Contacts of the strand formed by residues 31 - 38 (chain B) in PDB entry 3CFV
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 TYR 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B TRP* 2.7 45.1 + + - -
27B THR* 2.8 38.2 + - + +
28B PRO* 4.1 10.6 - - - +
29B PHE 3.6 0.4 - - - -
30B LEU* 1.3 94.6 - - + +
32B ASP* 1.3 62.4 + - - +
33B LEU 3.6 10.8 - - - +
34B VAL* 3.7 22.0 - - + +
367B PHE* 3.5 25.1 - + - -
368B ILE 4.7 0.5 + - - -
369B HIS* 2.9 29.0 + + - -
370B GLY 3.9 2.9 + - - -
401B TRP* 3.7 16.2 - + - -
402B GLN 3.3 16.8 - - - +
404B ALA* 3.8 4.7 - - - +
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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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31B TYR* 1.3 74.7 - - - +
33B LEU* 1.3 62.1 + - - +
88B ASP* 5.2 13.3 - - - +
402B GLN* 2.9 20.3 + - - +
403B MSE 3.8 7.7 - - - +
404B ALA* 3.9 6.5 - - - +
405B GLU* 2.9 37.9 + - - +
408B TYR* 4.9 1.4 + - - -
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Residues in contact with LEU 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 TYR* 3.3 1.9 - - - +
32B ASP* 1.3 83.1 - - - +
34B VAL* 1.3 76.1 + - - +
35B MSE 3.7 27.4 - - + -
85B ILE* 3.8 26.5 - - + -
86B PRO* 4.6 14.4 - - + +
111B THR* 5.7 2.2 - - - +
388B VAL* 4.5 17.9 - - + -
400B ILE* 4.4 18.6 - - + +
401B TRP* 3.3 1.4 - - - -
402B GLN* 2.8 46.9 + - + +
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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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23B TRP* 4.4 16.4 - - + -
27B THR* 4.3 17.5 - - + +
31B TYR* 3.7 42.2 - - + +
33B LEU* 1.3 83.8 - - - +
35B MSE 1.3 66.1 + - - +
36B THR* 5.4 4.9 - - + -
111B THR* 4.5 7.6 + - - -
369B HIS* 5.3 0.9 - - + -
399B GLN* 5.8 2.5 - - + +
400B ILE 3.7 2.2 - - - -
401B TRP* 3.9 10.3 - - + -
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Residues in contact with MSE 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 LEU* 3.7 24.2 - - + -
34B VAL* 1.3 78.5 - - - +
36B THR* 1.3 65.5 + - - +
83B VAL* 5.9 1.3 - - + -
84B HIS 3.6 7.2 - - - +
85B ILE* 4.6 7.2 - - - -
86B PRO* 4.1 13.5 - - - -
111B THR* 3.4 15.9 - - - +
112B GLY* 2.9 41.7 - - - -
113B LYS* 3.5 7.0 - - - +
398B MSE 4.0 0.2 - - - +
399B GLN* 3.2 6.8 - - - +
400B ILE* 2.8 63.4 + - + +
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Residues in contact with THR 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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20B TYR* 5.2 8.3 + - - +
23B TRP* 5.6 4.9 - - + -
34B VAL* 5.4 4.3 - - + -
35B MSE 1.3 81.6 - - - +
37B HIS* 1.3 64.3 + - - +
397B ILE* 4.9 8.7 - - + -
398B MSE 3.5 5.8 - - - -
399B GLN* 3.2 32.5 - - + +
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Residues in contact with HIS 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 THR* 1.3 76.8 - - - +
38B ALA* 1.3 80.6 + - - +
39B LEU* 3.7 22.5 + - + +
114B ILE* 3.6 46.8 - - + +
397B ILE* 3.6 5.0 - - - -
398B MSE 2.9 44.4 + - + +
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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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37B HIS* 1.3 89.9 + - - +
39B LEU* 1.3 66.8 + - - +
40B GLN 3.9 0.2 + - - -
396B ASN* 3.6 9.2 - - + +
397B ILE* 4.0 17.5 - - + -
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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