Contacts of the strand formed by residues 28 - 35 (chain B) in PDB entry 1U5Q
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 PHE 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B PRO* 3.1 25.8 + - + +
25B GLU* 3.9 14.9 - - - +
26B LYS 5.4 0.2 - - - -
27B LEU* 1.3 98.7 - - + +
29B SER* 1.3 62.3 + - - +
31B LEU* 4.1 11.9 - - + +
45B ALA* 4.3 2.0 - - + -
46B ARG 3.0 6.1 - - - +
47B ASP* 3.7 33.4 - - - -
48B VAL* 4.5 1.8 - - - -
49B ARG* 4.4 2.9 - - - -
54B VAL* 4.1 13.2 - - + -
56B ILE* 3.7 25.1 - - + -
95B TYR* 3.8 30.7 - + - -
102B TRP* 4.3 3.2 - + + -
104B VAL* 3.6 37.2 - - + -
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Residues in contact with SER 29 (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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28B PHE* 1.3 76.1 - - - +
30B ASP* 1.3 70.7 + - - +
31B LEU* 3.2 7.4 + - - +
45B ALA* 3.5 1.9 - - - -
46B ARG* 2.8 43.6 + - - +
48B VAL* 4.0 17.7 - - - +
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Residues in contact with ASP 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 SER* 1.3 81.2 - - - +
31B LEU* 1.3 65.6 + - - +
32B ARG* 3.3 18.7 + - - +
44B PHE* 3.5 24.7 - - - +
46B ARG* 3.0 35.9 + - + -
320B ALA* 3.9 12.5 - - - +
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Residues in contact with LEU 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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28B PHE* 4.1 11.0 - - + +
29B SER* 3.7 20.4 - - - +
30B ASP* 1.3 77.3 - - - +
32B ARG* 1.3 63.2 + - - +
43B TYR* 4.0 33.0 - - + -
44B PHE 3.2 6.7 - - - +
45B ALA* 3.7 17.5 - - + -
56B ILE* 4.2 7.0 - - + -
58B LYS* 4.0 24.7 - - - +
102B TRP* 4.2 14.6 - - + -
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Residues in contact with ARG 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 ASP* 3.5 26.0 + - - +
31B LEU* 1.3 79.4 - - - +
33B GLU* 1.3 64.7 + - - +
34B ILE* 3.4 0.5 + - - +
43B TYR* 3.8 3.3 - - - -
44B PHE* 2.7 48.0 + - + +
313B LYS* 3.7 22.6 - - - +
317B PHE* 3.2 64.3 - - + +
320B ALA* 4.7 16.2 + - - +
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Residues in contact with GLU 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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32B ARG* 1.3 73.1 - - - +
34B ILE* 1.3 63.9 + - - +
35B GLY 3.7 18.3 - - - +
36B HIS* 3.3 32.1 + - - +
41B ALA* 3.8 7.9 - - + +
42B VAL 3.6 6.5 - - - +
43B TYR* 3.6 24.3 + - + -
314B LYS* 5.0 1.0 - - - +
317B PHE* 3.6 11.3 - - - -
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Residues in contact with ILE 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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32B ARG 3.7 4.0 - - - +
33B GLU* 1.3 79.7 - - - +
35B GLY* 1.3 57.3 - - - +
42B VAL* 2.9 33.6 + - + +
43B TYR 3.8 5.6 - - - +
44B PHE* 3.7 21.5 - - + +
55B ALA* 4.8 4.3 - - + -
107B TYR* 4.3 19.7 - - + +
108B CYS 5.2 4.0 - - - +
314B LYS* 3.3 43.8 + - + +
317B PHE* 3.6 27.8 - - + -
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Residues in contact with GLY 35 (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 GLU* 3.6 8.3 - - - +
34B ILE* 1.3 82.1 - - - +
36B HIS* 1.3 64.4 + - - -
41B ALA* 3.5 4.9 - - - +
42B VAL* 2.8 34.9 + - - +
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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