Contacts of the helix formed by residues 11 - 25 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLY 3.3 5.1 + - - -
10B GLY* 1.3 77.5 - - - +
12B VAL* 1.3 67.3 + - - -
13B GLY 3.3 2.7 - - - -
14B GLY 4.0 1.0 - - - +
15B ILE* 2.9 25.5 + - - +
39B PHE* 3.8 11.9 - - - -
40B GLY 5.7 1.6 - - - -
441B FAD 3.3 28.0 + - - -
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Residues in contact with VAL 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLY* 1.3 70.1 - - - +
13B GLY* 1.3 58.6 + - - +
15B ILE* 4.4 1.0 - - - +
16B ALA* 3.0 33.4 + - - +
39B PHE* 3.7 24.8 - - + -
41B PHE* 5.9 1.3 - - + -
42B THR* 4.7 6.7 - - - +
43B PRO* 5.6 4.9 - - + -
314B GLY* 4.5 15.0 - - - +
317B ILE* 4.0 18.4 - - + -
318B GLU* 4.6 7.0 - - + -
389B PHE* 4.1 23.4 - - + -
441B FAD 3.2 40.3 + - - +
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Residues in contact with GLY 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 1.3 73.7 - - - +
14B GLY* 1.3 56.5 + - - +
16B ALA* 3.9 2.0 - - - +
17B THR* 2.8 38.1 + - - -
104B ALA* 3.9 7.6 - - - -
292B VAL* 3.7 11.4 - - - -
317B ILE* 3.6 19.2 - - - +
441B FAD 2.8 21.0 + - - -
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Residues in contact with GLY 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 3.5 19.9 - - - +
9B GLY 3.2 24.2 + - - -
11B GLY 3.5 5.0 + - - +
13B GLY* 1.3 76.9 - - - +
15B ILE* 1.3 56.9 + - - +
17B THR* 3.8 0.6 - - - -
18B ALA* 2.9 30.8 + - - +
32B LEU* 4.1 2.5 - - - -
104B ALA* 3.5 12.5 - - - +
441B FAD 4.2 0.6 + - - -
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Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLY 4.3 0.2 + - - -
10B GLY 4.0 11.9 - - - +
11B GLY 2.9 20.5 + - - +
12B VAL* 4.4 1.3 - - - +
14B GLY* 1.3 71.7 - - - +
16B ALA* 1.3 61.0 + - - +
18B ALA* 3.3 3.0 + - - -
19B TYR* 2.8 63.1 + - + +
32B LEU* 3.8 20.0 - - + -
39B PHE* 4.2 11.4 - - + -
62B LEU* 3.9 30.7 - - + -
66B LEU* 4.2 13.2 - - + -
389B PHE* 6.2 1.1 - - + -
393B VAL* 4.4 10.8 - - + -
398B ILE* 4.2 10.1 - - + -
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 3.0 21.8 + - + +
13B GLY* 3.9 0.7 - - - +
15B ILE* 1.3 76.3 - - - +
17B THR* 1.3 58.1 + - - +
19B TYR* 3.9 0.7 - - - +
20B ASN* 2.8 38.8 + - - +
318B GLU* 4.8 11.2 - - + -
321B ALA* 3.5 19.1 - - + -
389B PHE* 6.3 0.2 - - - -
398B ILE* 3.9 31.6 - - + +
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Residues in contact with THR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 5.0 2.0 - - + -
13B GLY 2.8 22.9 + - - -
14B GLY* 3.9 2.9 - - - -
16B ALA* 1.3 76.4 - - - +
18B ALA* 1.3 56.7 + - - +
20B ASN* 3.4 1.8 + - - +
21B LEU* 2.9 47.0 + - + +
102B VAL* 3.9 32.8 - - + -
292B VAL* 3.6 11.1 - - - +
321B ALA* 3.3 27.3 - - - +
324B VAL* 3.9 17.3 - - + -
325B ALA 4.5 0.7 - - - +
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 4.4 5.3 - - + +
14B GLY 2.9 18.3 + - - +
15B ILE* 3.8 4.3 - - - +
17B THR* 1.3 77.3 - - - +
19B TYR* 1.3 59.3 + - + +
21B LEU* 3.4 5.5 + - - -
22B ARG* 2.9 29.5 + - - +
30B ILE* 3.5 24.1 - - + +
32B LEU* 4.2 16.4 - - + -
