Contacts of the helix formed by residues 16 - 32 (chain A) in PDB entry 5TJ4
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 GLY 16 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 5.2 2.1 - - - +
15A LYS* 1.3 71.8 - - - +
17A TYR* 1.3 63.7 + - - -
19A GLY* 3.5 0.9 + - - -
20A LEU* 3.1 19.8 + - - +
293A VAL* 3.6 19.5 - - - +
296A ASP* 3.2 28.3 - - - -
297A LYS* 3.7 19.6 + - - +
299A LEU* 5.9 0.6 - - - +
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Residues in contact with TYR 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.7 27.3 - - + +
12A ASN 4.4 1.1 - - - -
13A GLY* 3.3 24.5 - - - -
15A LYS 3.1 16.0 + - - -
16A GLY* 1.3 70.3 - - - -
18A ASN* 1.3 99.4 + - - +
20A LEU* 3.2 5.7 + - - +
21A ALA* 2.9 27.3 + - - +
37A VAL* 3.8 14.5 - - + +
39A HIS* 3.2 49.4 + + + -
296A ASP* 3.5 0.8 + - - -
297A LYS* 6.3 2.0 - - + -
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Residues in contact with ASN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR* 1.3 108.1 + - - +
19A GLY* 1.3 58.4 + - - +
21A ALA* 3.1 9.1 + - - +
22A GLU* 2.9 36.8 + - - +
296A ASP* 3.1 18.9 + - - +
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Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY 3.5 3.8 + - - -
17A TYR 3.3 0.2 - - - -
18A ASN* 1.3 77.4 - - - +
20A LEU* 1.3 58.6 + - - +
22A GLU* 3.3 16.5 + - - +
23A VAL* 3.2 22.7 + - - +
292A ALA* 3.7 23.5 - - - +
293A VAL* 4.1 7.0 - - - -
296A ASP* 3.0 18.9 + - - -
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 3.9 26.2 - - + -
11A ILE* 3.8 26.2 - - + -
16A GLY 3.1 15.1 + - - +
17A TYR* 3.2 9.2 + - - +
19A GLY* 1.3 74.8 - - - +
21A ALA* 1.3 59.4 + - - +
23A VAL* 3.1 9.2 + - + +
24A GLY* 2.8 23.4 + - - -
37A VAL* 4.3 17.1 - - + +
61A PHE* 4.1 7.9 - - + -
279A PHE* 4.2 17.3 - - + -
284A LEU* 4.0 36.1 - - + -
293A VAL* 4.0 10.9 - - + +
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR 2.9 13.6 + - - +
18A ASN* 3.1 12.5 + - - +
20A LEU* 1.3 73.9 - - - +
22A GLU* 1.3 54.8 + - - +
24A GLY* 3.0 3.1 + - - +
25A LYS* 2.7 35.4 + - - +
35A VAL 5.6 2.9 - - - +
37A VAL* 4.0 21.5 - - + +
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Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASN* 2.9 23.1 + - - +
19A GLY* 3.3 19.1 + - - +
20A LEU 3.3 0.2 - - - -
21A ALA* 1.3 74.8 - - - +
23A VAL* 1.3 61.0 + - - +
25A LYS* 3.2 9.3 + - - +
26A LYS* 3.1 20.8 + - - +
292A ALA* 4.5 16.8 - - + +
296A ASP* 5.8 0.7 - - - +
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY 3.5 13.0 - - - +
20A LEU* 3.1 11.1 + - + +
22A GLU* 1.3 73.1 - - - +
24A GLY* 1.3 65.6 + - - +
26A LYS* 3.2 10.2 + - + +
27A PHE* 3.0 20.1 + - - +
279A PHE* 3.8 20.9 - - + -
283A TYR* 3.8 29.4 - - + +
284A LEU* 4.0 6.1 - - + +
289A GLY* 3.5 30.7 - - - +
292A ALA* 3.9 7.4 - - + -
293A VAL* 4.2 9.0 - - + -
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Residues in contact with GLY 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU 2.8 13.8 + - - -
21A ALA* 3.0 7.6 + - - -
23A VAL* 1.3 77.1 - - - +
25A LYS* 1.3 56.2 + - - +
27A PHE* 3.1 4.9 + - - +
28A GLU* 2.9 25.7 + - - +
