Contacts of the strand formed by residues 39 - 46 (chain B) in PDB entry 5F2R
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 39 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ASP* 4.3 5.7 - - - +
36B GLY* 3.4 14.3 - - - -
38B THR* 1.3 94.4 + - - +
40B SER* 1.3 62.3 + - - +
61B ILE* 3.7 33.9 - - + -
62B THR 3.2 5.6 - - - +
63B PRO* 3.6 33.6 - - + +
64B SER* 3.9 1.6 - - - -
65B TYR* 6.5 0.2 - + - -
78B ASP* 5.1 2.7 - - - -
81B LYS* 3.0 31.3 + - - +
293B GLU* 3.7 5.7 + - - -
297B ARG* 3.1 29.0 + - - -
501B ACP 2.9 50.7 + - - +
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Residues in contact with SER 40 (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 ASP 3.2 13.4 + - - -
35B LEU* 3.7 3.8 - - - +
36B GLY 3.2 12.3 + - - -
39B TYR* 1.3 73.3 - - - +
41B CYS* 1.3 61.7 + - - +
61B ILE* 3.3 6.4 - - - +
62B THR 2.6 35.6 + - - -
64B SER* 2.8 21.5 + - - -
149B VAL* 3.6 11.7 - - - +
153B MET* 3.7 30.9 - - - +
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Residues in contact with CYS 41 (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 ILE* 3.5 3.5 - - - +
34B ASP* 2.8 39.0 + - + +
39B TYR 5.5 0.2 - - - +
40B SER* 1.3 77.0 - - - +
42B VAL* 1.3 62.4 + - - +
52B ILE* 3.8 18.8 - - - -
60B ARG 3.4 23.3 - - - +
61B ILE* 4.3 3.1 - - + -
153B MET* 3.5 5.8 - - - +
391B ASP 4.2 11.9 - - - +
392B GLU* 4.1 19.1 - - - -
395B ALA* 3.5 23.2 - - + +
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Residues in contact with VAL 42 (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 VAL* 4.0 17.9 - - + -
32B GLY 3.3 9.6 - - - +
33B ILE* 3.9 15.7 - - + -
41B CYS* 1.3 77.9 - - - +
43B GLY* 1.3 62.3 + - - +
52B ILE* 3.7 5.1 - - - +
53B ILE* 2.9 37.7 + - + +
60B ARG 4.8 1.6 + - - -
153B MET* 3.7 27.1 - - + +
156B THR* 3.8 30.3 - - + -
157B ALA* 4.1 13.9 - - + +
395B ALA* 4.5 3.4 - - - -
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Residues in contact with GLY 43 (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 VAL* 3.6 1.7 - - - +
32B GLY* 2.8 34.5 + - - -
42B VAL* 1.3 75.3 - - - +
44B VAL* 1.3 68.2 + - - +
51B GLU 3.2 13.0 - - - -
52B ILE* 4.3 8.1 - - - -
53B ILE* 4.5 1.3 - - - -
395B ALA* 4.5 2.2 - - - +
399B ALA* 3.7 15.4 - - - +
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Residues in contact with VAL 44 (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 THR* 4.3 10.3 - - + -
30B VAL 4.2 8.7 - - - +
31B VAL* 3.7 25.4 - - + -
43B GLY* 1.3 78.6 - - - +
45B PHE* 1.3 56.7 + - - +
46B LYS* 4.5 7.9 - - + -
50B VAL* 3.4 3.1 - - - +
51B GLU* 2.7 41.0 + - + +
53B ILE* 3.8 23.3 - - + -
160B TYR* 3.9 22.0 - - + -
161B LEU* 4.2 18.8 - - + -
399B ALA* 3.9 9.6 - - - +
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Residues in contact with PHE 45 (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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45A PHE* 3.7 24.7 - + - -
48A GLY* 3.9 18.6 - - - -
29B THR* 4.8 8.9 - - - +
30B VAL 5.1 2.8 + - - -
44B VAL* 1.3 74.2 - - - +
46B LYS* 1.3 65.5 + - - +
47B ASN 5.2 0.2 - - - -
48B GLY* 3.3 38.6 - - - -
49B ARG* 3.4 19.1 - - - -
50B VAL* 3.8 17.0 - - + -
399B ALA 3.9 9.3 + - - +
400B VAL* 4.7 10.3 - - + -
403B GLY* 3.6 31.7 - - - +
406B SER* 6.0 1.7 - - - -
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Residues in contact with LYS 46 (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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44B VAL* 3.9 10.0 + - + -
45B PHE* 1.3 77.8 - - - +
47B ASN* 1.3 94.3 + - - +
48B GLY 3.2 1.8 - - - -
49B ARG* 2.8 28.1 + - - +
51B GLU* 4.6 11.0 - - + +
160B TYR* 4.1 39.3 + - + +
161B LEU* 4.4 18.5 + - + +
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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