residues in contact with ILE 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L LEU* 4.8 6.7 - - + +
22L SER* 3.1 25.8 + - - +
23L LYS* 3.5 23.8 - - + +
25L HIS* 1.3 77.4 - - - +
27L GLY* 1.3 70.5 + - - +
29L ILE* 3.7 1.1 - - - +
30L ALA* 2.9 28.7 + - + +
38L LEU* 4.1 24.3 - - + +
52L ALA* 5.9 8.3 - - + +
55L ALA* 6.1 2.9 - - + -
56L THR* 3.6 30.7 - - + -
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Residues in contact with GLY 27 (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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23L LYS 3.0 14.7 + - - -
24L ASN* 4.1 1.1 - - - -
26L ILE* 1.3 79.0 - - - +
28L ALA* 1.3 62.0 + - - +
30L ALA* 3.8 6.1 - - - +
31L GLN* 3.1 28.6 + - - +
302L PRO* 5.0 2.5 - - - -
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Residues in contact with ALA 28 (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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24L ASN 2.7 25.5 + - - +
25L HIS* 3.3 7.0 - - - +
26L ILE 2.8 3.8 + - - -
27L GLY* 1.3 73.2 - - - +
29L ILE* 1.3 63.8 + - - +
31L GLN* 3.6 6.2 + - - +
32L HIS* 3.5 18.7 - - - -
301L HIS* 3.9 2.9 - - + -
302L PRO* 3.8 30.3 - - + +
305L TYR* 3.7 25.6 - - + -
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Residues in contact with ILE 29 (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* 3.5 39.9 - - + -
15L LEU* 5.8 1.8 - - + -
25L HIS* 2.8 23.6 + - + +
26L ILE 3.7 0.9 - - - +
28L ALA* 1.3 67.0 - - - +
30L ALA* 1.3 54.2 + - - +
31L GLN 2.3 1.5 + - - -
32L HIS* 2.0 47.8 + - - -
36L ALA* 4.2 7.2 - - + -
37L GLU* 4.1 10.3 - - - +
38L LEU* 3.8 46.2 - - + +
77L VAL* 5.3 2.9 - - + -
305L TYR* 3.9 26.7 - - + +
309L ILE* 5.7 0.7 - - + -
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Residues in contact with ALA 30 (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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26L ILE* 2.9 26.8 + - + +
27L GLY* 3.8 7.0 - - - +
29L ILE* 1.3 78.6 - - - +
31L GLN* 1.3 54.9 + - - +
33L GLY* 2.8 26.1 + - - +
36L ALA 5.9 0.2 - - - -
38L LEU* 5.8 1.0 - - - +
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Residues in contact with GLN 31 (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 GLY 3.1 17.3 + - - +
28L ALA 3.6 5.8 - - - +
29L ILE 2.3 9.9 + - - -
30L ALA* 1.3 68.9 - - - +
32L HIS* 1.3 64.3 + - + -
33L GLY 3.4 1.7 + - - -
34L ASP* 4.9 3.5 - - - +
302L PRO* 3.7 30.6 - - + +
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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