Contacts of the strand formed by residues 47 - 59 (chain D) in PDB entry 3U8M
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 GLU 47 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D GLU 4.2 0.5 - - - +
41D VAL 3.7 1.0 - - - -
42D ASN* 2.9 31.5 + - + +
45D THR* 3.4 32.8 + - - +
46D ASN* 1.3 82.9 - - - +
48D VAL* 1.3 65.0 + - - +
92D ILE* 3.5 28.5 - - + +
120D ARG* 5.7 3.7 - - + +
121D PHE 3.0 7.6 - - - +
122D SER* 4.6 4.9 - - - -
125D VAL* 3.9 0.4 - - - +
39E LEU* 3.8 28.7 - - + +
118E ARG* 5.6 1.9 + - - -
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Residues in contact with VAL 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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38D ILE* 5.1 1.3 - - + -
40D GLU 3.4 5.8 - - - +
41D VAL* 4.1 10.8 - - + -
47D GLU* 1.3 78.8 - - - +
49D ASP* 1.3 60.5 + - - +
50D VAL* 3.9 20.0 - - + -
119D GLN 4.0 0.5 - - - +
120D ARG* 3.1 8.6 - - - +
121D PHE* 2.8 43.2 + - + +
123D CYS* 3.8 7.2 - - - -
125D VAL* 3.6 22.7 - - + -
136D CYS* 3.8 24.0 - - - -
199D LEU* 6.4 0.2 - - + -
201D PHE* 4.0 22.0 - - + -
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Residues in contact with ASP 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ILE* 3.5 4.5 - - - +
39D LEU* 2.8 33.8 + - + +
40D GLU* 2.7 33.3 + - + +
48D VAL* 1.3 72.6 - - - +
50D VAL* 1.3 63.0 + - - +
118D ARG* 2.9 49.5 + - - +
119D GLN 3.9 2.1 - - - +
120D ARG* 2.9 37.3 + - + -
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Residues in contact with VAL 50 (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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35D PHE* 3.5 35.7 - - + -
37D ASN 3.6 8.1 - - - +
38D ILE* 4.6 12.6 - - + -
39D LEU* 5.4 0.2 - - - -
48D VAL* 3.9 25.1 - - + -
49D ASP* 1.3 80.2 + - - +
51D VAL* 1.3 67.1 + - - +
52D PHE* 3.8 11.8 - - + -
117D ILE 3.6 1.2 - - - +
118D ARG* 3.3 4.3 - - - +
119D GLN 3.0 36.5 + - - +
121D PHE* 4.2 13.9 - - + -
136D CYS* 5.8 0.2 - - - -
138D ILE* 5.2 2.5 - - + -
199D LEU* 4.8 10.1 - - + -
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Residues in contact with VAL 51 (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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89C TYR 6.2 0.2 - - - +
91C ALA 5.1 4.7 - - - +
92C ILE* 4.7 8.5 - - + -
35D PHE* 3.7 1.2 - - - -
36D ILE* 2.7 49.1 + - + -
37D ASN* 2.8 27.9 + - + +
39D LEU* 3.9 24.2 - - + -
50D VAL* 1.3 79.0 - - - +
52D PHE* 1.3 58.6 + - - +
98D LEU* 4.1 11.0 - - + -
116D SER* 3.8 17.5 - - - +
117D ILE 3.2 4.9 - - - +
118D ARG* 3.7 22.2 - - + -
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Residues in contact with PHE 52 (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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33D LEU* 3.6 30.3 - - + -
34D LYS 3.3 15.0 - - - +
35D PHE* 4.0 18.6 - + + -
36D ILE* 3.9 1.6 - - - -
50D VAL* 3.8 15.0 - - + -
51D VAL* 1.3 80.0 - - - +
53D TRP* 1.3 66.4 + - - +
54D GLN* 3.5 29.1 + - + -
116D SER* 4.4 0.2 - - - -
117D ILE* 2.7 69.6 + - + -
119D GLN* 3.9 17.0 - - + -
121D PHE* 3.9 26.5 - + - -
140D ILE* 5.3 1.8 - - + -
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Residues in contact with TRP 53 (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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89C TYR* 4.2 21.8 + + - -
143C TRP* 3.4 35.4 - + - -
