Contacts of the helix formed by residues 18 - 35 (chain D) in PDB entry 2YYN
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 THR 18 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LYS 3.4 7.9 + - - +
17D LEU* 1.3 78.8 - - - +
19D PRO* 1.3 73.5 - - - +
20D ILE* 3.3 10.9 - - + +
21D ASP* 3.0 37.4 + - - +
22D LYS* 3.0 17.8 + - - +
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Residues in contact with PRO 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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17D LEU 4.1 3.6 - - - +
18D THR* 1.3 87.1 - - - +
20D ILE* 1.3 61.3 + - - +
22D LYS* 3.1 13.2 + - + +
23D ARG* 3.1 26.0 + - - +
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Residues in contact with ILE 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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39C LEU* 3.8 24.5 - - + -
40C ALA* 4.7 17.9 - - + +
102C GLU* 6.2 0.2 - - - +
103C VAL* 6.5 0.7 - - + -
18D THR* 3.2 15.4 - - + +
19D PRO* 1.3 79.6 - - - +
21D ASP* 1.3 78.9 + - - +
23D ARG* 3.0 11.4 + - + +
24D LYS* 2.9 57.3 + - + +
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Residues in contact with ASP 21 (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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102C GLU* 5.0 7.6 - - - +
17D LEU* 3.5 20.5 - - + +
18D THR* 3.0 25.0 + - - +
20D ILE* 1.3 87.8 - - - +
22D LYS* 1.3 57.3 + - - +
24D LYS* 3.5 7.8 + - - +
25D CYS* 3.0 27.0 + - - +
79D PRO* 3.1 25.8 - - + +
82D PHE* 3.7 5.9 - - + -
122D TYR* 2.5 37.2 + - - +
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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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17D LEU* 4.4 16.8 - - + +
18D THR 3.0 12.5 + - - +
19D PRO* 3.4 14.4 - - + +
20D ILE 3.1 0.4 - - - -
21D ASP* 1.3 76.3 - - - +
23D ARG* 1.3 59.9 + - + +
25D CYS* 3.3 3.3 + - - +
26D GLU* 2.8 42.1 + - - +
69D LEU* 3.7 32.5 + - + +
70D GLN* 2.7 40.6 - - - +
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Residues in contact with ARG 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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23B ARG* 6.0 0.8 - - - +
39C LEU* 4.1 37.7 + - + +
42C GLN* 3.1 34.2 + - - +
43C ASP* 3.7 19.4 + - - -
19D PRO 3.1 15.5 + - - +
20D ILE* 3.0 12.8 + - - +
22D LYS* 1.3 75.0 - - + +
24D LYS* 1.3 53.0 + - - +
26D GLU* 2.9 21.0 + - - +
27D ARG* 2.6 37.2 + - - +
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Residues in contact with LYS 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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36C GLU 5.4 1.6 - - - -
37C MET* 5.7 4.0 - - - -
39C LEU* 3.5 16.8 - - + +
102C GLU* 4.2 11.9 + - - +
20D ILE* 2.9 39.8 + - + +
21D ASP* 3.7 8.0 + - - +
22D LYS 3.3 0.2 - - - -
23D ARG* 1.3 76.2 - - - +
25D CYS* 1.3 58.3 + - - +
27D ARG* 3.2 11.0 + - - +
28D LEU* 3.0 31.8 + - - +
82D PHE* 5.3 0.2 - - - -
121D LEU* 2.8 37.9 + - + +
122D TYR* 3.3 50.9 - - + +
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Residues in contact with CYS 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 ASP 3.0 10.9 + - - +
22D LYS 3.6 4.7 - - - +
24D LYS* 1.3 75.8 - - - +
26D GLU* 1.3 65.1 + - - +
28D LEU* 3.2 6.7 + - - +
29D LEU* 2.9 29.8 + - - +
65D ILE* 4.6 4.0 - - - -
69D LEU* 3.8 21.5 - - + -
76D TYR* 5.0 0.2 - - - -
82D PHE* 3.5 52.7 - - + -
86D PHE* 3.9 15.9 - - - -
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Residues in contact with GLU 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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120B ASN* 6.0 0.2 + - - -
22D LYS* 2.8 35.2 + - - +
23D ARG* 2.9 31.0 + - - +
25D CYS* 1.3 75.7 - - - +
27D ARG* 1.3 61.1 + - - +
29D LEU* 3.5 7.2 + - - +
30D LEU* 3.1 24.8 + - - +
69D LEU* 3.5 17.9 - - + -
70D GLN* 2.9 26.3 + - - +
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Residues in contact with ARG 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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31B PHE* 5.4 8.9 - - + -
33C TYR 5.2 4.8 + - - -
34C CYS 3.2 25.9 + - - -
36C GLU* 3.4 32.1 + - - +
39C LEU* 3.9 24.7 - - + +
42C GLN* 5.8 0.2 + - - -
23D ARG 2.6 17.1 + - - +