66B LEU* 6.1 0.4 - - + -
71B ILE* 4.1 18.2 - - + +
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Residues in contact with TYR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 2.8 41.1 + - + +
16B ALA 4.0 2.2 - - - +
18B ALA* 1.3 71.1 - - + +
20B ASN* 1.3 60.5 - - - +
22B ARG* 3.4 5.0 + - - +
23B ASN* 2.9 37.4 + - - +
65B LEU* 3.6 11.1 - - - +
66B LEU* 3.7 25.1 - - + +
69B PHE* 3.5 23.8 - + + -
71B ILE* 3.9 12.8 - - + -
392B LYS 3.8 5.2 - - - -
393B VAL* 2.7 33.8 + - - +
396B GLY* 3.5 32.1 - - - +
397B ASN 3.7 0.7 - - - -
398B ILE* 3.5 28.5 - - + +
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Residues in contact with ASN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA* 2.8 33.7 + - - +
17B THR 3.7 1.1 - - - +
19B TYR* 1.3 77.2 - - - +
21B LEU* 1.3 56.3 + - - +
23B ASN* 3.3 4.5 + - - +
24B LEU* 2.9 36.8 + - + +
318B GLU 4.6 0.8 + - - -
321B ALA* 3.7 4.2 - - - +
322B MET* 3.6 35.2 - - - +
325B ALA* 3.6 20.9 - - + -
397B ASN* 4.9 2.8 - - - +
398B ILE* 4.9 3.7 + - - +
399B ALA* 3.5 28.7 + - - +
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL* 3.7 33.2 - - + -
7B VAL* 4.7 3.1 - - + -
17B THR* 2.9 36.0 + - + +
18B ALA* 3.6 9.0 - - - +
20B ASN* 1.3 75.9 - - - +
22B ARG* 1.3 57.0 - - - +
24B LEU* 3.3 5.5 + - - +
25B MET* 2.9 33.1 + - - +
28B LEU* 4.0 13.4 - - + +
30B ILE* 3.8 10.1 - - + -
325B ALA* 3.7 34.5 - - + +
328B ILE* 3.9 23.8 - - + -
329B VAL* 4.2 4.7 - - + +
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ALA 2.9 18.4 + - - +
19B TYR* 3.7 7.4 - - - +
20B ASN 3.4 0.2 - - - -
21B LEU* 1.3 75.0 - - - +
23B ASN* 1.3 71.4 + - - +
25B MET 2.8 40.2 + - - -
26B PRO* 3.1 24.1 + - - +
28B LEU 2.8 29.5 + - - -
29B LYS* 4.5 0.4 - - - +
30B ILE* 3.5 28.4 - - + +
69B PHE* 2.8 36.0 + - + +
70B ASN* 2.8 33.2 + - - +
71B ILE* 4.4 5.1 - - + +
396B GLY 6.0 0.9 - - - +
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Residues in contact with ASN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR 2.9 24.5 + - - +
20B ASN* 4.0 4.4 - - - +
22B ARG* 1.3 85.2 + - - +
24B LEU* 1.3 65.1 + - + +
26B PRO* 4.7 6.1 - - - +
396B GLY 3.1 23.7 + - - +
397B ASN* 3.6 23.6 - - - +
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ASN* 2.9 22.3 + - + +
21B LEU 3.7 3.6 - - - +
23B ASN* 1.3 82.1 - - + +
25B MET* 1.3 56.6 + - - +
26B PRO* 4.0 5.1 - - - +
325B ALA* 3.9 36.8 - - + +
326B HIS* 4.0 36.3 - - + +
329B VAL* 4.0 17.9 - - + -
333B ARG* 3.2 24.5 + - - +
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Residues in contact with MET 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU 2.9 13.0 + - - +
22B ARG* 2.8 25.1 + - - +
23B ASN 3.4 0.4 - - - -
24B LEU* 1.3 79.0 - - - +
26B PRO* 1.3 63.8 - - + +
27B ASP* 3.3 20.6 + - - +
28B LEU* 3.4 32.6 - - + +
329B VAL* 3.5 31.2 - - + +
332B ILE* 4.0 22.9 - - + -
333B ARG* 3.3 43.1 - - + +
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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
------------------------------------------------------------
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