Contacts of the strand formed by residues 41 - 50 (chain H) in PDB entry 6B0B
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 41 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138E PHE* 4.0 21.7 - - + -
142E ALA* 5.2 2.9 - - + -
163E LEU* 5.0 5.6 - - - +
35H GLY* 3.4 1.0 - - - -
36H ARG* 2.9 53.3 + - - +
39H GLU* 3.9 9.4 - - + +
40H GLY* 1.3 81.7 - - - +
42H GLN* 1.3 64.1 + - - +
72H TYR* 4.5 1.3 - - - +
214H TYR* 3.8 20.2 - - + +
215H GLU 3.4 3.8 - - - -
216H ARG* 3.7 25.4 - - - +
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Residues in contact with GLN 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E LEU* 6.3 1.1 - - - -
14H PHE* 3.9 19.0 - - - -
34H GLU 3.7 9.2 - - - +
35H GLY* 4.0 1.6 - - - -
41H THR* 1.3 76.9 - - - +
43H THR* 1.3 66.2 + - - +
44H ALA* 5.6 1.6 - - - +
65H PHE* 4.8 12.8 - - - +
70H LYS 5.1 1.9 + - - -
72H TYR* 3.3 53.1 + - + +
213H GLN 3.8 0.2 - - - +
214H TYR* 3.2 9.0 - - - -
215H GLU* 2.9 73.2 + - + +
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Residues in contact with THR 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E TYR* 3.7 47.3 - - + -
163E LEU* 4.8 11.6 - - + +
14H PHE* 4.3 2.7 - - - -
33H GLY* 3.3 1.6 - - - -
34H GLU* 2.9 50.5 + - - +
42H GLN* 1.3 81.2 - - - +
44H ALA* 1.3 61.7 + - - +
45H LYS* 5.8 1.7 - - - -
212H GLU* 5.9 2.2 - - - -
213H GLN 3.0 10.1 - - - +
214H TYR* 4.0 11.0 - - + -
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Residues in contact with ALA 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H PHE* 3.8 24.0 - - + -
32H GLU 3.8 5.8 - - - +
33H GLY* 3.9 0.4 - - - -
42H GLN* 5.6 2.0 - - - +
43H THR* 1.3 76.0 - - - +
45H LYS* 1.3 64.0 + - - +
46H LEU* 4.0 17.3 - - + +
65H PHE* 5.7 7.2 - - + -
211H VAL 3.7 0.9 - - - +
212H GLU* 3.0 8.4 - - - +
213H GLN* 2.9 40.7 + - + +
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Residues in contact with LYS 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E TYR* 5.3 2.0 - - - -
31H GLY* 3.2 3.8 - - - -
32H GLU* 2.9 43.3 + - + +
33H GLY* 6.0 0.2 - - - -
34H GLU* 5.5 5.8 + - - -
43H THR* 5.8 1.8 - - - -
44H ALA* 1.3 76.2 - - - +
46H LEU* 1.3 61.9 + - - +
47H LYS* 5.1 13.7 + - - +
210H ILE* 6.4 1.8 - - + -
211H VAL 3.6 4.5 - - - +
212H GLU* 3.4 36.6 - - + +
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Residues in contact with LEU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H VAL* 4.2 10.8 - - + -
29H ILE* 4.1 8.5 - - + -
30H GLU 3.8 1.1 - - - -
31H GLY* 3.7 16.6 - - - +
44H ALA* 4.0 19.1 - - + +
45H LYS* 1.3 83.0 - - - +
47H LYS* 1.3 71.4 + - - +
58H TRP* 3.7 40.2 - - + -
65H PHE* 4.1 22.7 - - + -
209H THR 4.6 1.1 - - - -
210H ILE* 3.8 8.9 - - - +
211H VAL 2.9 37.2 + - - +
213H GLN* 4.1 18.2 - - + -
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Residues in contact with LYS 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H ILE* 3.4 4.7 - - - -
30H GLU* 2.9 39.3 + - + +
32H GLU* 4.4 15.6 + - - +
45H LYS* 5.1 13.9 + - - +
46H LEU* 1.3 81.5 + - - +
48H VAL* 1.3 68.0 + - - +
49H THR* 3.6 6.4 + - + +
209H THR 3.8 5.2 - - - -
210H ILE* 3.7 23.1 - - + +
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Residues in contact with VAL 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H PHE* 5.2 0.2 - - + -
28H GLU 3.8 7.4 - - - +
29H ILE* 4.4 9.2 - - + -
47H LYS* 1.3 74.5 - - - +
49H THR* 1.3 60.8 + - - +
50H LYS 3.3 28.0 - - - +
52H GLY* 4.1 17.1 - - - +
54H LEU* 4.2 33.9 - - + -
58H TRP* 4.6 6.7 - - + -
208H TYR 4.5 2.7 - - - +
209H THR* 3.5 35.8 + - + +
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Residues in contact with THR 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H GLU* 3.0 32.7 + - - +
29H ILE 4.0 0.3 + - - -
30H GLU* 3.7 29.4 - - + +
47H LYS* 4.0 10.5 - - + +
48H VAL* 1.3 77.7 - - - +
50H LYS* 1.3 77.7 + - - +
52H GLY 5.5 0.2 - - - -
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Residues in contact with LYS 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H GLU 5.0 1.6 - - - +
27H PHE* 3.3 21.9 - - - +
28H GLU* 3.6 29.2 + - + +
48H VAL* 3.3 12.7 - - - +
49H THR* 1.3 96.0 + - - +
51H GLY* 1.3 62.9 + - - +
52H GLY 3.3 2.5 - - - -
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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