Contacts of the helix formed by residues 17 - 29 (chain B) in PDB entry 4B2B
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 17 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLY 3.8 1.3 + - - +
16B LYS* 1.3 77.5 - - - +
18B VAL* 1.3 64.6 + - - +
19B ASP* 3.5 5.0 + - - +
20B GLN* 3.0 41.8 + - - +
21B ALA* 2.9 21.9 + - - +
60B THR 5.6 0.4 - - - +
61B ASN* 3.1 26.7 - - + +
62B VAL* 4.3 9.6 - - + +
63B VAL* 4.5 0.4 - - - -
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 1.3 71.6 - - - +
19B ASP* 1.3 61.5 + - - +
21B ALA* 3.2 7.1 + - - +
22B ARG* 2.8 53.4 + - - +
36B PHE* 3.8 23.1 - - + -
56B TYR* 3.5 42.6 - - + -
61B ASN* 3.0 33.3 + - - +
63B VAL* 4.5 3.1 - - + -
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Residues in contact with ASP 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 3.2 5.8 + - - +
18B VAL* 1.3 81.2 - - - +
20B GLN* 1.3 63.0 + - + +
22B ARG* 2.9 33.0 + - - +
23B GLU* 3.1 30.9 + - - +
61B ASN* 4.6 10.7 + - - +
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLY 4.7 1.0 - - - +
16B LYS* 3.5 22.4 - - + +
17B THR* 3.0 46.4 + - - +
19B ASP* 1.3 77.7 - - + +
21B ALA* 1.3 56.8 + - - +
23B GLU* 3.3 12.7 + - - +
24B TYR* 3.0 25.6 + - - +
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Residues in contact with ALA 21 (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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13B VAL* 3.8 26.0 - - + -
16B LYS* 4.2 6.3 - - + -
17B THR 2.9 19.6 + - - +
18B VAL 3.7 0.2 - - - +
20B GLN* 1.3 70.2 - - - +
22B ARG* 1.3 65.1 + - - +
24B TYR* 3.1 8.3 + - - +
25B PHE* 3.0 30.6 + - + -
36B PHE* 3.6 23.3 - - + -
63B VAL* 4.0 5.8 - - + -
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 2.8 36.6 + - - +
19B ASP* 2.9 39.6 + - - +
21B ALA* 1.3 76.0 - - - +
23B GLU* 1.3 64.5 + - + +
25B PHE* 3.3 2.5 + - - +
26B THR* 3.0 35.1 + - - +
36B PHE* 3.6 30.8 - - + +
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Residues in contact with GLU 23 (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 ASP* 3.1 18.5 + - - +
20B GLN* 3.6 12.2 - - - +
22B ARG* 1.3 78.1 - - + +
24B TYR* 1.3 62.5 + - - +
26B THR* 3.4 5.5 + - - -
27B LEU* 3.1 26.5 + - - +
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Residues in contact with TYR 24 (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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10B PHE* 4.7 3.1 - + - -
12B GLU* 2.6 45.4 + - + +
13B VAL* 3.4 22.2 - - + -
16B LYS* 3.9 22.4 - - + -
20B GLN 3.0 13.9 + - - +
21B ALA* 3.1 12.5 + - - +
23B GLU* 1.3 76.5 - - - +
25B PHE* 1.4 66.4 + + - +
28B HIS* 3.0 57.6 + + - +
29B TYR* 3.7 28.9 + + - -
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Residues in contact with PHE 25 (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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10B PHE* 3.7 54.3 - + + -
13B VAL* 3.9 23.6 - - + -
21B ALA 3.0 27.6 + - - +
22B ARG* 4.1 3.1 - - - +
24B TYR* 1.4 77.8 - + - +
26B THR* 1.3 61.0 + - - +
29B TYR* 2.8 54.5 + + + +
32B TYR* 5.3 0.2 - + - -
34B VAL* 3.8 37.2 - - + -
36B PHE* 4.3 2.7 - + + -
52B VAL* 4.2 9.2 - - + -
54B VAL* 3.7 26.2 - - + -
67B PRO* 4.4 1.6 - - + -
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Residues in contact with THR 26 (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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22B ARG* 3.0 24.9 + - - +
23B GLU* 3.9 6.1 - - - -
25B PHE* 1.3 79.0 - - - +
27B LEU* 1.3 61.8 + - - +
30B PRO* 3.8 19.7 - - - +
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Residues in contact with LEU 27 (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 GLU 3.1 16.6 + - - +
24B TYR 4.1 1.3 - - - +
26B THR* 1.3 81.2 - - - +
28B HIS* 1.3 91.3 + - + +
30B PRO* 3.6 8.1 - - - +
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Residues in contact with HIS 28 (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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24B TYR* 3.0 53.2 + + - +
27B LEU* 1.3 105.8 - - + +
29B TYR* 1.3 86.4 + + + +
30B PRO* 3.3 5.5 - - - +
31B GLN* 4.1 2.6 + - - +
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Residues in contact with TYR 29 (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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8B LYS* 3.8 26.3 + - - -
10B PHE* 3.8 25.7 - + - -
12B GLU* 4.4 3.5 + - - -
24B TYR* 3.7 36.4 + + - -
25B PHE* 2.8 28.0 + + + +
28B HIS* 1.3 96.7 - - + +
30B PRO* 1.3 63.8 - - - +
31B GLN* 3.1 25.7 + - - -
32B TYR* 3.1 32.9 + + + +
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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