Contacts of the helix formed by residues 16 - 29 (chain C) in PDB entry 1EFP
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 16 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C LEU* 3.0 21.7 + - + +
15C ASN* 1.3 71.4 - - - +
17C ASP* 1.3 59.3 + - - +
19C THR* 3.4 0.6 + - - -
20C ALA* 2.7 52.3 + - - +
47C GLU* 3.5 32.8 + - - +
50C LYS 5.6 0.8 + - - -
51C ILE* 4.2 22.5 - - + +
154C ALA* 4.4 10.7 + - - +
156C GLY* 3.1 18.0 - - - +
157C GLU* 3.0 54.7 + - - +
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Residues in contact with ASP 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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15C ASN* 3.3 6.8 + - - +
16C ARG* 1.3 80.2 + - - +
18C ALA* 1.3 59.6 + - - +
20C ALA* 3.8 4.5 - - - +
21C LYS* 2.7 66.9 + - - +
149C THR* 5.9 0.7 - - - -
154C ALA* 3.6 13.2 - - - +
191C THR 4.4 2.8 - - - +
192C SER* 3.4 33.3 - - - +
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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
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8C GLU* 4.1 7.2 - - + -
15C ASN* 2.9 26.0 + - - +
17C ASP* 1.3 76.1 + - - +
19C THR* 1.3 67.0 + - - +
21C LYS* 3.3 2.8 + - - +
22C ALA* 3.0 24.3 + - - +
90C PRO* 3.9 24.1 - - + +
92C THR* 4.8 6.5 - - + -
149C THR* 3.9 15.0 - - + +
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Residues in contact with THR 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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5C LEU* 4.5 7.0 - - + -
7C GLY* 4.2 15.0 - - - -
8C GLU* 3.4 18.9 + - - +
14C LEU* 3.4 21.0 - - + +
15C ASN 2.7 18.1 + - - -
16C ARG* 3.8 4.0 - - - -
18C ALA* 1.3 76.3 - - - +
20C ALA* 1.3 58.4 + - - +
22C ALA* 3.3 6.9 + - - +
23C VAL* 3.0 37.8 + - + +
34C VAL* 4.3 13.5 - - + -
48C ALA* 5.3 0.7 - - + -
51C ILE* 4.1 17.0 - - + -
90C PRO* 5.0 2.0 - - - -
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Residues in contact with ALA 20 (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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16C ARG* 2.7 42.4 + - - +
17C ASP 3.8 0.2 - - - +
19C THR* 1.3 73.0 - - - +
21C LYS* 1.3 57.0 + - - +
23C VAL* 3.2 3.6 + - - +
24C ALA* 2.8 29.6 + - - +
51C ILE* 4.0 15.2 - - + +
154C ALA* 3.8 28.9 - - + +
155C ALA 3.8 7.4 - - - +
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Residues in contact with LYS 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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17C ASP* 2.7 52.8 + - - +
18C ALA 3.3 3.6 + - - +
20C ALA* 1.3 72.9 - - - +
22C ALA* 1.3 63.2 + - - +
24C ALA 3.9 0.4 - - - -
25C ALA* 3.1 21.8 + - - +
149C THR* 3.3 33.4 - - - +
150C ALA* 5.6 1.8 - - - +
152C PHE* 3.0 39.9 - - + +
153C ASP* 3.7 9.4 - - - +
154C ALA* 3.4 22.4 - - - +
191C THR 5.1 4.6 + - - -
192C SER* 5.3 1.6 - - - +
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Residues in contact with ALA 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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5C LEU* 3.9 26.0 - - + -
18C ALA 3.0 16.6 + - - +
19C THR 3.5 5.2 - - - +
21C LYS* 1.3 74.5 - - - +
23C VAL* 1.3 66.4 + - - +
25C ALA* 2.8 17.8 + - - +
26C VAL* 2.9 14.9 + - - +
89C ALA 4.7 0.2 - - - -
90C PRO* 4.1 20.4 - - + -
147C ILE* 4.5 14.6 - - + +
149C THR* 4.6 1.0 - - - +