35A VAL* 3.3 37.6 - - - +
279A PHE* 4.2 6.4 - - - -
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Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA 2.7 14.7 + - - +
22A GLU* 3.2 12.3 + - - +
24A GLY* 1.3 71.6 - - - +
26A LYS* 1.3 58.0 + - - +
28A GLU* 3.3 12.0 + - - +
29A LYS* 2.9 31.1 + - - +
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU 3.1 13.0 + - - +
23A VAL* 3.2 10.7 + - + +
25A LYS* 1.3 75.7 - - - +
27A PHE* 1.3 60.6 + - - +
29A LYS* 4.5 6.5 - - + -
30A ASP* 3.3 47.3 + - - +
283A TYR* 3.7 16.4 - - + -
288A GLU* 5.5 15.0 + - + -
354E ARG* 6.0 1.6 - - - +
1356E PRO* 5.4 2.6 - - - +
1360E ASP* 5.3 12.7 + - - -
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Residues in contact with PHE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.2 13.7 - - + -
23A VAL 3.0 11.7 + - - +
24A GLY 3.1 9.2 + - - +
26A LYS* 1.3 74.3 - - - +
28A GLU* 1.3 58.7 + - - +
30A ASP 3.2 1.4 + - - -
31A THR* 2.8 65.5 + - + +
33A ILE* 4.1 17.9 - - + -
35A VAL* 3.7 19.3 - - + -
275A LEU* 3.9 26.2 - - + -
278A GLU* 3.9 18.8 - - + -
279A PHE* 3.7 31.2 - + + -
283A TYR* 3.5 32.4 - + + -
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLY 2.9 15.0 + - - +
25A LYS* 3.5 13.3 - - - +
27A PHE* 1.3 73.7 - - - +
29A LYS* 1.3 57.8 + - - +
32A GLY* 2.8 32.0 + - - -
33A ILE 3.3 30.4 + - - +
34A LYS* 3.3 24.2 - - + +
35A VAL* 3.9 6.1 + - + +
1268E ARG* 5.9 0.7 + - - -
1502E NA 3.8 3.3 - - - -
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS 2.9 17.4 + - - +
26A LYS* 4.0 7.6 - - + +
27A PHE 3.2 0.2 - - - -
28A GLU* 1.3 74.0 - - - +
30A ASP* 1.3 72.1 + - - +
1257E GLU* 2.6 32.7 + - - -
1359E LYS* 3.3 17.3 - - - +
1397E SER 4.3 1.6 + - - -
1400E LEU* 3.2 39.5 - - + +
1401E GLU* 3.5 35.4 + - - +
1403E ALA 3.4 2.3 - - - +
1502E NA 2.8 24.2 - - - -
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Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LYS* 3.3 36.3 + - - +
27A PHE 3.2 2.5 + - - +
29A LYS* 1.3 90.9 - - - +
31A THR* 1.3 61.6 + - - +
283A TYR* 3.1 26.4 + - - +
1356E PRO* 3.3 33.4 - - + +
1400E LEU* 3.9 19.8 - - - +
1403E ALA* 4.5 1.9 - - - +
1405E GLY* 3.5 18.2 + - - -
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Residues in contact with THR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 2.8 59.0 + - + +
30A ASP* 1.3 75.1 - - - +
32A GLY* 1.3 61.3 + - - +
33A ILE* 3.3 37.5 - - + +
275A LEU* 4.9 1.7 - - - +
278A GLU* 5.7 2.5 - - - +
283A TYR* 5.1 3.1 - - - -
1404E GLU* 3.8 3.6 - - - +
1405E GLY* 3.7 16.6 + - - +
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Residues in contact with GLY 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 2.8 27.6 + - - -
29A LYS 4.4 0.2 + - - -
30A ASP 3.5 1.6 - - - -
31A THR* 1.3 73.9 - - - +
33A ILE* 1.3 60.1 + - - +
34A LYS 4.3 0.7 + - - -
1403E ALA 4.8 0.9 - - - -
1404E GLU* 3.7 39.8 - - - +
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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
------------------------------------------------------------
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