Contacts of the helix formed by residues 18 - 31 (chain A) in PDB entry 2YWE
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 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A HIS 5.1 1.6 - - - -
17A HIS* 1.3 76.0 - - - +
19A LYS* 1.3 65.1 + - - +
20A SER* 3.5 2.5 - - - -
21A THR* 3.7 14.9 + - - -
22A LEU* 3.5 16.6 + - - +
103A LEU* 3.7 9.5 - - - +
133A ASN* 4.4 5.1 + - - -
134A LYS* 5.1 10.0 - - - +
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Residues in contact with LYS 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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11A ILE* 3.6 40.2 - - + +
13A ALA* 4.2 26.0 - - + +
14A HIS 5.3 4.0 - - - -
17A HIS 3.6 1.2 - - - +
18A GLY* 1.3 75.1 - - - +
20A SER* 1.3 73.3 + - - +
22A LEU* 3.4 6.1 + - - +
23A ALA* 3.4 18.4 + - + +
58A MET* 6.0 1.1 - - + -
79A ASP* 2.8 31.4 + - - +
80A THR 3.4 21.1 + - - +
81A PRO* 5.4 1.3 - - - +
82A GLY 6.0 0.9 - - - +
103A LEU* 3.9 9.4 - - - -
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Residues in contact with SER 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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18A GLY* 5.1 1.2 - - - -
19A LYS* 1.3 88.7 + - - +
21A THR* 1.3 70.2 + - - +
23A ALA* 3.2 9.0 + - - +
24A ASP* 3.2 27.7 + - - +
58A MET* 6.1 1.8 - - - -
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Residues in contact with THR 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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18A GLY* 3.7 16.4 + - - -
19A LYS 3.3 0.6 - - - -
20A SER* 1.3 81.9 + - - +
22A LEU* 1.3 63.6 + - - +
24A ASP* 3.0 21.2 + - + +
25A ARG* 3.0 30.4 + - + +
165A ALA* 4.2 17.3 - - + -
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Residues in contact with LEU 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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11A ILE* 4.0 15.7 - - + -
18A GLY 3.5 9.2 + - - +
19A LYS 3.4 9.3 + - - +
20A SER 3.3 0.4 - - - -
21A THR* 1.3 78.9 - - - +
23A ALA* 1.3 58.3 + - - +
25A ARG* 3.2 24.8 + - + +
26A LEU* 2.9 41.3 + - + +
101A LEU* 4.0 13.7 - - + -
103A LEU* 3.4 38.1 - - + -
131A VAL* 4.9 3.6 - - + -
163A ALA* 5.5 2.9 - - + -
171A ILE* 5.4 1.6 - - + -
174A ILE* 3.6 27.6 - - + -
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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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11A ILE* 3.9 16.0 - - + +
19A LYS* 3.4 10.7 + - + +
20A SER* 3.2 11.6 + - - +
21A THR 3.2 0.4 - - - -
22A LEU* 1.3 79.4 - - - +
24A ASP* 1.3 62.4 + - - +
26A LEU* 3.4 8.7 + - - +
27A LEU* 3.1 28.8 + - - +
58A MET* 3.6 33.9 - - + -
63A MET* 6.1 0.2 - - - +
77A LEU* 4.9 6.7 - - + -
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Residues in contact with ASP 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 SER* 3.2 15.7 + - - +
21A THR* 3.0 13.4 + - + +
23A ALA* 1.3 77.9 - - - +
25A ARG* 1.3 59.9 + - + +
27A LEU* 3.2 9.3 + - - +
28A GLU* 2.9 47.6 + - + +
58A MET* 4.9 8.7 - - - +
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Residues in contact with ARG 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 THR* 3.0 34.2 + - + +
22A LEU* 3.2 18.5 + - + +
24A ASP* 1.3 75.9 - - + +
26A LEU* 1.3 61.6 + - - +
28A GLU* 4.0 11.9 - - - +
29A TYR* 3.1 26.7 + - - +
133A ASN* 5.8 1.8 - - - +
163A ALA* 4.4 7.9 - - - +
164A SER 3.0 19.6 + - - +
165A ALA* 2.9 36.7 + - - +
168A GLY* 3.6 5.7 - - - -
169A ILE 2.9 23.6 + - - +
171A ILE* 2.8 43.6 - - + +
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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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9A PHE* 3.9 33.0 - - + -
11A ILE* 4.4 11.4 - - + -
22A LEU* 2.9 37.0 + - + +
23A ALA* 3.5 7.4 - - - +
25A ARG* 1.3 79.0 - - - +
27A LEU* 1.3 59.9 + - - +
29A TYR* 3.8 4.2 - - - +
30A THR* 2.9 31.4 + - - +
63A MET* 4.2 12.3 - - + -
77A LEU* 5.3 1.6 - - + -
101A LEU* 4.3 12.3 - - + -
171A ILE* 4.4 17.9 - - + -
174A ILE* 4.3 16.4 - - + -
175A LEU* 4.5 15.9 - - + +
178A ILE* 5.1 0.4 - - + -
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Residues in contact with LEU 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 3.1 21.2 + - - +
24A ASP* 3.7 8.3 - - - +
26A LEU* 1.3 75.0 - - - +
28A GLU* 1.3 60.3 + - + +
30A THR* 2.8 3.4 + - - +
31A GLY* 2.7 34.0 + - - -
32A ALA 3.7 0.2 + - - -
58A MET* 4.6 18.4 - - + -
61A VAL* 3.4 31.0 - - + -
62A ARG 5.2 0.7 - - - +
63A MET* 3.4 23.1 - - + -
243A THR 5.8 0.7 - - - -
244A PRO* 4.1 30.5 - - + -
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Residues in contact with GLU 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 ASP* 2.9 34.5 + - + +
25A ARG* 4.0 11.2 + - - +
27A LEU* 1.3 75.6 - - + +
29A TYR* 1.3 61.9 + - - +
32A ALA* 2.8 50.1 + - + +
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Residues in contact with TYR 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 ARG 3.1 17.4 + - - +
26A LEU 3.8 3.4 - - - +
28A GLU* 1.3 80.7 - - - +
30A THR* 1.3 63.1 + - - +
32A ALA 4.1 5.9 - - - +
65A TYR* 4.2 15.3 - + - -
171A ILE* 3.4 26.7 - - + -
172A GLU* 3.0 41.0 + - + +
175A LEU* 3.4 26.0 - - + -
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Residues in contact with THR 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 2.9 15.5 + - - +
27A LEU* 2.8 22.9 + - - +
29A TYR* 1.3 78.7 - - - +
31A GLY* 1.3 65.4 + - - +
32A ALA 4.0 1.2 - - - +
63A MET* 3.6 29.1 - - + +
64A PHE 3.8 25.3 - - - +
65A TYR* 4.5 8.7 - - + -
175A LEU* 4.1 26.7 - - + -
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Residues in contact with GLY 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 LEU* 2.7 16.5 + - - +
30A THR* 1.3 74.3 + - - +
32A ALA* 1.3 67.9 + - - +
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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