Contacts of the helix formed by residues 16 - 28 (chain j) in PDB entry 5MQF
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 16 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14j MET 3.9 2.8 + - - -
15j VAL* 1.3 74.0 - - - +
17j PRO* 1.4 66.6 - - + +
18j ILE* 4.6 5.4 - - + +
19j ASN* 2.9 36.8 + - + +
20j LEU* 3.2 6.9 + - - +
34k PHE 4.8 7.4 - - - +
35k ASP* 5.6 3.1 - - + -
41k VAL* 5.1 0.4 - - - -
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Residues in contact with PRO 17 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15j VAL 3.8 2.0 - - - +
16j GLN* 1.4 84.0 - - + +
18j ILE* 1.3 63.4 + - - +
20j LEU* 3.2 24.9 + - + +
21j ILE* 3.3 7.4 + - - +
33k GLY 4.1 0.9 - - - -
34k PHE 3.8 23.8 - - - +
35k ASP* 4.2 6.7 - - + +
39k ASN* 3.2 46.0 - - + +
40k LEU 3.9 15.9 - - - +
41k VAL* 4.6 5.8 - - + +
61k VAL* 4.9 12.1 - - + +
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Residues in contact with ILE 18 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16j GLN* 3.3 4.7 - - + +
17j PRO* 1.3 79.4 - - - +
19j ASN* 1.3 58.6 + - - +
21j ILE* 3.4 9.7 + - - +
22j PHE* 3.0 24.3 + - - +
35k ASP* 6.1 0.8 - - - +
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Residues in contact with ASN 19 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15j VAL* 5.9 1.6 - - + -
16j GLN* 2.9 24.7 + - + +
18j ILE* 1.3 77.4 - - - +
20j LEU* 1.3 54.0 + - - +
22j PHE* 2.9 11.6 + - - +
23j ARG* 2.8 34.0 + - - +
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Residues in contact with LEU 20 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15j VAL* 6.0 4.2 - - + +
16j GLN 3.2 5.7 + - - +
17j PRO* 3.2 17.0 + - + +
19j ASN* 1.3 77.4 - - - +
21j ILE* 1.3 51.0 + - - +
23j ARG* 3.1 10.8 - - - +
24j TYR* 2.8 32.1 + - - +
41k VAL* 5.5 8.1 - - + -
60k VAL 5.9 2.5 - - - +
61k VAL* 5.3 10.8 - - + +
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Residues in contact with ILE 21 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17j PRO 3.3 8.0 + - - +
18j ILE* 3.4 11.9 - - - +
19j ASN 3.1 0.2 - - - -
20j LEU* 1.3 75.4 - - - +
22j PHE* 1.3 67.4 + - - +
23j ARG 3.0 1.1 - - - -
24j TYR* 2.8 11.7 + - - +
25j LEU* 2.8 23.7 + - - +
47j ILE* 5.6 0.9 - - - +
50j PHE* 6.0 6.3 - - + -
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Residues in contact with PHE 22 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18j ILE 3.0 13.6 + - - +
19j ASN* 2.9 13.8 + - - +
21j ILE* 1.3 74.0 - - - +
23j ARG* 1.3 56.2 + - - +
25j LEU* 3.3 9.2 - - - +
26j GLN* 3.0 28.2 + - - +
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Residues in contact with ARG 23 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19j ASN 2.8 11.5 + - - +
20j LEU* 3.1 16.8 - - - +
22j PHE* 1.3 75.1 - - - +
24j TYR* 1.3 57.3 + - - +
26j GLN* 3.4 6.2 + - - +
27j ASN* 2.8 33.8 + - - +
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Residues in contact with TYR 24 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20j LEU 2.8 15.4 + - - +
21j ILE* 2.8 15.9 + - - +
23j ARG* 1.3 71.1 - - - +
25j LEU* 1.3 56.8 - - - +
27j ASN* 4.5 4.7 - - - -
28j ARG* 3.0 25.6 + - - -
29j SER* 3.6 20.0 + - - +
31j ILE* 5.8 7.9 - - + -
47j ILE* 4.7 12.7 - - + +
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Residues in contact with LEU 25 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21j ILE 2.8 13.8 + - - +
22j PHE* 3.3 14.8 - - - +
24j TYR* 1.3 75.5 - - - +
26j GLN* 1.3 63.0 + - - +
28j ARG* 3.4 9.2 + - - +
47j ILE* 3.7 27.8 - - + +
48j ILE 5.1 9.2 - - - +
49j GLY* 5.6 3.6 - - - +
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Residues in contact with GLN 26 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22j PHE 3.0 13.1 + - - +
23j ARG* 3.4 6.9 + - - +
25j LEU* 1.3 80.7 - - - +
27j ASN* 1.3 61.5 + - - +
28j ARG* 3.5 2.1 + - - +
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Residues in contact with ASN 27 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23j ARG 2.8 18.5 + - - +
24j TYR* 3.8 4.5 - - - +
26j GLN* 1.3 76.5 - - - +
28j ARG* 1.3 70.7 + - - +
29j SER* 3.3 15.6 + - - +
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Residues in contact with ARG 28 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24j TYR 3.0 10.4 + - - -
25j LEU 3.4 7.4 + - - +
26j GLN 3.3 4.8 - - - +
27j ASN* 1.3 81.1 - - - +
29j SER* 1.3 65.7 + - - +
30j ARG 3.6 1.6 + - - -
46j CYS* 4.8 14.6 - - + +
47j ILE 5.3 3.4 - - - +
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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