Contacts of the helix formed by residues 16 - 29 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.0 23.7 + - + +
15A ASN* 1.3 72.0 - - - +
17A ASP* 1.3 60.1 + - - +
19A THR* 4.4 0.9 - - - -
20A ALA* 2.8 51.4 + - - +
47A GLU* 4.0 29.3 + - - +
50A LYS 6.1 0.2 - - - -
51A ILE* 4.1 21.8 - - + +
154A ALA* 4.1 12.3 + - - +
155A ALA 3.9 5.3 + - - -
156A GLY* 3.2 19.0 - - - +
157A GLU* 2.9 51.7 + - - +
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Residues in contact with ASP 17 (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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15A ASN* 3.3 8.2 + - - +
16A ARG* 1.3 80.8 - - - +
18A ALA* 1.3 60.4 + - - +
20A ALA* 3.6 4.5 - - - +
21A LYS* 2.7 67.4 + - - +
149A THR* 5.9 0.5 - - - -
154A ALA* 3.4 13.7 - - - +
191A THR* 4.3 4.9 + - - +
192A SER* 3.4 31.2 + - - -
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Residues in contact with ALA 18 (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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8A GLU* 4.2 7.9 - - + -
15A ASN* 3.0 24.7 + - - +
17A ASP* 1.3 75.5 - - - +
19A THR* 1.3 67.4 + - - +
21A LYS* 3.2 5.2 + - - +
22A ALA* 2.9 23.4 + - - +
90A PRO* 3.9 24.9 - - + -
92A THR* 4.8 6.1 - - + -
149A THR* 3.9 15.2 - - + +
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Residues in contact with THR 19 (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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5A LEU* 4.2 12.3 - - + -
7A GLY* 3.9 23.1 - - - -
8A GLU* 3.4 17.6 + - - +
14A LEU* 3.8 13.9 - - + +
15A ASN 2.7 19.3 + - - -
16A ARG 4.1 2.2 - - - -
18A ALA* 1.3 76.7 - - - +
20A ALA* 1.3 56.7 + - - +
22A ALA* 3.3 6.3 + - - +
23A VAL* 2.9 36.3 + - + +
34A VAL* 4.3 17.5 - - + -
48A ALA* 5.5 0.7 - - + -
51A ILE* 4.5 11.4 - - + -
90A PRO* 5.2 1.3 - - - -
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Residues in contact with ALA 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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16A ARG* 2.8 37.9 + - - +
17A ASP 3.6 3.8 - - - +
19A THR* 1.3 76.4 - - - +
21A LYS* 1.3 53.5 + - - +
23A VAL* 3.2 3.3 + - - +
24A ALA* 2.8 36.0 + - - +
51A ILE* 4.2 12.3 - - + +
154A ALA* 3.6 18.6 - - + -
155A ALA 3.8 16.8 - - - +
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Residues in contact with LYS 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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17A ASP* 2.7 59.3 + - - +
18A ALA 3.6 4.5 - - - +
20A ALA* 1.3 75.8 - - - +
22A ALA* 1.3 57.0 + - - +
24A ALA* 3.5 2.1 - - - +
25A ALA* 2.9 28.8 + - - +
147A ILE* 5.1 1.1 - - - -
149A THR* 3.4 35.0 + - - +
150A ALA* 5.8 1.9 - - - +
152A PHE* 3.2 33.6 - - + +
153A ASP* 4.0 4.9 - - - +
154A ALA* 3.4 25.1 - - + +
191A THR 4.5 10.1 + - - -
192A SER* 4.9 3.4 + - - +
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Residues in contact with ALA 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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5A LEU* 3.8 24.5 - - + -
18A ALA 2.9 14.0 + - - +
19A THR 3.5 7.4 - - - +
20A ALA 3.2 0.2 - - - -
21A LYS* 1.3 73.6 - - - +
23A VAL* 1.3 66.4 + - - +
25A ALA* 3.0 8.4 + - - +
26A VAL* 3.0 24.9 + - - +
89A ALA 4.6 2.2 - - - -
90A PRO* 4.3 23.1 - - + -
147A ILE* 4.4 11.1 - - + +
