Contacts of the helix formed by residues 8 - 24 (chain D) in PDB entry 5XBY
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 8 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ILE* 6.1 1.0 - - - +
28C LEU* 3.9 6.5 - - - +
6D PRO 3.5 0.2 + - - -
7D PRO* 1.3 72.9 - - - +
9D LEU* 1.3 63.9 + - - +
10D THR* 3.2 3.2 - - - +
11D GLU* 3.0 23.7 + - - +
12D LEU* 3.1 25.3 + - - +
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Residues in contact with LEU 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 4.2 15.9 - - + -
3B TRP* 5.8 2.9 - - + +
5B ILE* 5.1 5.8 - - + +
16C TYR* 3.9 21.3 - - + +
17C THR* 3.8 27.8 - - + +
20C VAL* 5.1 9.9 - - + -
21C LEU* 5.6 2.9 - - + -
28C LEU* 3.7 21.8 - - + +
5D ILE* 4.8 8.5 - - + -
6D PRO* 3.3 19.9 + - + +
7D PRO 3.3 3.6 + - - -
8D GLY* 1.3 77.9 - - - +
10D THR* 1.3 62.0 + - - +
12D LEU* 3.9 1.3 - - + +
13D LEU* 3.2 43.3 + - + +
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Residues in contact with THR 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B PRO* 5.2 0.4 - - + -
3B TRP* 2.7 29.6 + - - +
4B GLN* 3.0 30.3 - - + +
5B ILE* 3.8 10.7 + - - +
8D GLY* 3.2 1.4 - - - +
9D LEU* 1.3 75.2 - - - +
11D GLU* 1.3 75.7 + - + +
13D LEU* 3.4 1.7 + - - +
14D GLN* 2.8 57.4 + - - +
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Residues in contact with GLU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLY* 3.0 29.7 + - - +
10D THR* 1.3 88.6 - - + +
12D LEU* 1.3 62.4 - - - +
14D GLN* 3.9 8.5 - - - +
15D GLY* 3.0 20.3 + - - -
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Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TYR* 3.6 29.4 - - + +
28C LEU* 3.6 32.8 - - + +
29C VAL* 3.8 24.9 - - + -
8D GLY 3.1 17.5 + - - +
9D LEU* 3.9 5.8 - - + +
11D GLU* 1.3 80.4 - - - +
13D LEU* 1.3 68.5 + - + +
15D GLY* 3.5 0.9 + - - -
16D TYR* 3.4 19.2 + - - +
35D TYR* 4.7 2.9 + - - -
36D PHE* 3.5 36.0 - - + -
39D LEU* 5.1 7.1 - - + +
43D ARG* 5.0 3.8 - - - +
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TRP* 4.3 31.8 - - + +
13C LEU* 3.4 38.7 - - + +
16C TYR* 3.7 21.8 - - + -
17C THR* 3.4 24.9 - - - +
9D LEU* 3.2 35.8 + - + +
10D THR* 4.1 2.5 - - - +
12D LEU* 1.3 79.6 - - + +
14D GLN* 1.3 65.8 + - - +
16D TYR* 3.7 3.1 + - - +
17D THR* 3.2 24.4 + - - -
36D PHE* 5.1 2.7 - - + -
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Residues in contact with GLN 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B PRO* 3.8 14.9 - - + +
3B TRP* 3.7 20.9 + - + +
10D THR* 2.8 40.0 + - - +
11D GLU* 3.9 8.1 - - - +
13D LEU* 1.3 79.6 - - - +
15D GLY* 1.3 61.6 + - - +
17D THR* 3.3 7.6 + - - -
18D VAL* 3.2 31.5 + - + +
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Residues in contact with GLY 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLU 3.0 17.0 + - - -
12D LEU 4.0 0.4 - - - -
14D GLN* 1.3 74.9 - - - +
16D TYR* 1.3 64.6 + - - +
18D VAL* 3.3 10.0 + - - +
19D GLU* 3.2 25.8 + - - +
35D TYR* 3.7 15.4 + - - -
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Residues in contact with TYR 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LEU* 3.3 25.8 - - + -
