Contacts of the helix formed by residues 20 - 36 (chain C) in PDB entry 1YE2
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 HIS 20 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LYS 4.8 7.0 - - - -
17C VAL* 2.7 23.3 + - - +
19C ALA* 1.3 78.5 - - + +
21C ALA* 1.3 62.7 + - - -
22C GLY 3.1 2.9 - - - -
23C GLU* 2.8 44.9 + - - +
24C TYR* 2.9 45.6 + + + -
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Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C TRP* 4.3 13.3 - - + +
17C VAL* 3.5 19.8 - - + +
18C GLY 3.1 16.0 + - - +
19C ALA 3.2 1.6 - - - -
20C HIS* 1.3 77.0 - - - +
22C GLY* 1.3 58.8 + - - +
24C TYR* 3.2 3.7 + - - +
25C GLY 2.9 24.8 + - - -
63C ALA* 3.2 22.3 - - + +
64C ASP* 5.3 4.0 - - - +
67C THR* 4.6 8.7 - - - +
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Residues in contact with GLY 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ALA 4.6 3.0 + - - -
20C HIS 3.0 1.0 + - - -
21C ALA* 1.3 79.1 - - - +
23C GLU* 1.3 61.6 + - - +
25C GLY* 3.3 2.1 + - - -
26C ALA* 3.2 21.5 + - - +
56C LYS 4.8 1.5 - - - +
59C GLY 4.0 5.0 - - - -
60C LYS* 4.1 30.1 + - - -
63C ALA* 4.0 2.0 - - - +
64C ASP* 5.6 1.2 + - - -
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Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ALA 4.5 4.5 - - - +
20C HIS* 2.8 50.4 + - - +
22C GLY* 1.3 72.3 - - - -
24C TYR* 1.3 65.2 + - + +
26C ALA* 3.4 6.7 + - - +
27C GLU* 2.9 28.9 + - - +
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Residues in contact with TYR 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C TRP* 6.0 3.4 - - + -
17C VAL* 3.7 42.0 - - + -
20C HIS* 2.9 40.6 + + + +
21C ALA* 3.6 7.6 - - - +
23C GLU* 1.3 82.7 - - + +
25C GLY* 1.3 59.0 + - - +
27C GLU* 3.2 3.2 + - - +
28C ALA* 2.8 31.1 + - - +
105C LEU* 4.8 3.8 - - + +
108C THR* 3.7 16.6 - - + +
109C LEU* 4.5 13.2 - - + -
112C HIS* 3.1 63.7 + + + +
113C LEU* 4.7 9.5 - - + +
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Residues in contact with GLY 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA 2.9 12.9 + - - -
22C GLY 3.7 0.2 - - - -
23C GLU 3.3 0.4 - - - -
24C TYR* 1.3 76.0 - - - +
26C ALA* 1.3 60.5 + - - +
28C ALA* 3.3 7.0 + - - +
29C LEU* 3.1 27.4 + - - +
59C GLY* 3.6 24.2 - - - -
62C VAL* 5.4 4.0 - - - +
63C ALA* 4.4 7.2 - - - +
105C LEU* 4.8 8.3 - - - +
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLY 3.2 13.0 + - - +
23C GLU* 3.7 9.6 - - - +
25C GLY* 1.3 74.0 - - - +
27C GLU* 1.3 64.0 + - - +
29C LEU* 3.3 5.6 + - - +
30C GLU* 3.0 24.0 + - - +
55C VAL* 4.0 10.6 - - + +
56C LYS* 4.0 32.3 - - + +
59C GLY* 3.5 9.2 - - - -
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Residues in contact with GLU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLU 2.9 19.1 + - - +
24C TYR* 3.2 5.9 + - - +
26C ALA* 1.3 77.2 - - - +
28C ALA* 1.3 62.3 + - - +
30C GLU* 3.2 7.5 + - - +
31C ARG* 2.8 63.0 + - + +
108C THR* 3.7 13.0 - - + +
111C ALA* 4.8 0.3 - - - +
112C HIS* 2.7 35.7 + - - -
124D PRO* 5.0 7.2 - - + -
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Residues in contact with ALA 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C TYR 2.8 16.1 + - - +
25C GLY 3.7 3.4 - - - +
26C ALA 3.3 0.4 - - - -
27C GLU* 1.3 71.6 - - - +
29C LEU* 1.3 64.3 + - - +
31C ARG* 3.2 1.7 + - - +
32C MET* 2.9 20.0 + - - +
101C LEU* 4.5 7.0 - - + -
104C CYS* 3.5 12.1 - - - +
105C LEU* 3.3 44.0 - - + +
108C THR* 3.5 16.8 + - - +
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Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C GLY 3.1 8.9 + - - +
