Contacts of the strand formed by residues 22 - 33 (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 HIS 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B THR* 3.2 4.3 - - - -
19B VAL 2.9 34.7 + - - +
20B ASN 3.2 2.4 - - - +
21B ASN* 1.3 79.0 - - - +
23B HIS* 1.3 80.1 + - - +
24B PHE* 3.6 4.2 - - - -
48B GLY* 2.6 35.2 + - - -
50B PRO 4.8 0.6 + - - -
51B LEU* 4.2 5.3 - - + +
52B PRO* 3.3 41.9 - - + +
53B PHE* 4.2 8.4 - - + -
133B MET* 6.2 0.7 - - + -
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Residues in contact with HIS 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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16B GLU* 2.5 35.5 + - + +
17B GLY 3.3 17.3 - - - -
18B THR* 3.8 15.0 - - + +
21B ASN 3.9 3.8 + - - -
22B HIS* 1.3 94.3 + - - +
24B PHE* 1.3 68.7 + - - +
25B LYS* 4.0 3.4 - - + -
47B GLU* 3.3 34.0 + - - +
48B GLY* 3.4 7.6 - - - -
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Residues in contact with PHE 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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15B MET* 4.0 16.4 - - + -
16B GLU* 3.5 5.4 - - - +
17B GLY* 2.9 63.2 + - - +
18B THR* 3.7 3.6 - - - -
19B VAL* 3.9 8.7 - - + -
22B HIS* 3.6 10.3 - - + -
23B HIS* 1.3 78.0 - - - +
25B LYS* 1.3 69.8 + - - +
26B CYS* 4.0 15.0 - - - -
47B GLU 3.2 16.4 - - - +
48B GLY* 4.3 0.2 - - - -
51B LEU* 3.5 23.6 - - + -
53B PHE* 3.7 20.4 - + - -
58B LEU* 3.7 38.1 - - + -
121B ILE* 4.1 8.1 - - + -
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Residues in contact with LYS 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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15B MET 3.1 8.5 - - - +
16B GLU* 3.4 38.2 + - + -
23B HIS* 4.0 2.2 - - + -
24B PHE* 1.3 80.2 - - - +
26B CYS* 1.3 68.2 + - - +
45B VAL* 3.7 0.9 - - - +
46B VAL* 3.0 36.4 + - + -
47B GLU* 3.0 46.1 + - + +
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Residues in contact with CYS 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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13B LEU* 4.7 0.4 - - - -
14B TYR* 3.7 0.2 - - - -
15B MET* 2.7 44.0 + - + +
24B PHE* 4.0 18.1 - - - -
25B LYS* 1.3 80.4 - - - +
27B THR* 1.3 69.2 + - - +
43B ILE* 4.3 3.8 - - + -
44B LYS 3.2 8.1 - - - +
45B VAL* 3.9 25.1 - - - -
46B VAL* 4.4 1.6 - - - +
51B LEU* 5.0 0.2 - - - -
55B PHE* 4.7 1.3 - - - -
58B LEU* 4.5 6.7 - - - -
62B PHE* 4.0 33.2 - - + -
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Residues in contact with THR 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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13B LEU* 3.2 14.1 - - - +
14B TYR* 4.2 21.1 - - + -
26B CYS* 1.3 80.6 - - - +
28B SER* 1.3 65.7 + - - +
43B ILE* 3.6 1.6 - - - +
44B LYS* 2.8 41.5 + - - +
46B VAL* 3.7 28.8 - - + +
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Residues in contact with SER 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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12B LYS* 3.3 3.5 - - - +
13B LEU* 2.7 52.8 + - - +
27B THR* 1.3 80.0 - - - +
29B GLU* 1.3 66.4 + - - +
41B MET* 3.4 24.5 - - - +
42B ARG 3.3 15.3 - - - -
43B ILE* 3.7 20.0 - - - -
44B LYS* 6.1 0.2 - - - -
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Residues in contact with GLU 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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11B MET 3.3 4.7 - - - +
12B LYS* 3.6 29.6 - - + +
28B SER* 1.3 82.1 - - - +
30B GLY* 1.3 58.8 + - - +
41B MET* 4.5 2.0 - - - -
42B ARG* 2.8 50.5 + - - +
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Residues in contact with GLY 30 (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 HIS* 3.4 7.8 + - - +
11B MET* 2.8 41.7 + - - +
29B GLU* 1.3 77.0 - - - +
31B GLU* 1.3 75.2 + - - +
40B THR 3.2 14.4 - - - -
41B MET* 4.2 2.2 - - - +
42B ARG* 3.7 1.5 - - - +
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Residues in contact with GLU 31 (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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9B MET 3.2 11.9 - - - +
10B HIS* 4.5 18.3 + - + +
11B MET* 3.3 6.7 - - - +
30B GLY* 1.3 79.0 - - - +
32B GLY* 1.3 58.0 + - - +
40B THR* 3.0 31.6 + - - +
42B ARG* 2.4 47.5 + - - -
234B CIT 3.4 43.1 - - + +
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Residues in contact with GLY 32 (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 ASN* 3.5 4.5 - - - -
9B MET 3.0 32.1 + - - -
31B GLU* 1.3 76.1 - - - +
33B LYS* 1.3 60.8 + - - -
34B PRO* 3.5 2.6 - - - +
38B THR 3.2 12.8 - - - -
39B GLN* 3.9 1.3 - - - -
69B PHE* 3.4 15.2 - - - -
234B CIT 3.6 16.6 - - - +
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Residues in contact with LYS 33 (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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7B GLU* 3.4 18.7 + - - +
8B ASN* 3.0 33.8 + - - +
32B GLY* 1.3 71.3 - - - -
34B PRO* 1.3 68.9 - - - +
35B TYR 3.2 2.0 - - - +
36B GLU* 3.1 39.3 + - + +
37B GLY 3.0 19.6 + - - -
38B THR* 2.8 26.0 + - - +
69B PHE* 3.8 2.0 - - - -
234B CIT 3.6 25.4 - - - +
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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