Contacts of the helix formed by residues 14 - 27 (chain A) in PDB entry 1EBF
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 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLY 3.7 1.6 - - - -
13A ALA* 1.3 77.6 - - - +
15A VAL* 1.3 60.7 + - - -
16A VAL 3.3 3.1 - - - -
17A GLY* 3.9 4.0 - - - +
18A SER* 2.8 32.0 + - - -
2109A NAD 3.3 30.3 + - - -
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Residues in contact with VAL 15 (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 GLY* 1.3 71.6 - - - +
16A VAL* 1.3 62.3 + - + +
18A SER* 4.0 4.2 + - - -
19A ALA* 3.9 9.4 + - - +
341A ALA* 3.7 29.9 - - + +
2109A NAD 3.1 38.3 + - - +
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Residues in contact with VAL 16 (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 VAL* 1.3 74.4 - - + +
17A GLY* 1.3 67.2 + - - +
19A ALA 3.3 1.7 + - - -
20A PHE* 3.0 21.0 + - - +
92A ASN* 4.3 16.8 - - - +
115A PRO* 4.9 3.4 - - + -
341A ALA* 4.7 11.4 - - - -
344A THR* 4.1 22.0 - - + -
345A ALA* 3.7 24.8 - - - +
348A VAL* 5.1 0.7 - - + -
2109A NAD 2.8 64.1 + - + +
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Residues in contact with GLY 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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12A GLY 3.5 23.2 - - - +
13A ALA* 4.1 1.3 - - - -
14A GLY 3.3 9.3 + - - +
16A VAL* 1.3 80.9 - - - +
18A SER* 1.3 55.7 + - - +
20A PHE* 3.3 4.0 - - - +
21A LEU* 3.0 31.6 + - - +
92A ASN* 3.7 18.8 + - - +
2109A NAD 3.9 2.6 + - - -
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Residues in contact with SER 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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13A ALA 4.0 6.3 - - - -
14A GLY 2.8 24.9 + - - -
15A VAL* 4.0 5.0 + - - -
17A GLY* 1.3 69.5 - - - -
19A ALA* 1.3 66.2 + - - +
21A LEU* 3.5 1.9 + - - +
22A ASP* 3.1 31.3 + - - +
59A TRP* 3.4 34.0 - - - -
60A LYS* 5.8 1.1 - - - -
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL 3.9 11.4 + - - +
16A VAL 3.3 8.1 + - - +
18A SER* 1.3 77.2 + - - +
20A PHE* 1.3 60.5 + - - +
22A ASP* 3.2 9.6 + - - +
23A GLN* 2.9 35.1 + - - +
341A ALA* 4.0 26.7 - - + +
342A ALA* 4.4 6.7 - - + +
345A ALA* 4.0 4.5 - - + -
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Residues in contact with PHE 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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8A VAL* 4.9 0.4 - - + -
10A VAL* 3.9 19.1 - - + -
16A VAL 3.0 14.3 + - - +
17A GLY 3.3 9.4 - - - +
18A SER 3.2 0.2 - - - -
19A ALA* 1.3 77.7 - - - +
21A LEU* 1.3 61.4 + - + +
23A GLN* 3.1 5.2 + - - +
24A LEU* 2.7 57.8 + - + +
90A VAL* 3.7 26.7 - - + -
92A ASN* 3.5 18.6 - - - +
345A ALA* 3.5 28.7 - - + +
348A VAL* 3.9 19.3 - - + -
349A LEU* 3.8 29.4 - - + -
352A VAL* 4.0 7.9 - - + -
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Residues in contact with LEU 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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10A VAL* 4.0 30.5 - - + -
12A GLY 4.4 3.4 - - - +
13A ALA* 4.3 4.7 - - + -
17A GLY 3.0 22.5 + - - +
18A SER 3.7 5.4 - - - +
19A ALA 3.3 0.2 - - - -
20A PHE* 1.3 80.6 - - + +
22A ASP* 1.3 57.3 + - - +
24A LEU* 4.4 3.6 - - + -
25A LEU* 2.9 41.5 + - + +
35A LEU* 4.1 14.1 - - + -
38A LEU* 3.7 37.7 - - + -
59A TRP* 3.9 35.9 - - + +
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Residues in contact with ASP 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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18A SER* 3.1 15.8 + - - +
19A ALA* 3.2 10.8 + - - +
21A LEU* 1.3 75.8 - - - +
23A GLN* 1.3 63.5 + - + +
25A LEU* 3.6 4.0 + - - +
26A ALA* 3.2 26.2 + - - +
57A SER 5.1 2.8 - - - +
59A TRP* 3.2 25.1 + - - +
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Residues in contact with GLN 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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19A ALA* 2.9 21.4 + - - +
20A PHE* 3.5 4.3 - - - +
22A ASP* 1.3 76.6 - - + +
24A LEU* 1.3 65.5 + - - +
26A ALA* 3.3 3.9 + - - +
27A MET* 3.1 24.3 + - - +
342A ALA* 3.0 38.6 + - - +
345A ALA* 3.7 11.5 - - - +
346A ALA* 3.1 12.2 + - - -
349A LEU* 3.6 12.8 - - + +
162B THR* 2.8 32.1 - - - +
327B ARG* 3.6 25.3 - - - +
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Residues in contact with LEU 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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8A VAL* 4.3 15.9 - - + -
10A VAL* 4.8 0.2 - - + -
20A PHE* 2.7 47.7 + - + +
21A LEU* 3.8 5.8 - - + +
23A GLN* 1.3 74.9 - - - +
25A LEU* 1.3 69.5 + - + +
26A ALA 3.3 0.7 + - - -
27A MET* 3.4 17.2 + - + +
33A TYR* 4.0 33.7 - - + +
35A LEU* 4.2 31.0 - - + +
349A LEU* 4.0 18.5 - - + +
352A VAL* 5.7 1.3 - - + -
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Residues in contact with LEU 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 LEU* 2.9 24.5 + - + +
22A ASP* 4.2 4.0 - - - +
24A LEU* 1.3 83.8 - - + +
26A ALA* 1.3 57.6 + - - +
27A MET 3.5 1.5 - - - +
35A LEU* 4.3 31.9 - - + -
55A VAL* 4.8 5.8 - - + -
56A GLY 4.3 20.9 - - - +
57A SER* 4.7 13.3 - - - -
59A TRP* 3.7 32.3 - - + -
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Residues in contact with ALA 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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22A ASP 3.2 18.1 + - - +
23A GLN* 4.2 2.9 - - - +
24A LEU 3.2 0.2 - - - -
25A LEU* 1.3 76.8 - - - +
27A MET* 1.3 64.2 + - - +
28A LYS* 3.5 18.4 + - - +
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Residues in contact with MET 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 GLN 3.1 17.0 + - - +
24A LEU* 3.4 14.5 + - - +
25A LEU 5.0 1.9 - - - +
26A ALA* 1.3 77.3 - - - +
28A LYS* 1.3 70.4 + - - +
29A SER* 3.9 6.4 + - - -
33A TYR* 4.6 22.8 - - + -
349A LEU* 3.2 39.9 - - + -
353A ILE* 3.1 40.2 - - + -
161B GLN* 3.6 26.5 - - + +
162B THR* 4.0 3.4 - - - +
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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