Contacts of the strand formed by residues 27 - 42 (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 VAL 27 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ILE* 3.7 28.3 - - + -
20D PRO* 3.6 28.5 - - + +
21D THR* 3.7 6.5 - - + +
22D GLN 6.0 0.2 - - - +
26D PRO* 1.3 70.1 - - - +
28D ALA* 1.3 63.4 + - - +
29D VAL* 3.3 7.3 + - + +
58D TRP* 4.0 25.8 - - + -
59D SER* 4.1 14.8 - - - +
82D TRP* 4.3 15.9 - - + -
149D GLU 2.8 11.3 + - - +
150D ILE* 3.7 5.3 - - + -
151D SER* 3.1 21.8 + - - +
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Residues in contact with ALA 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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26D PRO 3.3 6.0 + - - +
27D VAL* 1.3 73.1 - - - +
29D VAL* 1.3 59.9 + - - +
30D SER* 4.0 1.1 + - - -
57D THR* 3.6 9.5 - - - +
58D TRP* 3.8 11.3 - - - +
59D SER 4.7 1.2 + - - -
151D SER* 3.6 14.8 - - - +
153D ASP* 5.7 2.0 - - - +
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Residues in contact with VAL 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D VAL* 3.9 15.9 - - + +
28D ALA* 1.3 75.3 - - - +
30D SER* 1.3 65.7 + - - +
31D VAL* 4.1 11.4 - - + -
56D THR* 3.8 27.6 - - + -
57D THR 3.3 6.1 - - - +
58D TRP* 4.3 9.6 - - + -
82D TRP* 4.9 0.9 - - + -
84D PRO* 4.1 25.6 - - + -
86D LEU* 4.3 5.4 - - + -
150D ILE* 4.0 17.0 - - + -
151D SER 2.8 13.2 + - - +
152D VAL* 3.3 8.5 - - + +
153D ASP* 3.0 26.0 + - - +
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Residues in contact with SER 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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28D ALA 4.0 1.3 + - - -
29D VAL* 1.3 74.5 + - - +
31D VAL* 1.3 61.0 + - - +
55D GLN* 3.5 1.8 + - - +
56D THR* 3.3 8.7 - - - +
57D THR* 2.8 55.2 + - - +
153D ASP* 3.3 12.1 + - - +
154D PRO 4.4 5.5 + - - -
155D THR* 4.1 15.5 + - - -
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Residues in contact with VAL 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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29D VAL* 4.1 9.4 - - + +
30D SER* 1.3 80.1 - - - +
32D SER* 1.3 68.9 + - - +
33D LEU* 4.8 0.9 - - + -
54D GLN* 4.5 16.2 - - + -
55D GLN 3.4 6.5 - - - +
56D THR* 4.8 0.9 - - - +
86D LEU* 3.8 32.3 - - + -
140D ILE* 4.5 22.2 - - + +
152D VAL* 4.4 17.5 - - + -
153D ASP 2.9 7.8 + - - +
154D PRO* 3.6 21.1 - - - +
155D THR* 3.7 1.4 + - - -
178D GLN* 3.6 4.5 - - - +
195D VAL* 4.9 14.5 - - + +
197D VAL* 6.1 1.7 - - + +
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Residues in contact with SER 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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31D VAL* 1.3 77.0 - - - +
33D LEU* 1.3 67.3 + - - +
34D LYS* 3.5 21.8 + - - +
53D TRP 3.6 0.7 - - - +
55D GLN* 2.9 47.7 + - - +
155D THR* 3.3 27.6 - - - -
178D GLN* 4.2 12.8 + - - +
197D VAL* 6.0 0.7 - - - -
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Residues in contact with LEU 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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31D VAL* 4.8 2.9 - - + -
32D SER* 1.3 80.7 + - - +
34D LYS* 1.3 64.4 + - - +
35D PHE* 3.7 36.7 + - + -
52D PHE* 3.6 36.6 - - + -
53D TRP 3.6 1.3 - - - +
54D GLN* 3.9 17.0 - - + -
138D ILE* 4.4 15.5 - - + -
140D ILE* 3.9 25.1 - - + -
176D VAL* 5.2 3.3 - - - +
178D GLN* 3.9 11.2 + - - +
197D VAL* 4.1 26.9 - - + -
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Residues in contact with LYS 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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187C CYS* 5.8 2.9 - - - -
32D SER* 3.5 22.6 + - - +
33D LEU* 1.3 73.9 - - - +
35D PHE* 1.3 63.9 + - - +
36D ILE* 3.5 4.0 - - - +
52D PHE* 3.3 1.5 - - - -
53D TRP* 2.8 56.4 + - + +
55D GLN* 3.7 29.4 + - + +
114D MET* 4.7 6.5 - - - -
155D THR* 4.9 6.9 - - - +
159D SER* 3.8 20.2 + - - -
160D ASP 6.0 2.0 - - - +
161D ASP 5.8 0.4 - - - -
163D GLU* 6.1 0.4 - - - +
164D TYR* 3.8 36.8 - - + -
