Contacts of the strand formed by residues 36 - 48 (chain D) in PDB entry 5J0Z
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 36 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D SER 4.2 1.4 + - - -
30D LEU* 3.4 7.1 - - - +
31D ASP* 2.9 34.0 + - - +
34D ALA* 3.3 23.3 - - + +
35D GLU* 1.3 83.8 - - - +
37D PHE* 1.3 71.3 + - - +
38D LYS* 6.1 0.2 - - - +
82D GLU* 3.5 24.0 - - - +
109D ARG* 3.4 27.5 + - - +
110D VAL 3.2 15.3 - - - +
111D LEU* 4.1 3.6 - - + +
112D SER 4.6 2.2 - - - +
114D LEU* 5.1 1.2 - - - +
126D LEU* 6.2 0.2 - - - -
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Residues in contact with PHE 37 (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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27D CYS* 5.0 6.7 - - + -
28D TYR 4.1 2.7 - - - +
29D SER 3.3 9.6 - - - -
30D LEU* 3.9 19.5 - - + -
36D THR* 1.3 82.3 - - - +
38D LYS* 1.3 72.2 + - - +
39D VAL* 4.0 22.4 - - + -
109D ARG* 4.6 1.1 - - - -
110D VAL* 2.9 64.8 + - + +
112D SER* 4.4 6.3 - - - -
126D LEU* 3.7 49.6 - - + -
127D HIS 4.7 0.4 - - - -
128D ILE* 4.1 14.1 - - + -
157D LEU* 5.2 3.4 - - + -
188D LEU* 4.4 13.0 - - + -
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Residues in contact with LYS 38 (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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27D CYS* 3.5 3.1 - - - -
28D TYR* 2.8 75.9 + - + +
29D SER* 3.9 17.4 + - - +
37D PHE* 1.3 78.4 - - - +
39D VAL* 1.3 59.7 + - - +
83D ASN* 4.4 8.7 + - - -
108D ALA 3.5 6.7 - - - +
109D ARG* 3.8 41.9 - - + +
82E GLU* 5.1 3.6 - - - +
402E SO4 4.4 13.6 + - - +
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Residues in contact with VAL 39 (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 LEU* 3.4 33.9 - - + -
26D GLU 3.4 10.1 - - - +
27D CYS* 4.8 4.9 - - - -
28D TYR* 4.3 4.1 + - - -
37D PHE* 4.0 14.1 - - + -
38D LYS* 1.3 75.0 - - - +
40D ASN* 1.3 63.4 + - - +
41D ALA* 4.4 4.7 - - + -
106D PHE* 3.9 25.8 - - + -
107D SER* 3.1 5.5 - - - -
108D ALA 3.0 39.4 + - - +
110D VAL* 4.0 15.9 - - + -
128D ILE* 4.3 10.5 - - + -
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Residues in contact with ASN 40 (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 ILE* 2.8 31.1 + - - +
26D GLU* 2.8 36.3 + - + +
28D TYR* 4.2 5.2 - - + -
39D VAL* 1.3 75.9 - - - +
41D ALA* 1.3 55.3 + - - +
105D ARG* 3.1 39.3 + - - +
106D PHE 3.3 12.4 - - - +
107D SER* 3.9 13.5 - - - -
81E VAL* 3.2 26.5 + - - +
82E GLU 4.5 4.4 + - - -
84E ALA* 5.9 3.4 - - - +
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Residues in contact with ALA 41 (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 ILE* 3.9 9.4 - - + -
23D TYR 3.3 17.0 - - - +
24D LEU* 3.7 16.2 - - + -
25D ILE* 3.8 8.1 - - - -
39D VAL* 4.4 1.3 - - + -
40D ASN* 1.3 76.9 + - - +
42D PHE* 1.3 58.5 + - - +
105D ARG* 3.5 1.3 - - - -
106D PHE* 2.8 62.7 + - + +
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Residues in contact with PHE 42 (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 GLY 3.5 0.3 - - - +
22D ILE* 3.2 8.3 - - - +
23D TYR* 2.9 54.2 + + + +
25D ILE* 3.6 3.7 - - + +
41D ALA* 1.3 71.7 - - - +
43D LEU* 1.3 59.4 + - - +
44D SER 5.0 0.2 - - - +
90D VAL* 4.5 2.9 - - + -