185C TYR* 4.4 21.1 - + + -
187C CYS* 5.7 0.7 - - - -
33D LEU* 3.6 4.0 - - - -
34D LYS* 2.8 42.3 + - + +
36D ILE* 3.4 29.5 - - + +
52D PHE* 1.3 71.8 - - - +
54D GLN* 1.3 60.1 + - - +
55D GLN 3.4 4.2 + - - -
114D MET* 3.8 40.2 - - + -
115D PRO 3.3 4.5 - - - +
116D SER* 3.4 25.1 + - - -
164D TYR* 3.8 43.3 - + + -
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Residues in contact with GLN 54 (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 VAL* 4.5 7.9 - - + -
32D SER 3.9 2.2 - - - -
33D LEU* 3.9 14.4 - - + -
52D PHE* 3.5 27.9 + - + -
53D TRP* 1.3 71.4 - - - +
55D GLN* 1.3 58.1 + - - +
56D THR* 3.2 18.3 + - - +
86D LEU* 4.3 23.8 + - - +
113D TYR 3.2 14.9 - - - +
114D MET* 4.1 2.2 - - - -
115D PRO* 2.9 24.1 + - + +
117D ILE* 3.9 22.6 - - + +
119D GLN* 5.4 1.0 - - - +
140D ILE* 4.0 15.8 - - - +
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Residues in contact with GLN 55 (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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187C CYS* 4.5 12.6 - - - +
30D SER 3.5 1.6 + - - +
31D VAL* 3.4 6.8 - - - +
32D SER* 2.9 46.5 + - - +
34D LYS* 3.7 21.9 + - + +
53D TRP 3.4 1.8 + - - -
54D GLN* 1.3 70.5 - - - +
56D THR* 1.3 62.1 + - - +
57D THR* 5.6 4.4 + - - +
112D LEU* 3.8 18.8 - - + +
113D TYR 3.8 0.2 - - - -
114D MET* 3.5 31.9 - - - +
155D THR* 3.3 35.6 + - - +
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Residues in contact with THR 56 (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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29D VAL* 3.8 19.3 - - + -
30D SER 3.3 2.9 - - - +
31D VAL* 4.8 0.3 - - - +
54D GLN* 3.2 28.6 + - - +
55D GLN* 1.3 74.6 + - - +
57D THR* 1.3 64.5 + - - +
58D TRP* 3.6 27.0 - - + -
83D VAL* 6.1 0.4 - - + -
84D PRO* 4.1 4.5 - - + -
86D LEU* 3.8 16.5 - - + +
111D VAL 3.7 0.5 - - - +
112D LEU* 3.5 6.3 - - - +
113D TYR* 2.8 45.3 + - - -
115D PRO* 5.3 0.2 - - - +
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Residues in contact with THR 57 (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 ALA 3.6 2.3 - - - +
29D VAL* 3.3 2.8 - - - +
30D SER* 2.8 56.4 + - - +
55D GLN* 5.6 4.7 + - - +
56D THR* 1.3 77.6 + - - +
58D TRP* 1.3 71.1 + - - +
110D GLU* 4.9 7.4 - - - +
111D VAL 3.3 11.2 + - - +
112D LEU* 3.8 13.9 - - - +
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Residues in contact with TRP 58 (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 VAL* 4.0 10.3 - - + -
28D ALA 3.8 14.4 - - - +
29D VAL* 4.3 6.3 - - + -
56D THR* 3.6 31.4 - - + -
57D THR* 1.3 86.0 - - - +
59D SER* 1.3 75.4 + - - +
60D ASP* 4.2 6.5 - - + +
81D LEU* 5.2 2.7 - - + -
82D TRP* 3.2 48.3 + + - -
83D VAL* 4.0 15.9 - - + -
84D PRO* 3.6 29.2 - - + -
103D ALA* 5.6 0.9 - - + -
110D GLU* 3.3 8.3 - - - +
111D VAL* 2.8 67.3 + - + +
113D TYR* 4.2 14.1 - + + -
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Residues in contact with SER 59 (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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20D PRO* 3.6 20.3 - - - +
27D VAL* 4.1 9.6 - - - +
28D ALA 4.7 1.8 + - - -
58D TRP* 1.3 81.1 - - - +
60D ASP* 1.3 59.7 + - - +
61D ARG* 3.2 32.3 + - - +
108D ASP 4.7 0.7 + - - -
109D GLY 3.6 8.2 + - - -
110D GLU* 3.7 19.5 + - - -
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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