Contacts of the helix formed by residues 55 - 69 (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 SER 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PHE* 3.5 20.5 - - - +
35B LEU* 3.0 31.1 - - - +
38B ILE* 3.1 32.3 - - - +
45B PRO* 4.7 3.3 - - - +
46B LEU* 3.8 23.4 + - - -
53B ILE* 3.6 5.7 - - - +
54B THR* 1.3 78.6 + - - +
56B HIS* 1.3 60.8 + - - +
58B SER* 4.2 0.2 - - - -
59B GLY 3.1 17.3 + - - -
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Residues in contact with HIS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 4.1 28.7 - - + +
34B PHE* 3.8 11.8 - - - -
35B LEU* 4.4 6.3 - - + -
53B ILE* 3.4 30.4 + - + -
54B THR* 3.9 2.9 - - - -
55B SER* 1.3 82.5 + - - +
57B LEU* 1.3 75.4 + - + +
60B LEU* 3.1 37.3 + - - +
130B LEU* 3.6 41.3 + - + +
133B ASP* 3.3 40.5 + - + +
134B ALA 4.8 1.0 + - - -
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ILE 5.0 0.2 - - - +
54B THR* 3.2 12.7 + - + +
56B HIS* 1.3 99.0 - - + +
58B SER* 1.3 65.3 + - - +
60B LEU* 4.5 0.9 - - - -
61B PHE* 3.1 21.7 + - - +
133B ASP* 3.5 43.3 - - + +
134B ALA* 4.4 2.2 - - - +
137B LEU* 3.3 29.3 - - + +
302B PHE* 3.7 13.0 - - + -
303B LEU* 4.3 4.5 - - + -
307B HIS* 4.1 34.1 - - + +
309B PHE* 4.0 11.2 - - + -
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 4.3 9.2 - - - +
46B LEU* 3.6 25.5 - - - +
54B THR 3.0 17.5 + - - -
55B SER* 3.6 5.2 - - - -
56B HIS 3.3 0.2 - - - -
57B LEU* 1.3 75.6 - - - +
59B GLY* 1.3 60.1 - - - +
61B PHE 3.3 0.7 + - - -
62B TYR* 2.9 54.8 + - - +
309B PHE* 3.7 15.6 - - - -
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Residues in contact with GLY 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 3.6 22.3 - - - -
38B ILE* 3.5 20.1 - - - +
55B SER 3.1 7.5 + - - -
58B SER* 1.3 80.9 - - - +
60B LEU* 1.3 57.7 + - - +
62B TYR* 5.2 0.7 - - - -
63B ARG* 2.8 37.4 + - - +
64B THR 3.5 0.5 + - - -
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA* 6.1 0.7 - - + -
30B ALA* 5.3 0.4 - - + -
31B ILE* 4.2 14.6 - - + -
34B PHE* 3.5 14.8 - - + -
56B HIS* 3.1 28.0 + - + +
57B LEU* 4.1 6.3 - - - +
58B SER 3.4 0.2 - - - -
59B GLY* 1.3 74.2 - - - +
61B PHE* 1.3 56.1 - - - +
64B THR* 2.5 27.2 + - - +
76B TYR* 3.5 40.4 - - + -
134B ALA* 3.4 40.8 - - + +
137B LEU* 4.1 10.5 - - + -
138B LEU* 4.2 13.0 - - + +
141B MET* 3.7 7.8 - - - +
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Residues in contact with PHE 61 (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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57B LEU 3.1 17.4 + - - +
58B SER 3.9 1.8 - - - +
59B GLY 3.1 0.8 - - - -
60B LEU* 1.3 79.3 - - - +
62B TYR* 1.3 95.2 + + + +
65B ILE* 3.0 56.9 + - + +
137B LEU* 4.0 4.5 - - + -
141B MET* 3.6 26.2 - - + +
299B ILE* 3.9 19.3 - - + -
303B LEU* 3.6 23.1 - - + -
309B PHE* 4.8 1.1 - - + -
314B VAL* 3.8 39.5 - - + -
317B GLY* 4.5 1.6 - - - -
318B LEU* 4.1 11.7 - - + -
321B LEU* 5.2 0.2 - - + -
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Residues in contact with TYR 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B SER* 2.9 41.0 + - - +
59B GLY* 5.2 0.7 - - - -
61B PHE* 1.3 95.1 - + - +
63B ARG* 1.3 59.0 + - - +
65B ILE* 3.2 7.3 + - + +
66B ASN* 2.9 36.2 + - - +
309B PHE* 3.7 34.7 - + - +
310B SER* 4.4 2.8 + - - -
313B ARG* 3.7 46.2 + - + +
314B VAL* 3.7 9.5 - - - +
317B GLY* 5.6 1.1 - - - -
320B ARG* 4.8 12.5 + - - +
