Contacts of the strand formed by residues 33 - 38 (chain B) in PDB entry 3UNF
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 CYS 33 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B GLY 4.1 5.6 - - - +
32B THR* 1.3 76.9 - - - +
34B LEU* 1.3 62.6 + - - +
44B LEU* 5.3 0.2 - - - -
45B ALA 3.6 3.8 - - - -
46B ALA* 3.9 10.5 - - + +
63B LYS* 4.6 0.7 - - - +
74B SER* 3.0 39.7 - - - -
75B VAL 4.2 11.0 - - - +
134B LEU* 3.3 12.4 - - - +
162B CYS* 3.3 2.0 - - - -
163B ILE* 2.8 61.7 + - + +
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Residues in contact with LEU 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 THR* 4.3 1.8 - - + -
33B CYS* 1.3 76.3 - - - +
35B GLY* 1.3 58.7 + - - +
36B ILE* 3.7 30.3 - - + -
43B LEU* 4.7 2.0 - - + -
44B LEU* 3.5 4.0 - - - +
45B ALA* 2.8 62.6 + - + +
134B LEU* 3.7 6.0 - - - +
161B THR 3.4 10.5 - - - +
162B CYS* 4.0 13.5 - - + -
174B LEU* 4.9 5.4 - - + -
192B ALA* 3.8 11.4 - - + +
195B VAL* 3.8 30.7 - - + -
196B LEU* 4.0 24.9 - - + -
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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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34B LEU* 1.3 75.1 - - - +
36B ILE* 1.3 64.7 + - - +
43B LEU 3.3 11.0 - - - -
44B LEU* 4.6 2.5 - - - -
134B LEU* 3.6 6.5 - - - +
146B LEU* 3.3 25.9 - - - +
160B ALA* 3.4 0.9 - - - -
161B THR 2.9 33.5 + - - +
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Residues in contact with ILE 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 LEU* 3.7 24.0 - - + -
35B GLY* 1.3 81.0 - - - +
37B LEU* 1.3 63.4 + - - +
42B VAL* 3.4 5.8 - - - +
43B LEU* 3.1 39.9 + - + +
146B LEU* 4.6 0.8 - - - +
159B LYS 3.8 2.7 - - - +
160B ALA* 4.3 2.5 - - + +
174B LEU* 3.9 26.2 - - + -
178B TYR* 3.7 29.4 - - + -
183B MET* 4.2 2.7 - - + -
188B ALA* 3.5 42.0 - - + +
191B LEU* 4.3 4.5 - - + -
192B ALA* 3.9 11.2 - - + +
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Residues in contact with LEU 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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36B ILE* 1.3 74.3 - - - +
38B ALA* 1.3 67.0 + - - +
42B VAL* 3.9 16.6 - - + -
144B PHE* 3.5 46.9 - - + +
145B GLN* 3.9 8.7 - - - +
146B LEU* 4.4 2.2 - - + +
158B TRP 4.1 8.5 - - - +
159B LYS* 2.7 43.3 + - + +
178B TYR* 2.7 33.2 + - - +
183B MET* 4.2 1.7 - - - +
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Residues in contact with ALA 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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36B ILE 3.9 0.8 + - - +
37B LEU* 1.3 85.9 - - - +
39B ASN* 1.3 67.8 + - - +
40B ASP 4.3 1.8 - - - +
41B GLY 2.8 27.7 + - - +
144B PHE* 4.6 3.8 - - - +
183B MET* 3.5 15.0 - - - +
184B THR 3.6 23.1 - - - +
185B LEU* 3.6 11.7 - - + +
188B ALA* 4.4 8.5 - - + -
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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