Contacts of the helix formed by residues 11 - 25 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9F GLY 3.4 5.5 + - - -
10F GLY* 1.3 78.0 - - - +
12F VAL* 1.3 66.4 + - - +
13F GLY 3.4 2.2 - - - -
14F GLY 4.0 1.2 - - - +
15F ILE* 2.9 25.1 + - - +
39F PHE* 3.7 12.8 - - - -
40F GLY 5.6 1.3 - - - -
441F FAD 3.2 27.0 + - - -
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Residues in contact with VAL 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F GLY* 1.3 71.5 - - - +
13F GLY* 1.3 58.2 + - - +
15F ILE* 4.4 0.6 - - - +
16F ALA* 3.0 33.6 + - - +
39F PHE* 3.7 23.1 - - + -
41F PHE* 5.9 1.1 - - + -
42F THR* 4.4 9.4 - - + +
43F PRO* 5.6 2.9 - - + -
314F GLY* 4.6 15.3 - - - +
317F ILE* 4.0 18.2 - - + -
318F GLU* 4.7 6.7 - - + -
389F PHE* 4.1 23.2 - - + -
441F FAD 3.1 38.5 + - - +
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Residues in contact with GLY 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F VAL* 1.3 75.0 - - - +
14F GLY* 1.3 52.9 + - - +
16F ALA* 3.9 2.6 - - - +
17F THR* 2.7 37.6 + - - -
104F ALA* 4.5 0.2 - - - -
292F VAL* 3.7 19.3 - - - -
317F ILE* 3.5 21.9 - - - +
441F FAD 2.8 19.2 + - - -
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Residues in contact with GLY 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F VAL* 3.5 20.6 - - - +
9F GLY 3.2 22.8 + - - -
11F GLY 3.5 4.2 + - - +
12F VAL 3.4 0.6 - - - -
13F GLY* 1.3 72.6 - - - +
15F ILE* 1.3 60.2 + - - +
17F THR* 3.9 1.2 - - - -
18F ALA* 2.9 31.0 + - - +
32F LEU* 4.1 2.2 - - - -
104F ALA* 3.5 12.6 - - - +
292F VAL* 4.8 0.2 - - - -
441F FAD 4.2 0.4 + - - -
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Residues in contact with ILE 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F GLY 4.2 0.4 + - - -
10F GLY 4.0 13.9 - - - +
11F GLY 2.9 19.3 + - - +
12F VAL* 4.4 1.3 - - - +
14F GLY* 1.3 70.9 - - - +
16F ALA* 1.3 61.2 + - - +
18F ALA* 3.3 2.8 + - - +
19F TYR* 2.8 62.7 + - + +
32F LEU* 3.9 13.9 - - + -
39F PHE* 4.3 12.1 - - + -
62F LEU* 3.9 21.3 - - + -
66F LEU* 3.8 27.8 - - + -
389F PHE* 6.3 0.4 - - + -
393F VAL* 4.5 10.8 - - + -
398F ILE* 4.2 10.8 - - + -
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Residues in contact with ALA 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F VAL* 3.0 22.4 + - + +
13F GLY* 3.9 0.9 - - - +
15F ILE* 1.3 77.8 - - - +
17F THR* 1.3 53.8 + - - +
19F TYR* 3.7 1.2 + - - +
20F ASN* 2.7 40.9 + - - +
318F GLU* 4.9 10.1 - - + -
321F ALA* 3.6 18.6 - - + -
398F ILE* 3.8 32.2 - - + +
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Residues in contact with THR 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F VAL* 5.1 0.9 - - + -
13F GLY 2.7 22.6 + - - -
14F GLY 4.0 2.7 - - - -
16F ALA* 1.3 74.6 - - - +
18F ALA* 1.3 59.6 + - - +
20F ASN* 3.3 3.6 + - - +
21F LEU* 2.9 47.5 + - + +
102F VAL* 4.0 24.2 - - + -
292F VAL* 3.6 10.6 - - - +
321F ALA* 3.4 26.1 - - - +
324F VAL* 3.9 26.6 - - + +
325F ALA 4.3 1.1 - - - +
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Residues in contact with ALA 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F VAL* 4.4 5.7 - - + +
14F GLY 2.9 18.9 + - - +
15F ILE* 3.7 3.8 - - - +
17F THR* 1.3 75.8 - - - +
19F TYR* 1.3 60.8 + - + +
21F LEU* 3.6 10.9 - - - +
22F ARG* 3.0 28.8 + - - +