103D LEU* 3.9 29.4 - - + -
104D GLU 3.3 8.1 - - - +
105D ARG* 3.6 30.5 - - + -
106D PHE* 4.1 1.6 - - - -
77E ARG* 3.9 8.5 - - - -
133E ARG* 4.4 7.2 - - - -
176E LEU* 3.5 30.3 - - + -
177E GLU* 4.5 14.8 - - - +
181E GLU* 3.6 11.4 - - - -
403E ACT 3.2 30.1 - - + -
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Residues in contact with LEU 43 (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 GLY 3.5 9.0 - - - +
22D ILE* 4.0 17.7 - - + -
41D ALA 3.8 2.2 + - - -
42D PHE* 1.3 72.4 - - - +
44D SER* 1.3 63.6 + - - +
45D LEU* 4.3 23.7 + - + -
76D ILE* 4.1 17.3 - - + -
78D PHE* 4.6 4.5 - - + -
85D ARG* 4.1 17.3 - - - +
102D TYR* 4.3 1.0 - - - +
103D LEU* 3.7 2.5 - - - -
104D GLU* 2.8 65.2 + - + +
106D PHE* 3.9 11.6 - - + -
130D LEU* 4.0 21.1 - - + -
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Residues in contact with SER 44 (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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19D ASN 3.3 1.7 - - - +
20D THR* 3.3 5.2 - - - -
21D GLY* 2.8 48.0 + - - -
42D PHE 5.4 0.2 - - - -
43D LEU* 1.3 72.7 - - - +
45D LEU* 1.3 64.5 + - - +
102D TYR 3.4 6.1 - - - -
103D LEU* 3.6 19.7 - - - -
148D LYS* 3.2 34.4 - - - +
177E GLU* 3.8 6.3 - - - -
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Residues in contact with LEU 45 (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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18D VAL* 4.5 4.7 - - + -
19D ASN 3.4 4.0 - - - -
20D THR* 3.8 26.5 - - + -
43D LEU* 4.3 15.7 - - + -
44D SER* 1.3 77.7 - - - +
46D SER* 1.3 62.6 + - - +
47D TRP* 4.0 8.3 - - + -
73D ILE* 5.1 2.2 - - + -
74D PRO* 4.9 9.6 - - + +
76D ILE* 3.4 45.8 - - + -
85D ARG* 5.6 1.6 - - - +
101D GLN* 3.7 3.1 + - - -
102D TYR* 2.8 70.3 + - + +
148D LYS* 5.1 0.6 - - - -
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Residues in contact with SER 46 (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 THR 4.2 1.4 - - - +
18D VAL* 3.7 0.9 - - - +
19D ASN* 2.7 54.1 + - - +
45D LEU* 1.3 78.5 - - - +
47D TRP* 1.3 62.6 + - - +
99D THR* 4.4 9.6 - - - +
100D VAL 3.0 17.0 + - - -
101D GLN* 3.0 21.2 + - - +
145D ASP* 5.0 5.3 + - - -
148D LYS* 5.2 1.6 - - - -
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Residues in contact with TRP 47 (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 PRO* 4.6 0.4 - - + -
16D LEU* 4.1 10.3 - - + -
17D THR 4.0 15.0 - - - +
18D VAL* 4.3 10.1 - - + -
45D LEU* 4.0 7.4 - - + -
46D SER* 1.3 83.4 - - - +
48D LYS* 1.3 62.7 + - - +
49D ASP* 4.0 17.1 - - + +
71D ILE* 3.7 6.3 - - + -
72D TRP* 3.1 48.6 + + - -
73D ILE* 3.7 15.9 - - + -
74D PRO* 3.6 30.1 - - + -
99D THR* 3.4 6.8 - - - +
100D VAL* 2.7 70.9 + - + +
102D TYR* 3.6 27.8 - + + -
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Residues in contact with LYS 48 (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 PRO* 3.7 16.6 - - - +
14D GLU* 5.9 0.2 - - - -
16D LEU* 4.1 15.5 - - + +
17D THR 4.8 0.6 + - - -
47D TRP* 1.3 75.0 - - - +
49D ASP* 1.3 60.4 + - - +
50D ARG* 3.5 47.0 + - + +
97D ASP* 4.5 13.5 - - - +
98D GLY 3.6 5.4 - - - +
99D THR* 4.1 19.7 - - + +
138D ARG* 5.0 1.2 + - - -
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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