Contacts of the helix formed by residues 11 - 25 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLY 3.4 5.3 + - - -
10C GLY* 1.3 77.1 - - - +
12C VAL* 1.3 61.2 + - - -
13C GLY 3.4 2.0 - - - -
14C GLY 4.0 1.4 - - - +
15C ILE* 2.9 31.2 + - - +
39C PHE* 3.8 13.0 - - - -
40C GLY 5.6 2.2 - - - -
441C FAD 3.3 26.9 + - - -
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Residues in contact with VAL 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLY* 1.3 71.0 - - - +
13C GLY* 1.3 62.4 + - - +
15C ILE* 4.4 0.8 - - - +
16C ALA* 3.0 29.2 + - + +
39C PHE* 3.7 23.1 - - + -
41C PHE* 5.8 1.1 - - + -
42C THR* 4.8 6.1 - - - +
43C PRO* 5.5 7.0 - - + -
314C GLY* 4.6 14.8 - - - +
317C ILE* 4.2 18.2 - - + -
318C GLU* 4.7 7.6 - - + +
389C PHE* 4.2 21.7 - - + -
441C FAD 3.2 38.9 + - - +
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Residues in contact with GLY 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C VAL* 1.3 74.0 - - - +
14C GLY* 1.3 54.3 + - - +
16C ALA* 4.0 2.0 - - - +
17C THR* 2.7 38.4 + - - -
104C ALA* 4.0 4.3 - - - -
292C VAL* 3.5 13.6 - - - +
317C ILE* 3.5 21.5 - - - +
441C FAD 2.7 20.7 + - - -
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Residues in contact with GLY 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 3.5 19.7 - - - +
9C GLY 3.3 22.6 + - - -
11C GLY 3.5 4.2 + - - +
13C GLY* 1.3 73.5 - - - +
15C ILE* 1.3 59.0 + - - +
17C THR* 3.4 1.2 + - - -
18C ALA* 3.0 31.2 + - - +
32C LEU* 4.1 2.7 - - - -
104C ALA* 3.5 12.5 - - - +
441C FAD 4.2 0.6 + - - -
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Residues in contact with ILE 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLY 4.3 0.2 + - - -
10C GLY* 4.0 13.5 - - - +
11C GLY 2.9 23.5 + - - +
12C VAL* 4.4 1.6 - - - +
14C GLY* 1.3 71.5 - - - +
16C ALA* 1.3 58.4 + - - +
18C ALA* 3.4 1.2 + - - +
19C TYR* 2.9 61.6 + - + +
32C LEU* 4.0 20.0 - - + -
39C PHE* 4.2 12.3 - - + -
62C LEU* 3.9 29.8 - - + -
66C LEU* 4.1 13.9 - - + -
389C PHE* 6.2 0.9 - - + -
393C VAL* 4.5 11.0 - - + -
398C ILE* 4.1 11.2 - - + -
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Residues in contact with ALA 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C VAL* 3.0 21.9 + - + +
13C GLY* 4.7 0.4 - - - -
15C ILE* 1.3 76.8 - - - +
17C THR* 1.3 58.9 + - - +
19C TYR* 3.9 0.9 - - - +
20C ASN* 2.9 38.5 + - - +
318C GLU* 4.9 10.8 - - + -
321C ALA* 3.6 18.2 - - + -
389C PHE* 5.8 0.2 - - + -
398C ILE* 3.8 33.3 - - + +
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Residues in contact with THR 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C VAL* 5.2 1.1 - - + -
13C GLY 2.7 25.2 + - - -
14C GLY 3.9 2.9 - - - -
16C ALA* 1.3 72.1 - - - +
18C ALA* 1.3 61.6 + - - +
20C ASN* 3.4 1.8 + - - +
21C LEU* 2.9 43.6 + - + +
102C VAL* 4.0 23.6 - - + -
292C VAL* 3.5 12.3 - - - +
321C ALA* 3.3 26.9 - - - +
324C VAL* 3.9 27.1 - - + -
325C ALA 4.4 2.9 - - - +
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Residues in contact with ALA 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 4.3 5.8 - - + +
14C GLY 3.0 18.2 + - - +
15C ILE 3.8 3.1 - - - +
17C THR* 1.3 77.2 - - - +
19C TYR* 1.3 61.8 + - + +
21C LEU* 3.4 10.7 + - - +
22C ARG* 2.9 29.8 + - - +
30C ILE* 3.7 18.6 - - + +