12C LEU* 3.7 7.8 - - + +
13C LEU* 3.6 28.5 - - + -
36C PHE* 6.0 0.4 - + - -
12D LEU 3.4 14.5 + - - +
13D LEU* 4.1 4.3 - - - +
14D GLN 3.4 0.4 - - - -
15D GLY* 1.3 75.7 - - - +
17D THR* 1.3 64.2 + - - +
19D GLU* 3.3 2.9 + - - +
20D VAL* 3.1 29.6 + - + +
28D LEU* 2.8 38.9 + - - +
31D PHE* 3.7 22.0 - + - -
32D ALA* 3.7 26.7 - - + -
35D TYR* 4.0 33.0 + + + -
36D PHE* 4.1 13.0 - + + -
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Residues in contact with THR 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B TRP* 5.1 3.3 - - - -
5C ILE* 3.5 20.9 - - + -
9C LEU* 3.4 25.5 - - + +
13C LEU* 3.5 18.2 - - - +
13D LEU 3.2 12.3 + - - -
14D GLN* 3.3 10.6 + - - -
15D GLY 3.2 0.6 - - - -
16D TYR* 1.3 81.5 - - - +
18D VAL* 1.3 63.7 + - + +
20D VAL* 3.3 6.9 + - - +
21D LEU* 3.1 24.9 + - + +
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Residues in contact with VAL 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLN* 3.2 19.9 + - + +
15D GLY* 3.5 11.7 - - - +
17D THR* 1.3 79.5 - - + +
19D GLU* 1.3 59.9 + - - +
21D LEU* 3.1 14.1 + - + +
22D ARG* 3.0 55.4 + - + +
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Residues in contact with GLU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLY 3.2 8.5 + - - +
16D TYR 3.8 6.1 - - - +
17D THR 3.3 0.2 - - - -
18D VAL* 1.3 75.6 - - - +
20D VAL* 1.3 65.8 + - - +
22D ARG* 2.5 49.1 + - - +
23D GLN* 3.1 44.0 + - - +
31D PHE* 3.9 19.8 - - + -
35D TYR* 3.4 30.4 - - + +
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C PRO* 3.7 33.4 - - + -
9C LEU* 4.5 4.5 - - + -
16D TYR* 3.1 52.2 + - + +
17D THR* 3.6 10.1 - - - +
19D GLU* 1.3 76.0 - - - +
21D LEU* 1.3 58.8 + - - +
24D GLN* 2.9 30.2 + - - +
25D PRO* 4.1 12.6 - - + -
28D LEU* 3.8 15.3 - - + -
31D PHE* 3.8 10.5 - - + -
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 3.9 46.0 - - + +
6C PRO* 4.0 11.9 - - + -
17D THR* 3.1 23.6 + - + +
18D VAL* 3.5 13.5 - - + +
20D VAL* 1.3 79.1 - - + +
22D ARG* 1.3 63.2 + - - +
24D GLN* 3.8 13.8 - - - +
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Residues in contact with ARG 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D VAL* 3.0 34.9 + - + +
19D GLU* 2.5 46.8 + - - +
21D LEU* 1.3 80.6 - - + +
23D GLN* 1.3 65.5 + - + +
24D GLN* 4.7 2.3 - - - +
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Residues in contact with GLN 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D GLU* 3.1 28.6 + - - +
22D ARG* 1.3 82.3 - - + +
24D GLN* 1.3 71.8 + - - +
25D PRO* 3.4 9.8 - - + +
31D PHE* 3.6 31.5 - - + -
38D ARG* 5.4 7.8 + - - +
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Residues in contact with GLN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D VAL* 2.9 13.0 + - - +
21D LEU* 3.8 17.0 - - - +
22D ARG 4.7 2.0 - - - +
23D GLN* 1.3 79.4 - - - +
25D PRO* 1.3 70.2 - - - +
26D PRO* 3.6 4.7 - - - +
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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