Contacts of the helix formed by residues 27 - 37 (chain B) in PDB entry 1B43
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 ALA 27 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE 3.0 4.7 + - - -
26B ASP* 1.3 70.9 - - - +
28B LEU* 1.3 56.6 + - - +
30B ALA* 3.4 2.1 + - - +
31B ILE* 2.9 37.3 + - + +
60B LEU* 6.1 0.7 - - + -
76B TYR* 4.1 16.1 - - + -
77B VAL 2.8 25.8 + - - +
78B PHE* 3.6 41.3 - - + -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 3.3 8.3 + - - +
27B ALA* 1.3 78.3 - - - +
29B ASN* 1.3 61.5 + - - +
31B ILE* 3.4 9.4 + - + +
32B TYR* 3.1 37.6 + - + +
77B VAL 4.4 1.2 + - - -
78B PHE* 5.4 1.4 - - + +
79B ASP* 3.1 29.6 - - - +
124B THR* 5.9 6.3 - - + -
127B ASN* 3.9 29.6 - - + +
130B LEU* 6.6 0.2 - - + -
131B ILE* 4.4 23.6 - - + -
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Residues in contact with ASN 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 2.8 24.4 + - + +
28B LEU* 1.3 73.5 - - - +
30B ALA* 1.3 59.5 + - - +
32B TYR* 3.3 5.6 + - - +
33B GLN* 2.9 40.2 + - - +
153B GLU* 4.3 1.3 - - - +
170B SER* 3.1 21.4 + - - +
171B GLN* 3.0 35.5 + - - +
172B ASP* 2.9 32.7 + - - +
188B THR* 5.1 0.7 + - - +
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 3.9 13.2 - - + -
26B ASP 3.1 17.3 + - - +
27B ALA 3.6 4.0 - - - +
29B ASN* 1.3 75.5 + - - +
31B ILE* 1.3 65.4 + - - +
33B GLN* 3.0 5.3 + - - +
34B PHE* 3.0 39.6 + - + -
60B LEU* 5.3 0.4 - - + -
76B TYR* 4.3 8.1 - - + -
188B THR* 3.7 29.2 - - + -
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Residues in contact with ILE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA* 2.9 24.9 + - + +
28B LEU* 3.6 10.8 - - + +
30B ALA* 1.3 75.7 - - - +
32B TYR* 1.3 70.8 + - + +
34B PHE* 3.4 11.0 + - - +
35B LEU* 3.1 27.0 + - + +
56B HIS* 4.1 18.0 - - + +
60B LEU* 4.2 20.6 - - + -
78B PHE* 4.9 4.3 - - + -
130B LEU* 4.3 31.4 - - + +
131B ILE* 4.6 11.4 - - + -
134B ALA* 3.8 26.2 - - + -
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Residues in contact with TYR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.1 32.9 + - + +
29B ASN* 3.8 6.1 - - - +
30B ALA 3.2 0.2 - - - -
31B ILE* 1.3 84.4 - - + +
33B GLN* 1.3 63.6 + - - +
34B PHE 3.1 1.3 - - - -
35B LEU* 3.8 19.7 - - + +
36B SER* 3.0 25.3 + - - -
104B TRP* 3.3 21.0 + - - -
108B LEU* 5.4 0.2 - - + -
113B ILE* 3.8 18.3 - - + +
116B ALA* 4.6 3.8 - - + -
117B ARG* 3.3 58.7 + - + +
120B ALA* 3.6 9.8 - - + +
127B ASN* 3.0 38.5 + - - -
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Residues in contact with GLN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASN* 2.9 33.0 + - - +
30B ALA 3.0 6.5 + - - +
32B TYR* 1.3 76.7 - - - +
34B PHE* 1.3 54.7 + - + +
36B SER* 3.3 3.2 + - - -
37B THR* 2.8 45.4 + - - +
117B ARG* 4.0 17.5 + - - +
171B GLN* 3.3 33.0 - - + +
188B THR* 3.3 29.2 - - - +
189B ILE* 3.8 22.6 - - + +
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Residues in contact with PHE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA* 3.0 26.7 + - + -
31B ILE* 3.5 11.2 - - - +
32B TYR 3.1 0.2 - - - -
33B GLN* 1.3 75.6 - - - +
35B LEU* 1.3 59.6 + - - +
37B THR* 4.1 3.1 - - - -
38B ILE* 2.9 45.4 + - + +
55B SER* 3.5 17.3 - - - +
56B HIS* 3.8 17.9 - - - -
59B GLY* 3.7 26.2 - - - -
60B LEU* 3.5 32.1 - - + -
63B ARG* 3.9 16.6 - - + -
76B TYR* 4.7 5.6 - - - -
188B THR* 3.7 42.6 - - + -
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Residues in contact with LEU 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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31B ILE* 3.1 24.3 + - + +
32B TYR* 3.4 23.1 + - + +
34B PHE* 1.3 76.3 - - - +
36B SER* 1.3 59.0 + - - +
37B THR 3.8 0.2 + - - -
38B ILE 4.6 1.0 - - - +
39B ARG* 4.0 11.3 + - - +
45B PRO* 5.2 6.4 - - + +
53B ILE* 3.6 22.0 - - + -
55B SER* 3.0 28.2 + - - +
56B HIS* 4.2 14.4 - - + +
108B LEU* 4.1 22.9 - - + -
113B ILE* 3.3 29.2 - - + +
130B LEU* 3.9 27.1 - - + -
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Residues in contact with SER 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR 3.0 17.4 + - - -
33B GLN* 3.7 7.2 + - - -
35B LEU* 1.3 80.0 - - - +
37B THR* 1.3 64.1 + - - +
39B ARG* 2.9 34.5 + - - +
112B GLU* 5.3 1.4 + - - -
113B ILE* 4.1 11.3 - - - +
117B ARG* 3.9 18.1 + - - -
193B ARG* 5.1 1.0 + - - -
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Residues in contact with THR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN* 2.8 29.8 + - - +
34B PHE* 4.1 0.5 - - - -
36B SER* 1.3 87.1 - - - +
38B ILE* 1.3 67.9 + - - +
39B ARG* 3.5 8.4 + - - +
63B ARG* 5.8 1.6 + - - -
188B THR 4.7 3.6 + - - -
189B ILE* 3.7 28.1 - - + +
193B ARG* 3.7 42.6 + - - +
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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