26C ALA 3.6 4.7 - - - +
28C ALA* 1.3 76.5 - - - +
30C GLU* 1.3 65.2 + - - +
32C MET* 3.1 24.5 + - + +
33C PHE* 2.9 46.2 + - + -
43C PHE* 5.2 1.1 - - + -
46C PHE* 6.2 0.2 - - + -
55C VAL* 4.0 13.9 - - + +
58C HIS* 3.6 26.0 - - + +
59C GLY* 3.6 35.4 - - - +
62C VAL* 4.8 7.2 - - + -
101C LEU* 4.3 14.6 - - + -
150C OXY 4.4 9.9 - - - +
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Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ALA 3.0 16.3 + - - +
27C GLU* 3.2 8.2 + - - +
29C LEU* 1.3 74.9 - - - +
31C ARG* 1.3 64.3 + - - +
33C PHE* 3.5 9.2 + - + +
34C LEU* 3.1 42.1 + - + +
48C LEU 6.1 0.7 - - - +
50C HIS* 3.0 52.9 + - - +
51C GLY 4.8 0.9 + - - -
55C VAL* 4.7 7.6 - - + +
124D PRO* 4.3 15.7 - - + +
125D PRO* 5.6 1.6 - - - +
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Residues in contact with ARG 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLU* 2.8 42.9 + - - +
28C ALA 3.6 6.3 - - - +
30C GLU* 1.3 77.4 - - - +
32C MET* 1.3 55.5 + - - +
34C LEU* 3.8 1.5 - - - +
35C SER* 2.9 34.1 + - - -
104C CYS* 3.8 11.9 - - + -
107C VAL* 3.9 18.8 - - - +
108C THR* 3.4 20.9 + - - +
111C ALA* 4.5 12.1 - - - +
119D GLY 5.2 0.6 + - - -
120D LYS* 6.0 1.8 - - - +
122D PHE* 2.8 32.3 + - - -
123D THR* 3.6 3.6 + - - +
124D PRO* 3.6 37.1 - - + +
127D GLN* 2.9 33.0 + - - +
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Residues in contact with MET 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ALA 2.9 13.5 + - - +
29C LEU* 3.1 19.7 + - + +
31C ARG* 1.3 73.5 - - - +
33C PHE* 1.3 91.7 + - + +
36C PHE* 2.7 46.7 + - + +
39C THR* 3.5 30.1 - - + +
43C PHE* 4.7 2.2 - - + -
97C ASN 4.9 0.7 - - - +
100C LEU* 4.5 4.9 - - - +
101C LEU* 3.9 34.8 - - + +
104C CYS* 3.5 15.1 - - + -
142C HEM 4.2 15.9 - - + -
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Residues in contact with PHE 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LEU* 2.9 40.1 + - + +
30C GLU* 4.0 7.0 - - + +
32C MET* 1.3 94.8 - - + +
34C LEU* 1.3 64.2 + - + +
37C PRO* 3.5 21.5 - - - +
39C THR* 3.6 16.8 - - - -
40C LYS* 3.7 33.2 + - + +
43C PHE* 3.6 46.7 - + + -
46C PHE* 5.5 1.6 - + - -
48C LEU* 3.8 27.8 - - + +
55C VAL* 4.4 13.0 - - + -
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLU* 3.1 30.7 + - + +
31C ARG* 3.9 2.7 - - - +
33C PHE* 1.3 82.4 - - + +
35C SER* 1.3 63.3 + - - +
36C PHE 3.7 0.2 + - - -
37C PRO* 4.0 9.7 - - - +
40C LYS* 6.3 1.1 - - - +
124D PRO* 3.7 27.6 - - + +
125D PRO* 4.0 22.2 - - + -
128D ALA* 3.7 19.3 - - + +
132D LYS* 6.1 0.9 - - - -
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Residues in contact with SER 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ARG 2.9 18.7 + - - -
34C LEU* 1.3 77.1 - - - +
36C PHE* 1.3 86.1 - - - +
37C PRO* 3.5 7.2 - - - +
124D PRO 4.6 1.0 + - - -
127D GLN* 3.5 21.2 - - - +
128D ALA* 3.4 26.6 + - - +
131D GLN* 3.6 15.8 - - - +
132D LYS* 6.0 1.7 - - - +
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Residues in contact with PHE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C MET* 2.7 18.8 + - - +
35C SER* 1.3 93.3 - - - +
37C PRO* 1.3 62.9 - - - +
38C THR* 3.1 5.8 - - - +
39C THR* 2.7 34.6 + - + -
100C LEU* 4.0 54.7 - - + -
103C HIS* 4.1 13.7 - + - -
104C CYS* 3.9 22.0 - - - -
108D ASN* 5.3 2.7 - - - -
131D GLN* 3.8 31.0 - - + -
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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
------------------------------------------------------------
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