149A THR* 4.7 0.6 - - - +
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Residues in contact with VAL 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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5A LEU* 4.4 4.5 - - + -
19A THR* 2.9 25.8 + - + +
20A ALA* 3.6 5.8 - - - +
22A ALA* 1.3 73.5 - - - +
24A ALA* 1.3 55.9 + - - +
26A VAL* 3.8 8.3 - - - -
27A LYS* 2.8 35.5 + - - +
32A VAL* 4.0 28.0 - - + -
34A VAL* 4.0 18.6 - - + -
51A ILE* 4.7 13.7 - - + -
52A ALA 4.4 6.7 - - - +
53A GLY* 4.0 27.6 - - - -
54A VAL* 4.1 4.5 - - + +
155A ALA 5.6 0.4 - - - +
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Residues in contact with ALA 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 ALA 2.8 15.8 + - - +
21A LYS 3.5 3.8 - - - +
23A VAL* 1.3 79.0 - - - +
25A ALA* 1.3 61.3 + - - +
27A LYS* 3.6 26.8 - - - +
28A ALA* 5.9 0.3 - - - +
152A PHE* 5.2 2.7 - - + -
153A ASP 3.1 29.2 - - - +
155A ALA* 3.9 16.8 + - + +
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Residues in contact with ALA 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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21A LYS 2.9 17.7 + - - +
22A ALA 3.0 5.3 + - - +
24A ALA* 1.3 78.9 - - - +
26A VAL* 1.3 58.6 + - - +
27A LYS 3.7 0.2 - - - -
28A ALA* 4.7 7.3 + - - +
29A LEU* 5.5 0.3 - - - +
117A ILE* 3.3 17.9 - - + +
147A ILE* 3.9 16.4 - - + -
152A PHE* 3.4 45.1 - - + -
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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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3A VAL* 3.4 27.8 - - + +
5A LEU* 3.4 24.7 - - + -
22A ALA 3.0 19.4 + - - +
23A VAL* 3.6 6.1 - - - +
25A ALA* 1.3 76.6 - - + +
27A LYS* 1.3 66.0 + - - +
28A ALA* 3.0 4.0 - - - -
29A LEU* 2.8 37.9 + - + +
30A GLY 4.3 1.0 + - - -
32A VAL* 3.9 12.6 - - + +
88A ALA* 5.1 2.5 - - + -
117A ILE* 4.1 8.1 - - + -
145A PHE* 4.7 9.6 - - + -
147A ILE* 5.3 4.7 - - + -
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Residues in contact with LYS 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 VAL* 2.8 18.4 + - + +
24A ALA* 3.6 32.1 - - - +
26A VAL* 1.3 71.4 - - - +
28A ALA* 1.3 62.3 + - + +
29A LEU 2.9 6.4 + - - -
30A GLY* 3.1 17.4 + - - +
32A VAL* 3.6 17.9 - - + -
52A ALA* 3.1 29.6 + - - +
53A GLY* 4.5 10.4 - - - +
155A ALA* 4.3 15.9 - - - +
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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 ALA 5.9 0.2 - - - +
25A ALA 4.7 6.7 + - - +
26A VAL 2.9 2.3 + - - -
27A LYS* 1.3 82.6 - - + +
29A LEU* 1.3 67.4 + - + +
30A GLY 3.7 0.2 - - - -
117A ILE* 6.6 0.4 - - + -
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Residues in contact with LEU 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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2A ALA 4.9 9.0 + - - +
3A VAL* 4.8 4.9 - - + -
25A ALA 5.5 0.2 - - - +
26A VAL* 2.8 34.5 + - + +
28A ALA* 1.3 85.2 - - + +
30A GLY* 1.3 58.5 + - - +
86A HIS* 3.4 37.3 + - + +
117A ILE* 3.8 22.7 - - + -
119A ASP* 3.4 33.7 - - - +
120A ALA* 3.8 10.8 - - + +
145A PHE* 4.3 5.4 - - + -
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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
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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