30F ILE* 3.7 18.6 - - + +
32F LEU* 4.1 17.5 - - + -
71F ILE* 4.1 18.1 - - + +
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Residues in contact with TYR 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ILE* 2.8 40.5 + - + +
16F ALA 4.1 2.7 - - - +
18F ALA* 1.3 74.2 - - + +
20F ASN* 1.3 58.6 + - - +
22F ARG* 3.4 5.8 + - + +
23F ASN* 2.9 37.1 + - - +
65F LEU* 3.4 17.5 - - - +
66F LEU* 3.8 24.6 - - + +
69F PHE* 3.4 19.6 - + + -
71F ILE* 3.9 13.9 - - + -
392F LYS 3.7 5.4 - - - -
393F VAL* 2.6 33.6 + - - +
396F GLY* 3.5 30.5 - - - +
397F ASN 3.7 0.7 - - - -
398F ILE* 3.4 28.3 - - + +
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Residues in contact with ASN 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ALA* 2.7 33.3 + - - +
17F THR 3.3 1.1 + - - +
19F TYR* 1.3 75.1 - - - +
21F LEU* 1.3 64.3 + - - +
23F ASN* 3.4 6.0 + - - +
24F LEU* 3.0 31.3 + - + +
318F GLU 4.6 0.6 + - - -
321F ALA* 3.7 4.6 - - - +
322F MET* 3.6 34.1 - - - +
325F ALA* 3.5 20.9 - - + -
326F HIS* 6.5 0.2 - - + -
397F ASN* 5.0 2.1 - - - +
398F ILE* 5.2 3.4 + - - +
399F ALA* 3.5 29.0 + - - +
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Residues in contact with LEU 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F VAL* 3.8 31.9 - - + -
7F VAL* 4.6 3.4 - - + -
17F THR* 2.9 34.4 + - + +
18F ALA* 3.6 9.0 - - - +
20F ASN* 1.3 75.9 - - - +
22F ARG* 1.3 56.2 + - - +
24F LEU* 3.3 5.3 + - - +
25F MET* 2.9 34.5 + - - +
28F LEU* 4.0 12.4 - - + +
30F ILE* 3.8 11.2 - - + -
325F ALA* 3.7 33.6 - - + +
328F ILE* 3.8 26.9 - - + -
329F VAL* 4.2 4.0 - - + +
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Residues in contact with ARG 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ALA 3.0 17.6 + - - +
19F TYR* 3.7 7.9 - - + +
20F ASN 3.3 0.2 - - - -
21F LEU* 1.3 74.5 - - - +
23F ASN* 1.3 70.7 + - - +
25F MET 2.9 37.9 + - - -
26F PRO* 3.2 21.5 + - - +
28F LEU 2.8 30.1 + - - -
29F LYS* 4.5 0.4 - - - +
30F ILE* 3.5 31.5 - - + +
69F PHE* 2.8 35.1 + - + +
70F ASN* 2.7 36.9 + - - +
71F ILE* 4.5 4.7 - - + +
396F GLY 5.8 1.3 - - - +
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Residues in contact with ASN 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F TYR 2.9 21.1 + - - +
20F ASN* 4.0 5.5 - - - +
21F LEU 3.3 0.2 - - - -
22F ARG* 1.3 86.1 - - - +
24F LEU* 1.3 63.8 + - + +
26F PRO* 4.7 5.1 - - - +
396F GLY 3.0 23.8 + - - +
397F ASN* 3.7 25.8 - - - +
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Residues in contact with LEU 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ASN* 3.0 22.1 + - + +
21F LEU 3.7 3.8 - - - +
23F ASN* 1.3 80.4 - - + +
25F MET* 1.3 60.7 + - - +
26F PRO* 4.0 5.5 - - - +
325F ALA* 3.8 35.4 - - + +
326F HIS* 3.9 39.0 - - + +
329F VAL* 3.9 23.2 - - + +
333F ARG* 5.3 5.5 + - - -
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Residues in contact with MET 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F LEU 2.9 11.8 + - - +
22F ARG* 2.9 23.8 + - - +
24F LEU* 1.3 81.7 - - - +
26F PRO* 1.3 65.4 - - - +
27F ASP* 3.1 31.4 + - - +
28F LEU* 3.2 23.3 + - + +
329F VAL* 3.9 20.6 - - + +
332F ILE* 4.0 34.5 - - + -
333F ARG* 3.5 39.7 - - + +
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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