Contacts of the helix formed by residues 11 - 25 (chain A) in PDB entry 3HYW
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 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLY 3.4 5.3 - - - -
10A GLY* 1.3 77.4 - - - +
12A VAL* 1.3 66.4 + - - +
13A GLY 3.3 2.7 - - - -
14A GLY 4.0 1.5 - - - +
15A ILE* 2.9 24.9 + - - +
39A PHE* 3.7 12.1 - - - -
40A GLY 5.6 1.8 - - - -
441A FAD 3.3 27.6 + - - -
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Residues in contact with VAL 12 (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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11A GLY* 1.3 71.3 - - - +
13A GLY* 1.3 58.4 + - - +
15A ILE* 4.3 1.1 - - - +
16A ALA* 3.0 31.9 + - - +
39A PHE* 3.6 23.0 - - + -
40A GLY 5.2 0.2 - - - +
41A PHE* 5.9 1.1 - - + -
42A THR* 4.7 5.2 - - - +
43A PRO* 5.5 6.5 - - + -
314A GLY* 4.6 15.5 - - - +
317A ILE* 4.0 18.6 - - + -
318A GLU* 4.7 7.4 - - + +
389A PHE* 4.1 22.6 - - + -
441A FAD 3.1 39.9 + - - +
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Residues in contact with GLY 13 (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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12A VAL* 1.3 74.9 - - - +
14A GLY* 1.3 53.7 + - - +
16A ALA* 3.9 2.2 - - - +
17A THR* 2.6 39.1 + - - -
104A ALA* 4.0 7.0 - - - -
292A VAL* 3.6 11.3 - - - +
317A ILE* 3.5 20.6 - - - +
441A FAD 2.8 20.7 + - - -
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Residues in contact with GLY 14 (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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7A VAL* 3.6 17.8 - - - +
9A GLY 3.3 23.8 + - - -
11A GLY 3.5 4.6 + - - +
12A VAL 3.5 0.2 - - - -
13A GLY* 1.3 73.1 - - - +
15A ILE* 1.3 59.5 + - - +
17A THR* 3.5 1.2 + - - -
18A ALA* 2.9 31.7 + - - +
32A LEU* 4.0 3.8 - - - -
104A ALA* 3.5 12.5 - - - +
441A FAD 4.2 0.4 + - - -
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Residues in contact with ILE 15 (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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9A GLY 4.2 0.2 + - - -
10A GLY 4.0 14.1 - - - +
11A GLY 2.9 20.4 + - - +
12A VAL* 4.3 1.8 - - - +
14A GLY* 1.3 74.5 - - - +
16A ALA* 1.3 58.1 + - - +
18A ALA* 4.6 1.1 - - - -
19A TYR* 2.9 61.2 + - + +
32A LEU* 4.0 19.1 - - + -
39A PHE* 4.1 12.3 - - + -
62A LEU* 3.9 28.7 - - + -
66A LEU* 4.2 13.7 - - + -
389A PHE* 6.1 0.9 - - + -
393A VAL* 4.5 10.1 - - + -
398A ILE* 3.9 13.2 - - + -
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Residues in contact with ALA 16 (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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12A VAL* 3.0 22.1 + - + +
13A GLY* 3.9 0.9 - - - +
15A ILE* 1.3 75.9 - - - +
17A THR* 1.3 57.5 + - - +
19A TYR* 3.9 0.7 - - - +
20A ASN* 2.8 39.6 + - - +
318A GLU* 4.8 10.8 - - + -
321A ALA* 3.5 19.5 - - + -
398A ILE* 3.8 31.1 - - + +
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Residues in contact with THR 17 (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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7A VAL* 5.1 1.8 - - + -
13A GLY 2.6 23.9 + - - -
14A GLY* 4.0 2.7 - - - -
16A ALA* 1.3 74.3 - - - +
18A ALA* 1.3 59.5 + - - +
20A ASN* 3.3 1.2 + - - +
21A LEU* 2.9 43.2 + - + +
102A VAL* 3.9 24.6 - - + +
292A VAL* 3.5 12.8 - - - +
321A ALA* 3.5 24.1 - - - +
324A VAL* 3.8 28.7 - - + -
325A ALA 4.4 2.7 - - - +
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Residues in contact with ALA 18 (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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7A VAL* 4.3 9.0 - - + +
14A GLY 2.9 18.9 + - - +
15A ILE* 3.9 3.1 - - - +
17A THR* 1.3 76.3 - - - +