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Residues in contact with PHE 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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33D LEU* 3.7 28.9 + - + -
34D LYS* 1.3 72.4 - - - +
36D ILE* 1.3 61.1 + - - +
38D ILE* 5.7 1.1 - - + -
50D VAL* 3.5 33.0 - - + -
51D VAL 3.8 1.6 - - - +
52D PHE* 4.0 10.1 - + + -
138D ILE* 4.3 15.5 - - + -
161D ASP 4.4 9.2 + - - +
164D TYR* 3.7 4.3 + - - +
165D PHE* 3.5 27.0 + - + +
173D ILE* 3.7 19.3 - - + -
176D VAL* 4.2 15.7 - - + -
197D VAL* 4.1 20.9 - - + -
199D LEU* 3.8 45.5 - - + -
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Residues in contact with ILE 36 (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 4.6 14.8 - - - +
90C ASN* 6.0 1.8 - - - -
34D LYS 3.5 16.2 - - - +
35D PHE* 1.3 74.2 - - - +
37D ASN* 1.3 61.8 + - + +
51D VAL* 2.7 31.8 + - + +
52D PHE* 3.9 1.3 - - - -
53D TRP* 3.4 44.2 - - + +
116D SER* 4.5 0.9 - - - +
164D TYR* 3.6 37.0 - - + +
165D PHE* 3.6 3.8 - - - -
166D SER* 2.7 33.0 + - - +
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Residues in contact with ASN 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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92C ILE* 4.3 3.7 - - + +
122C SER* 2.9 37.8 + - - -
35D PHE* 5.3 0.2 - - - -
36D ILE* 1.3 83.1 + - + +
38D ILE* 1.3 86.6 + - - +
39D LEU* 3.5 20.8 - - + +
50D VAL* 3.6 3.8 - - - +
51D VAL* 2.8 40.1 + - + +
165D PHE* 3.6 7.8 - - - -
166D SER* 3.5 13.2 - - - -
169D SER* 3.1 21.7 + - - +
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Residues in contact with ILE 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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35D PHE* 5.7 0.9 - - + -
37D ASN* 1.3 87.8 + - - +
39D LEU* 1.3 63.1 + - - +
40D GLU 4.7 0.4 - - - +
41D VAL* 3.9 28.3 - - + -
48D VAL* 5.1 1.3 - - + -
49D ASP 3.5 10.1 - - - +
50D VAL* 4.6 14.6 - - + -
165D PHE* 3.8 21.5 - - + -
169D SER* 3.2 17.7 + - - +
170D ARG 4.8 1.2 + - - -
171D PHE* 3.6 21.5 - - + -
172D GLU 5.4 0.2 - - - +
173D ILE* 4.8 3.1 - - + -
199D LEU* 4.0 17.7 - - + -
201D PHE* 3.6 37.5 - - + -
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Residues in contact with LEU 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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45C THR* 5.0 1.6 - - - +
47C GLU* 3.7 31.0 - - + +
92C ILE* 3.7 24.2 - - + -
37D ASN* 3.5 34.1 - - + +
38D ILE* 1.3 75.5 - - - +
40D GLU* 1.3 61.5 + - + +
49D ASP* 2.8 19.5 + - + +
51D VAL* 3.9 13.5 - - + -
118D ARG* 3.1 54.7 - - - +
170D ARG* 3.3 17.0 + - - -
171D PHE* 4.8 0.4 - - - -
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Residues in contact with GLU 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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38D ILE 3.8 0.2 - - - -
39D LEU* 1.3 84.0 - - + +
41D VAL* 1.3 76.0 + - - +
42D ASN* 4.6 14.0 + - - +
47D GLU 4.2 0.4 - - - +
48D VAL* 3.4 2.3 - - - -
49D ASP* 2.7 40.8 + - + +
118D ARG* 5.8 1.3 - - - +
120D ARG* 6.1 1.4 - - - -
170D ARG* 4.1 10.5 - - - +
171D PHE* 5.0 0.2 - - - -
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Residues in contact with VAL 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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38D ILE* 3.9 9.2 - - + -
40D GLU* 1.3 88.8 - - - +
42D ASN* 1.3 63.8 + - - +
43D GLU* 4.2 2.0 - - + +
47D GLU 3.7 3.8 - - - -
48D VAL* 4.1 5.6 - - + -
125D VAL* 3.0 35.4 - - + -
128D VAL* 4.4 13.2 - - + -
170D ARG* 4.7 1.4 - - - +
171D PHE* 3.4 36.4 - - + -
201D PHE* 3.6 19.3 - - + -
203D LYS* 6.4 0.2 - - - -
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Residues in contact with ASN 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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40D GLU* 4.6 12.9 + - - +
41D VAL* 1.3 78.4 - - - +
43D GLU* 1.3 57.7 + - - +
44D ILE* 2.9 16.2 + - - +
45D THR* 2.9 46.2 + - - +
46D ASN* 2.8 32.1 + - - -
47D GLU* 2.9 16.0 + - + +
125D VAL* 4.1 1.1 - - - +
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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