Contacts of the helix formed by residues 14 - 30 (chain D) in PDB entry 2WY2
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 MET 14 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A VAL* 6.4 4.3 - - + -
76A HIS* 3.5 34.8 - - + +
59C ILE* 3.5 22.0 - - + -
62C ASP* 4.0 11.1 - - - +
70C VAL* 4.1 22.9 - - + -
74C LEU* 3.5 27.4 - - + -
75C VAL* 6.4 1.6 - - + -
78C GLN* 5.7 3.6 - - - +
10D CYS* 3.8 0.6 - - - -
13D GLY* 1.3 66.8 - - - -
15D SER* 1.3 60.2 + - - +
16D THR 2.8 3.8 - - - -
17D SER* 2.3 36.4 + - - -
18D LEU* 3.4 3.3 + - - +
200D PO3 2.4 24.1 + - - +
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Residues in contact with SER 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU* 3.6 35.2 + - - +
8A VAL* 4.8 6.8 - - - +
9A MET* 3.0 45.7 + - - +
76A HIS* 4.9 2.9 - - - -
14D MET* 1.3 76.9 - - - +
16D THR* 1.3 57.2 + - - -
18D LEU* 3.8 10.3 + - - +
19D LEU* 4.3 2.6 + - - +
84D TYR* 3.4 9.2 + - - -
200D PO3 2.7 14.8 + - - -
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Residues in contact with THR 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A MET* 4.2 0.7 - - - +
8D LEU* 3.5 42.6 - - + -
9D PHE 4.7 3.1 + - - +
10D CYS* 3.3 32.0 - - + +
13D GLY 5.0 0.2 - - - -
14D MET 2.6 2.2 + - - +
15D SER* 1.3 72.8 - - - +
17D SER* 1.3 60.0 + - - +
18D LEU 3.2 2.7 - - - -
19D LEU* 3.0 5.5 + - + +
20D VAL* 2.9 28.8 + - + +
38D ALA* 4.5 6.1 - - + -
57D GLY* 5.5 1.0 - - - -
79D ILE* 5.3 0.2 - - + -
84D TYR* 2.3 37.1 + - + +
200D PO3 4.2 0.2 + - - -
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Residues in contact with SER 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ILE 2.6 32.1 + - - -
60C GLU* 3.1 19.1 - - - +
62C ASP* 3.9 9.6 - - - +
13D GLY 2.2 30.2 + - - -
14D MET* 2.3 29.9 + - - -
16D THR* 1.3 69.9 - - - +
18D LEU* 1.3 58.9 + - - -
20D VAL* 3.4 5.5 + - - +
21D SER* 3.1 21.1 + - - -
38D ALA* 4.3 2.9 - - - +
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU* 4.0 16.8 - - - +
62C ASP* 4.9 3.9 + - - +
63C ALA* 5.2 8.1 - - + -
67C LYS* 3.9 22.4 - - + +
68C MET* 3.7 31.2 - - + -
14D MET 3.4 3.5 + - - +
15D SER* 4.0 9.6 - - - +
16D THR 3.2 0.8 - - - -
17D SER* 1.3 78.4 - - - +
19D LEU* 1.3 62.1 - - - +
21D SER* 2.7 26.9 + - - +
22D LYS* 3.2 14.6 + - + +
87D VAL* 4.0 22.0 - - + -
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 3.7 24.2 - - + -
15D SER 4.3 2.8 + - - +
16D THR* 3.0 14.5 + - - +
18D LEU* 1.3 77.3 - - - +
20D VAL* 1.3 60.1 + - - +
22D LYS* 3.2 2.8 + - - +
23D MET* 2.9 33.9 + - + +
79D ILE* 4.2 6.3 - - + -
83D LEU 4.7 2.0 - - - +
84D TYR* 3.8 31.0 - - + +
87D VAL* 3.9 32.2 - - + +
88D ASP 4.0 23.3 - - - +
89D GLY* 4.1 4.0 - - - +
92D VAL* 4.0 17.9 - - + -
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C GLU* 3.6 32.3 - - + +
8D LEU* 4.0 20.4 - - + -
16D THR 2.9 16.9 + - - +
17D SER* 3.7 9.9 - - - +
18D LEU 3.3 0.2 - - - -
19D LEU* 1.3 76.1 - - - +
21D SER* 1.3 62.6 + - - +
23D MET* 3.2 8.4 + - - +
24D ARG* 3.0 28.3 + - - +
36D ILE* 3.8 24.9 - - + +
38D ALA* 3.6 26.2 - - + +
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Residues in contact with SER 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C GLU 4.8 5.1 + - - -
61C GLY* 5.9 1.6 - - - -
63C ALA* 4.0 23.2 - - - +
17D SER 3.1 13.2 + - - -
18D LEU* 2.7 34.5 + - - +
