Contacts of the strand formed by residues 27 - 38 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19F ILE* 3.7 23.3 - - + -
20F PRO* 3.6 34.5 - - + +
21F THR* 3.8 4.5 - - - +
25F ARG 3.8 0.4 + - - -
26F PRO* 1.3 70.8 - - - +
28F ALA* 1.3 59.3 + - - +
29F VAL* 3.3 9.7 + - + +
58F TRP* 4.1 24.9 - - + -
59F SER* 4.2 14.8 - - - +
82F TRP* 4.3 16.4 - - + -
149F GLU 2.9 11.6 + - - +
150F ILE* 3.7 4.8 - - + -
151F SER* 3.2 22.1 + - - -
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Residues in contact with ALA 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F ARG* 6.3 1.6 - - - +
26F PRO 3.3 5.6 + - - +
27F VAL* 1.3 72.8 - - - +
29F VAL* 1.3 59.5 + - - +
30F SER* 4.0 0.9 + - - -
57F THR* 3.6 8.8 - - - +
58F TRP* 3.8 11.6 - - - +
59F SER 4.6 1.2 + - - -
151F SER* 3.8 13.9 - - - +
153F ASP* 6.0 0.7 - - - +
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Residues in contact with VAL 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F VAL* 3.9 22.2 - - + +
28F ALA* 1.3 74.3 - - - +
30F SER* 1.3 64.9 + - - +
31F VAL* 4.0 10.3 + - + -
56F THR* 3.8 28.0 - - + -
57F THR 3.3 5.8 - - - +
58F TRP* 4.4 3.8 - - + -
82F TRP* 4.8 0.2 - - + -
84F PRO* 4.0 25.1 - - + -
86F LEU* 4.4 5.6 - - + -
150F ILE* 3.9 18.2 - - + -
151F SER 2.9 11.7 + - - +
152F VAL* 3.4 8.6 - - + +
153F ASP* 3.0 26.3 + - - +
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Residues in contact with SER 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F ALA 4.0 1.1 + - - -
29F VAL* 1.3 74.2 + - - +
31F VAL* 1.3 63.2 + - - +
55F GLN* 3.5 2.5 - - - +
56F THR* 3.3 8.1 - - - +
57F THR* 2.7 56.8 + - - +
153F ASP* 3.3 11.9 + - - +
154F PRO 4.4 5.0 + - - -
155F THR* 4.5 17.1 - - - -
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Residues in contact with VAL 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F VAL* 4.1 9.6 - - + +
30F SER* 1.3 78.8 - - - +
32F SER* 1.3 69.4 + - - +
33F LEU* 4.8 1.6 - - + -
54F GLN* 4.5 15.7 - - + -
55F GLN 3.4 6.5 - - - +
56F THR* 4.8 0.9 - - - +
86F LEU* 3.8 31.6 - - + -
140F ILE* 4.5 22.4 - - + +
152F VAL* 4.4 18.6 - - + -
153F ASP 3.0 7.3 + - - +
154F PRO* 3.5 23.6 - - - +
155F THR* 4.6 1.1 - - - -
178F GLN* 3.8 3.8 - - - +
195F VAL* 4.9 15.4 - - + +
197F VAL* 6.5 0.9 - - + -
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Residues in contact with SER 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F VAL* 1.3 79.0 - - - +
33F LEU* 1.3 67.2 + - - +
34F LYS* 3.5 21.2 + - - +
54F GLN 3.8 0.9 - - - -
55F GLN* 2.9 59.2 + - - +
155F THR* 3.6 20.0 + - - -
178F GLN* 4.2 11.3 + - - -
197F VAL* 6.1 0.4 - - - -
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Residues in contact with LEU 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F VAL* 4.8 2.9 - - + -
32F SER* 1.3 81.0 + - - +
34F LYS* 1.3 65.9 + - - +
35F PHE* 3.8 36.7 + - + -
52F PHE* 3.6 33.0 - - + -
53F TRP 3.6 1.3 - - - +
54F GLN* 3.9 12.1 - - + -
138F ILE* 4.4 16.4 - - + -
140F ILE* 3.8 28.7 - - + -
176F VAL* 5.3 2.4 - - - +
178F GLN* 3.9 12.2 + - - +
197F VAL* 3.9 30.0 - - + +
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Residues in contact with LYS 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F SER* 3.5 21.5 + - - +
33F LEU* 1.3 73.9 - - - +
35F PHE* 1.3 64.8 + - - +
36F ILE* 3.5 3.9 - - - +
52F PHE* 3.3 2.0 - - - -
53F TRP* 2.7 61.0 + - + +
55F GLN* 3.4 27.8 + - - +
114F MET* 4.6 5.8 - - - -
155F THR* 5.1 1.2 + - - +
157F GLU* 2.9 40.7 + - - +
164F TYR* 4.0 29.6 - - + -
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Residues in contact with PHE 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU* 4.1 29.6 - - + -
34F LYS* 1.3 72.2 - - - +
36F ILE* 1.3 63.5 + - - +
37F ASN 5.0 0.4 - - - +
38F ILE* 5.7 0.9 - - + -
50F VAL* 3.6 31.2 - - + -
51F VAL 3.9 1.3 - - - -
52F PHE* 4.0 10.3 - + + -
138F ILE* 4.2 14.8 - - + -
161F ASP 5.0 7.7 + - - +
164F TYR* 3.8 3.1 + - - +
165F PHE* 3.7 24.4 + - + +
173F ILE* 3.8 19.6 - - + +
176F VAL* 4.0 17.9 - - + -
197F VAL* 4.0 22.9 - - + -
199F LEU* 3.9 44.0 - - + -
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Residues in contact with ILE 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F LYS 3.5 15.9 - - - +
35F PHE* 1.3 76.3 - - - +
37F ASN* 1.3 65.0 - - + +
51F VAL* 2.8 28.7 + - + +
52F PHE* 3.9 1.3 - - - -
53F TRP* 3.5 45.5 - - + +
116F SER* 4.5 1.1 - - - +
164F TYR* 3.7 33.4 - - + +
165F PHE* 3.5 5.2 - - - -
166F SER* 2.8 30.4 + - - -
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Residues in contact with ASN 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F PHE* 5.4 0.3 - - - -
36F ILE* 1.3 81.7 - - + +
38F ILE* 1.3 81.5 + - - +
39F LEU* 3.5 25.3 - - + +
50F VAL* 3.6 3.6 - - - +
51F VAL* 2.9 40.5 + - + +
165F PHE* 3.5 8.0 - - - -
166F SER* 3.5 22.8 + - - -
168F TYR 5.6 0.4 - - - -
169F SER* 3.1 22.8 + - - +
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Residues in contact with ILE 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F PHE* 5.7 0.9 - - + -
37F ASN* 1.3 85.2 + - - +
39F LEU* 1.3 60.5 + - - +
41F VAL* 3.8 28.7 - - + -
48F VAL* 5.2 1.8 - - + -
49F ASP 3.6 9.0 - - - +
50F VAL* 4.6 11.7 - - + +
165F PHE* 3.7 25.6 - - + -
169F SER* 3.1 16.1 + - - -
170F ARG 4.7 1.0 + - - -
171F PHE* 3.5 21.3 - - + -
172F GLU 5.2 0.2 - - - +
173F ILE* 4.6 3.6 - - + -
199F LEU* 3.9 21.3 - - + -
201F PHE* 3.6 38.1 - - + -
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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
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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