32C LEU* 4.2 17.3 - - + -
71C ILE* 4.0 16.6 - - + -
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Residues in contact with TYR 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 2.9 38.2 + - + +
16C ALA 3.9 2.9 - - - +
18C ALA* 1.3 75.5 - - + +
20C ASN* 1.3 65.9 + - - +
22C ARG* 3.3 5.8 + - + +
23C ASN* 3.0 31.0 + - - +
65C LEU* 3.5 10.4 - - - +
66C LEU* 3.7 25.8 - - + +
69C PHE* 3.3 24.9 - + + -
71C ILE* 4.0 11.9 - - + -
392C LYS 3.6 6.1 - - - -
393C VAL* 2.6 32.9 + - - +
396C GLY* 3.5 31.2 - - - +
397C ASN* 3.6 0.7 - - - -
398C ILE* 3.5 28.3 - - + +
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Residues in contact with ASN 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ALA* 2.9 29.2 + - - +
17C THR 3.6 1.3 - - - +
19C TYR* 1.3 75.8 - - - +
21C LEU* 1.3 62.6 + - - +
23C ASN* 3.2 5.9 + - - +
24C LEU* 3.0 30.0 + - + +
318C GLU 4.6 0.8 + - - -
321C ALA* 3.5 8.1 - - - +
322C MET* 3.4 39.2 - - - +
325C ALA* 3.5 20.4 - - + -
326C HIS* 6.5 0.2 - - + -
397C ASN* 4.9 2.1 - - - +
398C ILE* 5.0 3.2 + - - +
399C ALA* 3.6 28.2 + - - +
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Residues in contact with LEU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C VAL* 3.8 32.8 - - + -
7C VAL* 4.7 3.1 - - + -
17C THR* 2.9 41.4 + - + +
18C ALA* 3.6 8.7 - - - +
20C ASN* 1.3 72.0 - - - +
22C ARG* 1.3 57.6 + - - +
24C LEU* 3.4 3.7 + - - +
25C MET* 2.9 34.7 + - - +
28C LEU* 4.0 13.5 - - + +
30C ILE* 4.0 10.5 - - + -
325C ALA* 3.7 34.1 - - + +
328C ILE* 3.9 25.8 - - + -
329C VAL* 4.1 4.5 - - + -
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Residues in contact with ARG 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ALA 2.9 17.3 + - - +
19C TYR* 3.6 5.8 - - - +
20C ASN 3.3 0.2 - - - -
21C LEU* 1.3 75.7 - - - +
23C ASN* 1.3 70.2 + - - +
25C MET 3.0 35.9 + - - -
26C PRO* 3.4 20.6 + - - +
28C LEU 2.8 29.7 + - - -
29C LYS* 4.6 0.6 - - - +
30C ILE* 3.5 32.8 - - + +
69C PHE* 2.8 35.8 + - + +
70C ASN* 2.8 34.8 + - - +
71C ILE* 4.3 6.9 - - + +
396C GLY 5.9 0.9 - - - +
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Residues in contact with ASN 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TYR 3.0 22.5 + - - +
20C ASN* 4.0 4.4 - - - +
22C ARG* 1.3 85.2 + - - +
24C LEU* 1.3 67.0 + - + +
26C PRO* 4.6 6.4 - - - +
396C GLY 3.0 24.3 + - - +
397C ASN* 3.6 24.3 - - - +
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ASN* 3.0 21.0 + - + +
21C LEU 3.8 3.4 - - - +
23C ASN* 1.3 81.1 - - + +
25C MET* 1.3 58.3 + - - +
26C PRO* 3.9 5.6 - - - +
325C ALA* 4.0 14.6 - - + +
326C HIS* 3.9 56.5 - - + +
329C VAL* 3.9 23.3 - - + +
333C ARG* 5.4 5.0 + - - -
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Residues in contact with MET 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LEU 2.9 13.1 + - - +
22C ARG* 3.0 19.5 + - - +
23C ASN 3.4 0.2 - - - -
24C LEU* 1.3 80.8 - - - +
26C PRO* 1.4 69.6 - - - +
27C ASP* 3.1 22.3 + - + +
28C LEU* 3.3 21.8 - - + +
329C VAL* 3.5 35.7 - - + +
332C ILE* 3.9 36.1 - - + -
333C ARG* 3.6 27.4 - - + +
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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
------------------------------------------------------------
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