Contacts of the helix formed by residues 19 - 32 (chain A) in PDB entry 5EN4
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 ARG 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLY 3.7 6.6 - - - +
17A GLY 3.4 1.0 - - - -
18A GLY* 1.3 78.9 - - - +
20A GLY* 1.3 69.8 + - - +
22A GLY 3.4 5.4 + - - -
23A ALA* 3.2 16.7 + - - -
42A ASP* 5.6 5.6 - - - -
45A GLY* 5.7 1.3 - - - -
190A PRO* 3.5 25.3 - - + +
191A LEU* 3.8 6.1 - - - +
194A GLU* 3.1 39.0 + - - -
301A NAD 2.9 65.2 + - - +
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Residues in contact with GLY 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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19A ARG* 1.3 77.8 - - - +
21A ILE* 1.3 64.1 + - - -
23A ALA* 3.2 3.5 + - - +
24A GLY 3.1 16.5 + - - -
189A THR* 4.0 4.3 - - - -
190A PRO* 3.8 24.6 - - - +
221A PRO* 3.6 15.5 - - - +
301A NAD 3.6 10.1 - - - -
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Residues in contact with ILE 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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20A GLY* 1.3 71.6 - - - -
22A GLY* 1.3 64.0 + - - +
24A GLY* 3.0 3.6 + - - -
25A ILE* 2.9 26.9 + - + +
89A ASN* 3.4 17.9 - - - +
139A ILE* 4.8 3.1 - - + -
184A PRO* 4.5 7.9 - - + -
187A ILE* 3.9 27.4 - - + -
189A THR* 3.8 10.7 - - + +
221A PRO* 4.0 7.6 - - + +
224A VAL* 3.7 30.5 - - + -
301A NAD 2.9 59.2 + - + +
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Residues in contact with GLY 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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14A VAL* 3.8 6.8 - - - +
16A GLY 3.5 8.7 - - - -
17A GLY* 3.8 9.2 - - - -
19A ARG 3.4 2.8 + - - -
20A GLY 3.2 1.0 - - - -
21A ILE* 1.3 78.7 - - - +
23A ALA* 1.3 55.8 + - - +
25A ILE* 3.2 5.7 + - - +
26A VAL* 2.9 30.7 + - - +
89A ASN* 3.4 29.2 - - - +
301A NAD 4.4 0.2 + - - -
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Residues in contact with ALA 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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17A GLY 3.3 19.3 + - - +
18A GLY 4.1 0.7 - - - +
19A ARG* 3.2 27.2 + - - -
20A GLY 3.2 4.5 + - - +
22A GLY* 1.3 75.5 - - - +
24A GLY* 1.3 58.2 + - - +
26A VAL* 3.4 2.6 + - - +
27A ARG* 3.0 39.4 + - - +
49A LEU* 3.8 18.1 - - + +
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Residues in contact with GLY 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 GLY 3.1 7.5 + - - -
21A ILE 3.0 7.8 + - - -
23A ALA* 1.3 78.1 - - - +
25A ILE* 1.3 56.7 + - - +
27A ARG* 3.5 9.8 + - - +
28A ALA* 3.0 28.2 + - - +
221A PRO* 4.0 28.6 - - - +
222A ALA* 4.6 4.8 - - - -
225A GLY* 4.0 2.4 - - - -
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Residues in contact with ILE 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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14A VAL* 4.0 15.3 - - + -
21A ILE* 2.9 37.0 + - + +
22A GLY* 3.5 9.0 - - - +
24A GLY* 1.3 74.2 - - - +
26A VAL* 1.3 65.7 + - - +
28A ALA* 3.2 1.7 + - - +
29A PHE* 3.0 48.2 + - + -
87A VAL* 3.9 26.0 - - + -
89A ASN* 4.4 3.8 - - + +
139A ILE* 4.0 15.7 - - + -
224A VAL* 4.3 3.6 - - + -
225A GLY* 3.9 23.6 - - - +
228A ALA* 4.2 9.6 - - + -
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Residues in contact with VAL 26 (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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14A VAL* 3.9 24.5 - - + -
