Contacts of the strand formed by residues 38 - 47 (chain B) in PDB entry 3BX9
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 THR 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B GLY* 3.2 1.2 - - - -
33B LYS* 2.8 48.3 + - - +
36B GLU* 4.1 16.6 + - + +
37B GLY* 1.3 80.7 - - - +
39B GLN* 1.3 63.0 + - - +
69B PHE* 3.6 5.5 + - - -
214B HIS* 4.2 7.0 - - + +
215B GLU 3.3 4.7 - - - -
216B VAL* 4.2 18.8 - - + -
234B CIT 3.0 25.0 + - - +
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Residues in contact with GLN 39 (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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11B MET* 3.5 13.6 - - + +
31B GLU 3.5 11.2 - - - +
32B GLY* 3.9 0.7 - - - -
38B THR* 1.3 78.3 - - - +
40B THR* 1.3 63.6 + - - +
63B NRQ 3.4 25.5 - - + +
66B SER* 2.5 51.0 + - - -
69B PHE* 3.4 25.4 + - + +
214B HIS* 3.0 17.9 - - - -
215B GLU* 3.0 47.8 + - + +
234B CIT 3.9 3.4 + - - -
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Residues in contact with THR 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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11B MET* 3.6 2.8 - - - +
30B GLY* 3.2 3.2 - - - -
31B GLU* 3.0 36.0 + - - +
39B GLN* 1.3 72.5 - - - +
41B MET* 1.3 66.8 + - - +
42B ARG* 5.3 3.8 - - + +
63B NRQ 4.2 0.9 - - - -
202B ILE* 5.1 1.1 - - + -
212B GLU* 3.6 33.0 - - + +
213B GLN 3.2 12.3 - - - +
214B HIS* 3.3 19.2 - - + +
234B CIT 3.2 31.4 + - - +
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Residues in contact with MET 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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11B MET* 3.7 20.6 - - + -
13B LEU* 4.3 3.4 - - + -
28B SER* 3.4 24.0 - - - +
29B GLU 3.7 3.4 - - - +
30B GLY* 4.2 4.3 - - - +
39B GLN* 4.6 0.7 - - - +
40B THR* 1.3 76.9 - - - +
42B ARG* 1.3 64.0 + - - +
43B ILE* 3.9 13.0 - - + +
62B PHE* 2.8 48.5 - - - +
63B NRQ 3.5 19.3 - - + +
117B TYR* 3.6 26.2 - - + -
211B VAL 3.5 1.0 - - - +
212B GLU* 3.3 7.4 - - - +
213B GLN* 2.8 34.9 + - + +
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Residues in contact with ARG 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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28B SER* 3.3 3.3 - - - -
29B GLU* 2.8 65.3 + - - +
30B GLY* 3.7 1.4 - - - -
31B GLU* 2.4 45.8 + - - -
40B THR* 5.1 4.6 + - + +
41B MET* 1.3 73.5 - - - +
43B ILE* 1.3 62.4 + - - +
44B LYS* 5.0 6.9 - - + +
211B VAL 3.6 4.3 - - - +
212B GLU* 4.7 16.4 - - + +
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Residues in contact with ILE 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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26B CYS* 4.3 2.7 - - + -
27B THR 3.6 8.1 - - - +
28B SER* 3.7 15.3 - - - -
41B MET* 4.2 9.9 - - + -
42B ARG* 1.3 74.0 - - - +
44B LYS* 1.3 76.0 + - - +
45B VAL* 4.8 0.4 - - + +
55B PHE* 3.8 29.6 - - + -
62B PHE* 3.7 45.1 - - + -
209B THR 3.7 0.3 - - - +
210B TYR* 3.3 6.2 - - - +
211B VAL* 2.6 47.8 + - + +
213B GLN* 4.0 25.8 - - + +
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Residues in contact with LYS 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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26B CYS* 3.2 3.9 - - - -
27B THR* 2.8 47.1 + - - +
42B ARG* 5.0 6.3 - - + +
43B ILE* 1.3 81.3 - - - +
45B VAL* 1.3 63.9 + - - +
46B VAL* 3.4 16.8 + - + +
209B THR 3.3 4.7 - - - +
210B TYR* 3.9 27.8 - - + -
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Residues in contact with VAL 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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25B LYS 3.7 6.3 - - - +
26B CYS* 3.9 11.9 - - - -
44B LYS* 1.3 69.6 - - - +
46B VAL* 1.3 60.6 + - - +
47B GLU 3.5 22.0 - - - +
49B GLY* 3.7 26.8 - - - +
51B LEU* 3.8 32.1 - - + +
55B PHE* 4.4 5.4 - - + -
208B GLU 3.4 25.4 - - - +
209B THR* 2.9 35.1 + - + +
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Residues in contact with VAL 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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25B LYS* 3.0 32.8 + - + +
26B CYS* 4.4 0.7 - - - +
27B THR* 3.7 36.6 - - + +
44B LYS* 3.4 16.1 + - + +
45B VAL* 1.3 78.6 - - - +
47B GLU* 1.3 61.5 + - + +
49B GLY 5.5 0.2 - - - -
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Residues in contact with GLU 47 (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 HIS* 3.3 34.3 + - - +
24B PHE* 3.2 6.3 - - - +
25B LYS* 3.0 57.6 + - + +
45B VAL* 3.5 3.9 - - - +
46B VAL* 1.3 78.6 - - + +
48B GLY* 1.3 65.4 + - - +
49B GLY 3.3 3.1 - - - +
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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