20D VAL* 1.3 77.3 - - - +
22D LYS* 1.3 61.3 + - - +
24D ARG* 3.4 12.8 + - - +
25D ALA* 3.2 21.0 + - - +
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Residues in contact with LYS 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C LYS* 4.1 22.6 - - - +
18D LEU* 3.2 11.6 + - + +
19D LEU 3.2 8.8 + - - +
21D SER* 1.3 78.0 + - - +
23D MET* 1.3 65.9 + - - +
25D ALA* 3.3 11.3 + - + +
26D GLN* 3.2 33.1 + - + +
87D VAL* 4.1 25.8 - - + +
89D GLY* 4.0 14.8 - - - +
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Residues in contact with MET 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 4.3 17.9 - - + -
8D LEU* 4.1 14.4 - - + -
19D LEU* 2.9 32.4 + - + +
20D VAL* 3.6 5.4 - - - +
22D LYS* 1.3 78.4 - - - +
24D ARG* 1.3 56.9 + - - +
26D GLN* 3.2 3.6 + - - +
27D ALA* 2.9 29.3 + - - +
36D ILE* 3.7 33.9 - - + +
55D LEU* 4.7 0.7 - - + -
89D GLY* 3.5 28.5 - - - +
92D VAL* 3.9 28.5 - - + +
93D LEU* 4.0 23.2 - - + +
96D ALA* 4.9 0.4 - - + -
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Residues in contact with ARG 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C GLU* 4.1 21.0 + - - +
61C GLY* 4.8 15.0 - - - -
20D VAL* 3.0 18.3 + - - +
21D SER* 3.7 10.9 - - - +
22D LYS 3.3 0.2 - - - -
23D MET* 1.3 76.4 - - - +
25D ALA* 1.3 62.3 + - - +
27D ALA* 3.4 4.6 + - + +
28D GLU* 3.1 23.7 + - - +
34D VAL 5.9 2.5 - - - +
36D ILE* 3.7 27.0 + - + +
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Residues in contact with ALA 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D SER 3.2 13.2 + - - +
22D LYS* 3.5 17.3 - - + +
23D MET 3.2 0.6 - - - -
24D ARG* 1.3 75.3 - - - +
26D GLN* 1.3 63.8 + - + +
28D GLU* 3.2 7.2 + - - +
29D LYS* 3.0 28.0 + - - +
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Residues in contact with GLN 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LYS* 3.2 19.7 + - + +
23D MET 3.2 7.8 + - - +
25D ALA* 1.3 79.7 - - - +
27D ALA* 1.3 65.2 + - - +
29D LYS* 3.2 13.3 + - - +
30D TYR* 3.1 54.7 + - - +
89D GLY* 3.9 0.9 - - - -
90D LEU* 3.5 40.9 - - + +
93D LEU* 4.0 13.9 - - + +
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D MET 2.9 15.8 + - - +
24D ARG* 3.8 10.5 - - + +
25D ALA 3.4 0.2 - - - -
26D GLN* 1.3 77.1 - - - +
28D GLU* 1.3 57.4 + - - +
31D GLU* 3.0 8.1 + - - -
32D VAL* 2.9 37.6 + - + +
34D VAL* 3.8 31.0 - - + +
36D ILE* 4.4 2.0 - - + -
93D LEU* 3.7 14.1 - - + +
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Residues in contact with GLU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ARG 3.1 14.2 + - - +
25D ALA* 3.5 10.3 - - - +
27D ALA* 1.3 74.8 - - - +
29D LYS* 1.3 66.3 + - - +
31D GLU* 3.3 17.5 + - - +
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Residues in contact with LYS 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ALA 3.0 14.1 + - - +
26D GLN* 3.2 19.9 + - - +
28D GLU* 1.3 78.1 - - - +
30D TYR* 1.3 94.5 + - + +
31D GLU* 3.8 4.9 + - - +
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Residues in contact with TYR 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLN* 3.1 42.1 + - - +
29D LYS* 1.3 105.0 - - + +
31D GLU* 1.3 69.4 + - - +
32D VAL* 3.2 17.7 + - + +
90D LEU* 4.1 25.2 - - + +
93D LEU* 5.8 0.9 - - + -
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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