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Residues in contact with VAL 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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5C LEU* 4.1 4.5 - - + -
19C THR* 3.0 25.5 + - + +
20C ALA 3.5 6.7 - - - +
22C ALA* 1.3 73.1 - - - +
24C ALA* 1.3 58.8 + - - +
26C VAL* 4.0 8.1 - - - -
27C LYS* 2.8 33.4 + - - +
32C VAL* 4.2 17.9 - - + -
34C VAL* 4.2 25.6 - - + -
51C ILE* 4.5 14.1 - - + -
52C ALA 4.0 20.4 - - - +
53C GLY* 4.2 4.3 - - - -
54C VAL* 4.2 15.0 - - + +
155C ALA 5.2 0.4 - - - +
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Residues in contact with ALA 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 ALA 2.8 14.8 + - - +
21C LYS 3.8 3.1 - - - +
23C VAL* 1.3 77.2 - - - +
25C ALA* 1.3 63.4 + - - +
27C LYS* 3.8 25.6 - - - +
28C ALA* 5.0 0.9 + - - +
152C PHE* 5.1 2.9 - - + -
153C ASP 3.2 28.9 - - - +
155C ALA* 3.6 19.5 + - + -
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Residues in contact with ALA 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 LYS 3.1 12.1 + - - +
22C ALA 2.8 10.7 + - - +
24C ALA* 1.3 81.7 - - - +
26C VAL* 1.3 57.0 + - - +
28C ALA* 4.7 7.4 + - - +
29C LEU* 5.6 0.2 - - - +
117C ILE* 3.5 18.1 - - + +
147C ILE* 3.7 15.0 - - + -
152C PHE* 3.5 46.1 - - + -
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Residues in contact with VAL 26 (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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3C VAL* 3.5 24.8 - - + +
5C LEU* 3.4 33.2 - - + -
22C ALA 2.9 10.4 + - - +
23C VAL 3.7 3.8 - - - +
25C ALA* 1.3 77.3 - - + +
27C LYS* 1.3 59.7 + - - +
28C ALA* 2.8 13.1 + - - -
29C LEU* 2.8 37.8 + - + +
30C GLY 4.3 1.0 + - - -
32C VAL* 3.9 13.3 - - + +
88C ALA* 5.2 2.7 - - + -
117C ILE* 4.3 6.5 - - + -
145C PHE* 4.6 11.9 - - + -
147C ILE* 5.2 5.4 - - + -
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Residues in contact with LYS 27 (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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23C VAL* 2.8 24.0 + - + +
24C ALA* 3.8 20.4 - - - +
25C ALA 3.7 0.2 - - - -
26C VAL* 1.3 71.3 - - - +
28C ALA* 1.3 59.8 + - + +
29C LEU 3.1 5.1 + - - -
30C GLY 3.3 15.1 + - - +
32C VAL* 3.6 18.8 - - + -
52C ALA* 3.1 35.3 + - - +
53C GLY* 3.9 11.2 - - - +
155C ALA* 4.8 10.6 - - - +
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Residues in contact with ALA 28 (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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24C ALA 5.0 0.9 + - - +
25C ALA 4.7 6.7 + - - +
26C VAL 2.8 5.7 + - - -
27C LYS* 1.3 78.9 - - + +
29C LEU* 1.3 68.1 + - + +
30C GLY 3.7 0.7 - - - -
117C ILE* 6.4 0.9 - - + -
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Residues in contact with LEU 29 (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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2C ALA 4.5 11.4 + - - +
3C VAL* 4.9 4.9 - - + -
25C ALA 5.6 0.2 - - - +
26C VAL* 2.8 34.3 + - + +
28C ALA* 1.3 89.0 - - + +
30C GLY* 1.3 58.3 + - - +
86C HIS* 4.0 33.6 + - + +
117C ILE* 3.7 29.2 - - + -
119C ASP* 3.4 33.0 - - - +
120C ALA* 3.7 11.9 - - + +
123C PHE* 5.1 0.4 - - + -
145C PHE* 4.5 2.5 - - + -
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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