19A TYR* 1.3 58.8 + - + +
21A LEU* 3.5 4.3 + - - +
22A ARG* 2.9 29.6 + - - +
30A ILE* 3.8 22.7 - - + +
32A LEU* 4.1 17.7 - - + -
71A ILE* 4.1 18.1 - - + +
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Residues in contact with TYR 19 (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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15A ILE* 2.9 42.0 + - + +
16A ALA 4.1 0.7 - - - +
18A ALA* 1.3 71.6 - - + +
20A ASN* 1.3 66.2 + - - +
22A ARG* 3.3 5.1 + - - +
23A ASN* 2.9 31.3 + - - +
65A LEU* 3.6 5.5 - - - +
66A LEU* 3.5 31.9 - - + +
69A PHE* 3.6 16.6 - + + -
71A ILE* 3.9 16.8 - - + -
392A LYS 3.7 5.8 - - - -
393A VAL* 2.6 32.3 + - - +
396A GLY* 3.4 32.5 - - - +
397A ASN 3.5 0.4 - - - -
398A ILE* 3.5 29.2 - - + +
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Residues in contact with ASN 20 (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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16A ALA* 2.8 31.5 + - - +
17A THR 3.3 1.3 + - - +
19A TYR* 1.3 75.8 - - - +
21A LEU* 1.3 61.8 + - - +
23A ASN* 3.9 4.2 - - - +
24A LEU* 3.1 32.7 + - + +
318A GLU 4.5 0.2 + - - -
321A ALA* 3.5 7.1 - - - +
322A MET* 3.5 36.5 - - - +
325A ALA* 3.5 21.3 - - + -
397A ASN* 5.3 0.7 - - - +
398A ILE* 5.3 2.0 + - - +
399A ALA* 3.4 29.6 + - - +
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Residues in contact with LEU 21 (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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5A VAL* 3.8 33.9 - - + -
7A VAL* 4.9 1.8 - - + -
17A THR* 2.9 34.5 + - + +
18A ALA* 3.7 8.3 - - - +
20A ASN* 1.3 77.0 - - - +
22A ARG* 1.3 56.4 + - - +
24A LEU* 3.4 3.5 + - - +
25A MET* 2.9 34.5 + - - +
28A LEU* 3.9 12.5 - - + +
30A ILE* 3.8 12.8 - - + -
325A ALA* 3.6 33.9 - - + +
328A ILE* 3.8 24.2 - - + -
329A VAL* 3.9 5.8 - - + -
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Residues in contact with ARG 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 ALA 2.9 18.3 + - - +
19A TYR* 3.3 8.0 + - - +
21A LEU* 1.3 75.6 - - - +
23A ASN* 1.3 68.6 + - - +
25A MET 2.9 36.5 + - - -
26A PRO* 3.2 25.3 + - - +
28A LEU 2.7 31.5 + - - -
29A LYS* 4.4 0.8 - - - +
30A ILE* 3.7 33.1 - - + +
69A PHE* 2.9 34.5 + - + +
70A ASN* 2.7 34.2 + - - +
71A ILE* 4.4 5.1 - - + +
396A GLY 5.9 1.6 - - - +
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Residues in contact with ASN 23 (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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19A TYR 2.9 23.2 + - - +
20A ASN* 4.0 4.7 - - - +
22A ARG* 1.3 81.1 - - - +
24A LEU* 1.3 65.4 + - + +
26A PRO* 4.5 7.5 - - - +
396A GLY 3.0 25.0 + - - +
397A ASN* 3.9 26.4 - - - +
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Residues in contact with LEU 24 (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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20A ASN* 3.1 23.0 + - + +
21A LEU 3.7 3.6 - - - +
23A ASN* 1.3 83.3 - - + +
25A MET* 1.3 57.7 + - - +
26A PRO* 3.8 4.7 - - - +
325A ALA* 3.9 36.3 - - + +
326A HIS* 4.0 34.5 - - + +
329A VAL* 3.9 20.0 - - + -
333A ARG* 3.3 21.8 + - - +
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Residues in contact with MET 25 (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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3A LYS* 6.0 0.4 - - - -
21A LEU 2.9 12.6 + - - +
22A ARG* 2.9 24.3 + - - +
24A LEU* 1.3 78.9 - - - +
26A PRO* 1.3 62.9 - - + +
27A ASP* 3.2 21.5 - - - +
28A LEU* 3.2 34.1 + - + +
329A VAL* 3.6 36.1 - - + +
332A ILE* 3.8 26.9 - - + -
333A ARG* 3.5 33.4 - - + +
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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