24D LYS* 3.2 10.5 - - - +
25D CYS 3.1 0.2 - - - -
26D GLU* 1.3 71.5 - - - +
28D LEU* 1.3 64.9 + - - +
30D LEU* 3.4 6.2 + - - +
31D PHE* 3.1 63.0 + - + -
117D LEU* 6.1 1.6 - - - +
121D LEU* 3.7 25.6 - - + +
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Residues in contact with LEU 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 LYS 3.0 20.0 + - - +
25D CYS* 3.7 5.6 - - - +
27D ARG* 1.3 74.8 - - - +
29D LEU* 1.3 63.1 + - - +
31D PHE* 4.1 3.3 - - - -
32D LEU* 3.0 30.6 + - + +
82D PHE* 4.3 14.8 - - + -
86D PHE* 3.9 29.6 - - + -
114D PHE* 4.0 23.3 - - + -
117D LEU* 3.9 30.1 - - + -
118D LEU* 4.2 24.7 - - + +
121D LEU* 4.0 15.0 - - + -
122D TYR* 5.3 2.5 - - + -
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Residues in contact with LEU 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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120B ASN* 6.0 0.4 - - - +
25D CYS* 2.9 27.3 + - - +
26D GLU* 3.5 7.2 - - - +
28D LEU* 1.3 77.7 - - - +
30D LEU* 1.3 62.4 - - - +
32D LEU* 3.7 3.0 - - - +
33D TYR* 2.9 40.4 + - + -
62D LEU* 4.1 21.1 - - + +
65D ILE* 4.0 12.8 - - + -
66D LYS* 4.2 33.9 - - + +
69D LEU* 3.8 23.8 - - + -
86D PHE* 3.7 25.4 - - + -
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Residues in contact with LEU 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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27B ARG* 4.5 6.7 - - - +
31B PHE* 3.4 34.1 - - + -
116B GLU 4.8 1.8 - - - +
117B LEU* 3.3 38.6 - - + +
120B ASN* 4.0 38.3 + - + +
121B LEU* 6.4 0.9 - - + -
26D GLU 3.1 14.5 + - - +
27D ARG* 3.8 6.1 - - - +
29D LEU* 1.3 80.0 - - - +
31D PHE* 1.3 68.9 + - + +
33D TYR* 3.2 9.4 + - + +
34D CYS* 3.0 31.9 + - - -
66D LYS* 6.4 0.2 - - - +
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Residues in contact with PHE 31 (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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31B PHE* 4.4 20.6 - + - -
113B TYR* 3.3 31.4 - + - -
27D ARG* 3.1 63.2 + - + +
28D LEU 4.2 0.2 - - - +
30D LEU* 1.3 83.3 - - + +
32D LEU* 1.3 63.1 + - - +
34D CYS* 3.3 6.6 + - + +
35D HIS* 3.2 15.9 + - - -
113D TYR* 3.6 23.9 + - - +
117D LEU* 3.5 37.7 - - + -
121D LEU* 6.4 0.2 - - + -
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Residues in contact with LEU 32 (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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28D LEU* 3.0 18.1 + - - +
29D LEU 3.7 2.9 - - - +
31D PHE* 1.3 73.6 - - - +
33D TYR* 1.3 68.1 + - - +
35D HIS* 3.0 15.7 + - - +
38D SER* 3.1 18.8 + - - -
62D LEU* 3.9 18.8 - - + -
86D PHE* 3.7 36.3 - - + -
90D PHE* 4.7 5.6 - - + -
110D LEU* 3.6 18.8 - - + +
113D TYR* 3.9 23.3 - - + -
114D PHE* 3.7 32.8 - - + -
117D LEU* 4.3 7.0 - - + -
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Residues in contact with TYR 33 (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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116B GLU* 3.7 30.0 - - + +
29D LEU* 2.9 36.2 + - + -
30D LEU* 3.5 12.6 - - + +
32D LEU* 1.3 74.1 - - - +
34D CYS* 1.3 63.5 + - - +
35D HIS 3.1 1.7 + - - +
38D SER* 3.0 19.4 + - - -
42D GLN* 3.6 45.8 + - + -
62D LEU* 3.8 24.0 - - + +
63D SER* 3.3 34.8 + - - -
66D LYS* 4.1 28.9 - - - -
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Residues in contact with CYS 34 (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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113B TYR* 3.8 36.7 - - + +
116B GLU* 3.8 27.8 - - + -
117B LEU* 3.8 29.4 - - - -
30D LEU* 3.0 23.7 + - - +
31D PHE* 3.7 8.1 - - + +
32D LEU 3.2 0.2 - - - -
33D TYR* 1.3 77.5 - - - +
35D HIS* 1.3 58.6 + - - +
36D GLU* 3.6 2.3 + - - -
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Residues in contact with HIS 35 (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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31D PHE 3.2 10.2 + - - +
32D LEU 3.0 14.4 + - - +
33D TYR 3.5 1.9 - - - +
34D CYS* 1.3 75.3 - - - +
36D GLU* 1.3 75.8 + - + +
37D MET* 2.9 50.4 + - + +
38D SER* 3.1 20.1 + - - -
109D LYS* 4.9 8.9 + - + +
110D LEU* 4.3 9.1 - - + +
113D TYR* 3.2 49.2 - + + +
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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