Contacts of the strand formed by residues 33 - 38 (chain B) in PDB entry 5LTU
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 33 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B PHE* 3.3 9.6 - - - -
27B ARG* 3.1 60.2 + - + +
28B SER 6.0 0.4 - - - +
32B ASP* 1.3 85.1 - - + +
34B VAL* 1.3 61.1 + - - +
119B TRP* 3.8 20.4 - - + +
120B PHE 3.4 10.5 - - - +
121B LYS* 4.5 14.1 - - + -
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Residues in contact with VAL 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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24B LEU* 4.3 12.8 - - + -
25B CYS 3.3 24.2 - - - +
26B PHE* 4.0 18.6 - - + -
32B ASP 4.2 0.4 - - - -
33B GLU* 1.3 73.8 - - - +
35B LEU* 1.3 69.9 + - - +
36B LEU* 3.7 10.6 + - + -
48B VAL* 6.5 0.2 - - + -
119B TRP* 3.5 3.8 - - - -
120B PHE* 2.8 40.2 + - - +
122B VAL* 4.7 5.2 - - + -
125B ALA* 3.7 26.7 - - + -
140B LEU* 4.4 16.6 - - + -
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Residues in contact with LEU 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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25B CYS* 2.9 26.7 + - + +
34B VAL* 1.3 76.9 - - - +
36B LEU* 1.3 69.2 + - - +
37B VAL* 5.1 1.8 - - + -
49B PRO* 4.0 15.8 - - + +
71B ALA* 4.5 14.6 - - + +
73B VAL* 3.7 30.3 - - + -
100B VAL* 5.1 0.2 - - + -
117B ARG* 4.1 15.0 - - + -
118B GLU* 3.4 35.7 - - - +
119B TRP* 3.5 36.3 - - + +
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Residues in contact with LEU 36 (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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34B VAL* 3.7 16.4 + - + +
35B LEU* 1.3 82.5 - - - +
37B VAL* 1.3 71.3 + - - +
46B TRP* 3.8 12.8 - - + -
47B ILE 3.7 9.4 - - - +
48B VAL* 3.9 28.9 - - + -
49B PRO* 4.9 0.2 - - - -
117B ARG* 3.5 1.2 - - - +
118B GLU 3.1 29.9 + - - -
120B PHE* 3.6 34.1 - - + -
125B ALA* 3.8 19.7 - - + -
128B VAL* 4.0 17.3 - - + -
129B LEU* 4.2 13.5 - - + -
140B LEU* 5.4 0.7 - - + -
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Residues in contact with VAL 37 (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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35B LEU* 5.1 2.9 - - + -
36B LEU* 1.3 82.1 - - - +
38B SER* 1.3 65.2 + - - +
46B TRP* 3.3 9.7 - - - -
47B ILE* 2.8 50.6 + - + +
49B PRO* 4.5 17.7 - - + -
70B GLU* 4.3 2.2 - - + +
71B ALA* 3.9 28.9 - - + -
115B ARG* 4.2 18.6 - - - +
116B LYS 3.3 13.5 - - - +
117B ARG* 4.1 13.5 - - + -
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Residues in contact with SER 38 (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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37B VAL* 1.3 78.4 - - - +
39B SER* 1.3 61.3 - - - +
40B SER 5.4 1.8 - - - -
45B GLN 3.6 8.3 - - - -
46B TRP* 3.7 8.7 - - - -
47B ILE* 4.3 0.6 - - - +
115B ARG* 2.8 41.7 + - - +
116B LYS* 3.1 39.9 + - - +
203B EDO 5.6 2.7 - - - -
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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