Contacts of the helix formed by residues 21 - 32 (chain A) in PDB entry 1EYN
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 ALA 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A GLY* 1.3 68.1 - - - -
22A LYS* 1.3 65.3 + - - +
23A ASN* 4.2 3.4 - - + +
24A ALA 4.0 7.6 - - - +
25A ALA* 2.9 20.6 + - - +
45A PRO* 4.5 1.1 - - - -
190A GLU* 4.5 11.2 - - + +
228A VAL* 3.6 6.1 - - - +
229A LEU* 2.9 35.9 + - + +
230A PRO 3.9 0.7 - - - +
231A ASP* 3.6 26.3 - - + +
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Residues in contact with LYS 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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20A GLY 3.4 5.9 + - - -
21A ALA* 1.3 71.2 - - - +
23A ASN* 1.3 74.5 + - - +
25A ALA* 4.3 3.4 - - - -
26A LEU* 2.9 45.7 + - + +
45A PRO* 3.9 9.0 - - + -
47A LEU* 3.8 27.6 - - + +
49A ASP* 3.1 35.1 + - + -
50A ILE* 4.3 8.7 - - + -
231A ASP* 4.8 5.1 + - - +
370A LEU* 5.9 2.0 - - - +
371A ARG* 6.2 1.6 - - - +
397A ARG* 3.4 31.1 + - - +
398A GLY* 4.7 6.6 - - - +
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Residues in contact with ASN 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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21A ALA* 3.1 3.1 - - + +
22A LYS* 1.3 96.4 - - - +
24A ALA* 1.3 55.5 - - - +
26A LEU* 4.6 7.9 - - - +
27A PRO* 3.1 20.9 - - - +
95A TRP* 4.9 3.9 - - - -
163A VAL* 6.0 1.4 - - - +
190A GLU* 3.4 27.1 - - + +
233A ILE* 6.1 1.8 - - - +
305A ASP* 4.9 8.3 + - - -
371A ARG* 4.6 15.6 - - - +
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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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21A ALA* 3.0 7.1 + - + +
23A ASN* 1.3 76.2 - - - +
25A ALA* 1.3 68.5 + - - +
26A LEU 3.2 1.6 - - - -
27A PRO* 3.1 8.5 - - - +
28A ILE* 3.1 27.9 + - - +
190A GLU* 3.7 17.4 - - + +
193A ASP* 3.7 15.9 - - + +
228A VAL* 3.9 2.7 - - + -
229A LEU* 3.4 32.5 - - + -
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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 ALA 2.9 16.0 + - - +
22A LYS* 3.8 5.6 - - - +
24A ALA* 1.3 78.2 - - - +
26A LEU* 1.3 56.7 + - - +
28A ILE* 3.7 2.2 - - - +
29A LEU* 2.8 37.6 + - + +
41A ILE* 5.5 0.4 - - - -
44A VAL* 4.1 18.4 - - + -
45A PRO* 4.3 3.8 - - + -
50A ILE* 3.9 19.1 - - + -
228A VAL* 3.9 21.6 - - + +
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Residues in contact with LEU 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 LYS* 2.9 30.6 + - + +
23A ASN* 4.6 8.5 - - - +
25A ALA* 1.3 76.3 - - - +
27A PRO* 1.4 70.3 - - + +
29A LEU* 3.1 4.7 + - + +
30A PHE* 3.1 30.9 + - + -
49A ASP* 3.7 36.1 - - + +
50A ILE* 4.0 14.4 - - + -
53A THR* 3.1 29.8 - - + +
90A MET* 4.4 2.5 - - - -
92A ALA* 4.5 15.5 - - + -
95A TRP* 3.9 12.8 - - + -
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Residues in contact with PRO 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 ASN 3.1 26.9 - - - +
24A ALA* 3.1 15.7 - - - +
26A LEU* 1.4 91.4 - - + +
28A ILE* 1.3 54.4 + - - -
30A PHE* 3.4 3.6 + - + +
31A ALA* 2.9 28.8 + - - +
95A TRP* 3.5 25.8 - - + -
163A VAL* 6.5 0.2 - - + -
167A VAL* 3.8 29.6 - - + +
171A SER* 5.3 0.2 + - - -
190A GLU* 4.6 2.7 - - + +
194A THR* 3.3 25.1 - - + +
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Residues in contact with ILE 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 3.1 22.0 + - - +
25A ALA* 3.7 3.6 - - - +
27A PRO* 1.3 75.8 - - - +
29A LEU* 1.3 58.0 + - - +
31A ALA* 3.1 8.5 + - - +
32A ALA* 2.9 25.8 + - - +
41A ILE* 3.8 27.1 - - + -
193A ASP* 3.7 31.2 - - - +
194A THR* 3.9 13.7 - - - +
197A PHE* 3.5 38.1 - - + -
226A TYR* 4.0 19.7 - - + -
228A VAL* 4.3 7.9 - - + -
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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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25A ALA* 2.8 26.1 + - + +
26A LEU* 3.1 5.1 + - - +
28A ILE* 1.3 76.2 - - - +
30A PHE* 1.3 63.2 + - - +
32A ALA* 3.3 16.0 + - - +
33A LEU 4.0 1.9 + - - -
41A ILE* 3.5 27.4 - - + -
44A VAL* 4.9 2.9 - - + -
50A ILE* 4.0 37.7 - - + +
53A THR* 3.7 27.4 - - + -
54A MET* 5.3 3.1 - - + -
57A LEU* 3.8 18.4 - - + +
70A VAL* 3.9 26.0 - - + -
72A ILE* 4.5 9.2 - - + -
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Residues in contact with PHE 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 LEU* 3.1 27.7 + - + -
27A PRO 4.0 5.2 - - - +
29A LEU* 1.3 73.3 - - - +
31A ALA* 1.3 66.0 + - - +
33A LEU* 3.0 32.9 + - + +
53A THR* 3.7 28.5 - - + -
56A LEU* 3.9 27.6 - - + -
57A LEU* 4.6 4.0 - - + -
90A MET* 3.8 23.1 - - + -
92A ALA* 3.7 17.9 - - + -
93A SER* 3.9 4.5 - - - -
95A TRP* 3.6 35.0 - + + +
96A ALA* 3.5 31.4 - - + -
99A PRO* 3.7 7.4 - - + +
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Residues in contact with ALA 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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27A PRO 2.9 18.7 + - - +
28A ILE* 3.5 5.4 - - - +
30A PHE* 1.3 76.5 - - - +
32A ALA* 1.3 57.9 + - - +
33A LEU 3.0 0.7 - - - -
34A LEU* 3.0 32.7 + - - +
35A ALA 4.2 0.3 + - - -
99A PRO* 4.5 9.2 - - - +
171A SER* 4.4 9.9 - - - +
194A THR* 4.7 3.1 - - + -
197A PHE* 3.9 13.4 - - + -
198A LEU* 3.8 26.7 - - + -
201A LEU* 4.5 2.4 - - - +
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Residues in contact with ALA 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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28A ILE 2.9 12.0 + - - +
29A LEU* 3.3 15.7 - - - +
30A PHE 3.1 0.4 - - - -
31A ALA* 1.3 73.0 - - - +
33A LEU* 1.3 59.6 + - - +
34A LEU 2.9 6.7 - - - -
35A ALA* 2.9 22.4 + - - +
39A VAL* 5.0 4.5 - - + -
41A ILE* 4.5 3.8 - - + -
72A ILE* 4.0 31.6 - - + +
74A ALA* 3.5 11.1 - - - +
197A PHE* 3.9 17.2 - - + -
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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