17A GLY* 3.9 14.8 - - - +
22A GLY 2.9 18.0 + - - +
23A ALA* 3.4 9.2 + - - +
25A ILE* 1.3 77.0 - - - +
27A ARG* 1.3 62.9 + - - +
29A PHE* 3.3 2.0 + - - +
30A VAL* 3.0 26.7 + - + +
36A VAL* 4.0 20.0 - - + +
38A ILE* 4.0 27.1 - - + -
49A LEU* 4.4 3.8 - - + -
53A LEU* 3.9 22.2 - - + -
56A ALA* 4.4 1.1 - - + -
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Residues in contact with ARG 27 (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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23A ALA* 3.0 26.4 + - - +
24A GLY* 3.8 7.9 - - - +
26A VAL* 1.3 76.1 - - - +
28A ALA* 1.3 63.8 + - - +
30A VAL* 3.4 2.7 + - - +
31A ASN* 3.0 36.9 + - - +
49A LEU* 3.4 18.9 - - + +
52A GLU* 2.8 44.2 + - - -
53A LEU* 4.0 25.7 - - + +
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Residues in contact with ALA 28 (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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24A GLY 3.0 18.7 + - - +
25A ILE 3.2 4.0 + - - +
27A ARG* 1.3 76.8 - - - +
29A PHE* 1.3 61.8 + - - +
31A ASN* 3.4 9.6 + - - +
32A SER* 3.1 25.6 + - - -
222A ALA* 5.2 2.2 - - - +
225A GLY* 3.6 31.9 - - - +
226A ALA* 4.2 2.5 - - - +
229A VAL* 3.8 7.7 - - + +
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Residues in contact with PHE 29 (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 TYR* 3.7 31.2 - + + -
12A VAL* 3.7 23.3 - - + -
14A VAL* 4.9 1.1 - - + -
25A ILE* 3.0 45.6 + - + +
26A VAL 3.9 0.4 - - - +
28A ALA* 1.3 74.4 - - - +
30A VAL* 1.3 65.0 + - - +
32A SER* 3.1 11.8 + - - +
33A GLY 3.3 0.2 + - - -
34A ALA* 3.1 23.5 + - + +
36A VAL* 3.7 19.7 - - + -
85A CYS* 4.2 10.5 - - - -
87A VAL* 4.1 9.9 - - + -
137A ILE* 4.6 0.4 - - + -
228A ALA* 3.8 31.6 - - + -
229A VAL* 4.0 16.6 - - + -
232A ALA* 3.7 16.6 - - + -
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Residues in contact with VAL 30 (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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26A VAL* 3.0 21.1 + - + +
27A ARG* 3.8 6.1 - - - +
29A PHE* 1.3 74.0 - - - +
31A ASN* 1.3 67.6 + - - +
33A GLY* 3.0 14.9 + - - -
34A ALA 3.9 11.9 + - - +
36A VAL* 3.8 16.4 - - + -
53A LEU* 4.3 27.4 - - + -
54A PRO* 5.1 9.2 - - + -
55A GLY* 5.2 6.3 - - - -
56A ALA* 4.2 25.8 - - + +
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Residues in contact with ASN 31 (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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4A GLY* 3.3 22.2 + - - +
27A ARG* 3.0 28.3 + - - +
28A ALA* 3.7 8.1 - - - +
29A PHE 3.2 0.2 - - - -
30A VAL* 1.3 82.4 - - - +
32A SER* 1.3 57.5 + - - +
33A GLY 3.3 1.1 + - - -
53A LEU* 5.8 2.6 - - - +
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Residues in contact with SER 32 (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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4A GLY* 3.7 10.1 - - - +
6A ARG* 3.5 28.6 + - - +
7A TYR* 2.9 33.0 + - - -
8A ALA 3.4 1.2 + - - -
28A ALA 3.1 16.5 + - - -
29A PHE* 3.1 8.3 + - - -
31A ASN* 1.3 76.0 - - - +
33A GLY* 1.3 57.8 + - - +
34A ALA 3.5 2.0 - - - -
229A VAL* 3.5 23.8 - - - +
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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