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Residues in contact with ARG 63 (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 PHE* 3.9 21.9 - - + -
37B THR* 5.8 1.4 + - - -
38B ILE* 6.1 2.2 - - + +
59B GLY* 2.8 26.9 + - - +
62B TYR* 1.3 73.6 - - - +
64B THR* 1.3 61.1 + - - +
66B ASN* 3.2 18.8 + - - +
67B LEU* 3.0 36.8 + - + +
76B TYR* 5.2 1.1 - - - +
187B LEU 3.5 18.8 + - - +
188B THR* 3.4 21.6 + - + -
189B ILE* 3.9 5.7 - - - +
190B THR* 2.9 49.7 + - - +
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Residues in contact with THR 64 (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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59B GLY 3.5 1.0 + - - -
60B LEU* 2.5 28.6 + - - +
61B PHE 3.8 1.8 - - - -
62B TYR 3.2 0.8 - - - -
63B ARG* 1.3 78.1 - - - +
65B ILE* 1.3 57.2 + - - +
67B LEU* 3.3 8.4 + - - +
68B MET* 3.0 33.7 + - - +
74B PRO* 3.8 23.6 - - + -
76B TYR* 2.7 32.9 + - + -
138B LEU* 5.0 0.2 - - + -
141B MET* 4.1 5.4 - - + -
143B ILE* 4.0 26.2 - - + -
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Residues in contact with ILE 65 (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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61B PHE* 3.0 58.7 + - + +
62B TYR* 3.7 5.6 - - + +
64B THR* 1.3 75.4 - - - +
66B ASN* 1.3 52.8 + - - +
68B MET* 3.3 6.8 + - - +
69B GLU* 2.8 37.5 + - + +
141B MET* 3.9 12.3 - - + -
317B GLY* 3.6 25.1 - - - +
320B ARG* 3.5 37.9 - - + +
321B LEU* 4.1 19.1 - - + +
324B ALA* 6.2 0.2 - - + -
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Residues in contact with ASN 66 (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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15B LEU* 5.2 6.6 - - + +
62B TYR* 2.9 22.4 + - - +
63B ARG* 3.4 24.0 + - - +
64B THR 3.2 0.2 - - - -
65B ILE* 1.3 77.4 - - - +
67B LEU* 1.3 63.8 + - + +
69B GLU* 3.2 11.8 + - - +
70B ALA* 3.1 21.9 + - - +
320B ARG* 3.2 20.8 - - - +
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Residues in contact with LEU 67 (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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15B LEU* 4.1 27.4 - - + -
25B ILE* 4.0 26.2 - - + -
63B ARG* 3.0 23.2 + - + +
64B THR* 3.6 11.7 - - - +
66B ASN* 1.3 77.7 - - + +
68B MET* 1.3 59.4 + - - +
70B ALA* 3.1 13.4 + - - +
72B ILE* 3.0 42.3 + - + +
74B PRO* 4.6 8.7 - - + -
76B TYR* 4.9 2.2 - - - +
187B LEU* 4.1 37.2 - - + +
188B THR* 6.1 2.2 - - + -
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Residues in contact with MET 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B THR* 3.0 22.6 + - - +
65B ILE* 3.7 5.6 - - - +
67B LEU* 1.3 71.0 - - - +
69B GLU* 1.3 60.4 + - - +
70B ALA 3.0 2.0 - - - -
71B GLY* 2.8 21.0 + - - -
72B ILE 3.3 9.6 - - - +
73B LYS* 5.7 1.1 - - + -
74B PRO* 3.5 19.5 - - + -
143B ILE* 3.3 22.4 - - + -
291B TRP* 3.7 26.9 - - + +
321B LEU* 3.3 30.5 - - + -
324B ALA* 3.6 22.3 - - + +
325B ILE* 4.2 24.0 - - + +
327B SER* 5.9 0.9 - - - -
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Residues in contact with GLU 69 (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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19B TYR* 5.5 1.6 - - - -
65B ILE* 2.8 20.5 + - + +
66B ASN* 3.4 14.5 + - - +
68B MET* 1.3 73.1 - - - +
70B ALA* 1.3 58.5 + - - +
71B GLY 3.2 1.1 + - - -
320B ARG* 2.7 56.9 + - + +
324B ALA* 4.1 9.8 - - + +
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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