Contacts of the strand formed by residues 28 - 34 (chain B) in PDB entry 3EOV
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 LYS 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B VAL* 4.6 9.4 - - + -
26B THR 6.0 0.2 - - - -
27B ALA* 1.3 80.3 - - - +
29B VAL* 1.3 68.8 + - - +
44B THR* 4.8 8.7 - - + +
45B ILE 3.3 5.8 - - - +
155B LEU* 3.7 30.2 - - + +
186B GLU* 3.6 4.9 - - - +
187B LEU* 2.9 54.7 + - + +
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA* 5.8 0.2 - - + -
28B LYS* 1.3 80.2 - - - +
30B TYR* 1.3 68.1 + - - +
31B PHE* 5.9 0.4 - - + -
44B THR* 3.7 5.2 - - - +
45B ILE* 2.9 46.1 + - + +
47B LEU* 4.1 19.3 - - + -
59B PHE* 3.6 31.4 - - + -
60B ARG* 4.4 16.4 - - + +
63B CYS* 3.8 20.0 - - + -
185B GLY 3.2 16.2 - - - +
186B GLU* 4.3 5.8 - - + +
187B LEU* 4.9 1.2 - - - +
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Residues in contact with TYR 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 1.3 82.0 - - - +
31B PHE* 1.3 70.8 + - - +
32B ASP* 4.3 5.4 - - - -
42B ARG* 3.5 49.2 + - - -
43B ILE 3.1 13.2 - - - +
44B THR* 4.4 3.6 - - - +
45B ILE* 4.6 1.1 - - - +
63B CYS* 4.8 0.5 - - - -
183B ALA* 4.4 5.6 - - + +
184B SER* 3.1 49.6 + - - -
185B GLY* 3.1 21.7 + - - -
186B GLU 3.2 22.6 + - - -
187B LEU* 3.6 25.4 - - + -
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Residues in contact with PHE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 5.9 0.2 - - + -
30B TYR* 1.3 82.6 - - - +
32B ASP* 1.3 63.4 + - - +
33B VAL* 3.6 12.9 + - + -
41B GLY 3.7 0.2 - - - +
42B ARG* 3.2 3.6 - - - -
43B ILE* 2.8 51.7 + - + +
45B ILE* 3.9 27.4 - - + -
59B PHE* 3.7 22.7 - + - -
63B CYS* 4.0 10.3 - - - -
71B TYR* 4.0 26.9 - + + -
76B PHE* 4.8 3.8 - + - -
134B PHE* 3.7 29.8 - + - -
136B ILE* 5.3 1.3 - - + -
181B ILE* 3.6 30.7 - - + -
183B ALA 3.6 1.8 - - - -
184B SER* 3.6 8.1 - - - -
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Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B TYR* 4.4 4.1 - - - -
31B PHE* 1.3 72.1 - - - +
33B VAL* 1.3 59.8 + - - +
41B GLY 3.5 4.1 - - - +
42B ARG* 2.9 53.7 + - - +
181B ILE* 3.6 4.0 - - - -
182B VAL* 3.0 43.3 + - + +
183B ALA* 2.6 26.5 + - + +
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Residues in contact with VAL 33 (chain B).
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* 4.2 13.5 - - + +
32B ASP* 1.3 77.2 - - - +
34B MET* 1.3 76.8 + - - +
39B PRO* 3.9 1.2 - - - +
40B LEU* 3.0 36.8 + - + -
41B GLY 2.7 17.9 + - - +
43B ILE* 4.0 26.5 - - + -
76B PHE* 4.5 10.1 - - + -
160B VAL* 4.3 6.5 - - + -
164B ILE* 3.8 23.6 - - + -
179B VAL* 3.9 7.4 - - + -
180B LYS 3.6 10.5 - - - +
181B ILE* 4.7 2.2 - - + -
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Residues in contact with MET 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B VAL* 1.3 81.9 - - - +
35B ILE* 1.3 65.7 + - - +
36B ASP 3.6 5.4 - - - +
37B SER* 3.3 26.2 - - - +
38B GLU 3.3 10.8 - - - +
39B PRO* 3.1 38.8 - - + -
40B LEU* 4.0 1.3 - - - -
178B PRO 3.8 0.2 - - - +
179B VAL* 3.4 3.6 - - - -
180B LYS* 2.8 34.1 + - + +
182B VAL* 3.6 36.6 - - + -
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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