Contacts of the strand formed by residues 20 - 28 (chain B) in PDB entry 4IHB
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 20 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 2.5 46.7 + - - -
13B HIS* 3.6 0.2 - - - -
14B THR* 3.4 25.8 + - - -
19B ILE* 1.3 77.5 - - - +
21B ASP* 1.3 64.4 + - - +
22B ALA* 3.5 6.0 + - - -
38B ILE 3.6 1.7 - - - +
40B ASN 3.2 4.7 + - - -
41B SER 2.9 32.5 + - - +
71B ASP* 4.2 1.8 - - - -
81B LEU* 4.6 4.0 - - - -
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Residues in contact with ASP 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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19B ILE* 5.3 0.6 - - - +
20B SER* 1.3 71.5 - - - +
22B ALA* 1.3 61.8 + - - +
37B VAL* 3.5 16.9 - - + +
38B ILE 3.4 8.3 - - - +
39B LYS* 3.7 11.9 - - + +
40B ASN* 2.9 38.0 + - - -
71B ASP* 2.9 13.9 + - - +
72B HIS* 3.0 43.9 + - + +
73B GLU* 5.1 3.8 - - - +
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 4.1 13.0 - - + -
20B SER* 3.5 7.0 - - - -
21B ASP* 1.3 73.0 - - - +
23B TYR* 1.3 59.4 + - - +
37B VAL* 3.5 0.6 - - - -
38B ILE* 2.9 30.7 + - - +
41B SER 5.4 0.9 + - - +
44B PRO* 4.0 15.5 - - + -
46B TRP* 3.2 25.1 + - + -
69B VAL* 4.1 14.4 - - + -
70B LYS 3.3 10.5 - - - +
71B ASP* 4.6 0.9 - - - +
81B LEU* 4.6 0.7 - - + -
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Residues in contact with TYR 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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22B ALA* 1.3 72.8 - - - +
24B CYS* 1.3 69.9 - - - +
25B SER* 4.5 12.6 - - - -
32B LYS* 6.1 0.7 - - - -
34B ARG* 4.3 21.8 - - + -
35B THR 3.8 12.3 - - - +
36B LYS 3.6 17.7 - - - +
37B VAL* 4.1 18.4 - - + -
46B TRP* 3.6 10.3 - - - +
69B VAL* 3.4 4.9 - - - +
70B LYS* 2.9 77.8 + - + +
71B ASP 4.6 2.0 - - - -
72B HIS* 4.3 7.4 - - + -
78B ASN* 2.7 36.8 + - - +
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Residues in contact with CYS 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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6B ILE* 3.5 33.8 - - + +
23B TYR* 1.3 77.8 - - - +
25B SER* 1.3 69.2 + - - +
34B ARG* 3.2 4.0 - - - +
35B THR* 2.8 52.8 + - + +
46B TRP* 4.1 12.1 - - + -
67B VAL* 4.2 5.6 - - - -
68B VAL 3.4 11.0 - - - -
69B VAL* 4.4 4.3 - - + -
117B LEU* 4.1 20.2 - - - -
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Residues in contact with SER 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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23B TYR* 4.1 12.5 + - - -
24B CYS* 1.3 75.6 - - - +
26B ALA* 1.3 63.3 + - - +
27B VAL* 4.6 2.1 - - - +
32B LYS* 3.3 31.1 - - - +
33B LYS 3.5 4.0 - - - -
34B ARG* 4.3 4.3 - - - -
66B HIS 3.8 0.6 - - - +
67B VAL* 3.3 3.1 - - - -
68B VAL* 2.7 55.5 + - - +
70B LYS* 4.4 12.8 + - - -
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Residues in contact with ALA 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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4B VAL* 5.9 0.4 - - + -
6B ILE* 4.1 17.3 - - + -
24B CYS 4.2 0.2 - - - -
25B SER* 1.3 75.7 + - - +
27B VAL* 1.3 63.7 + - - +
32B LYS* 3.4 1.7 - - - -
33B LYS* 2.7 40.0 + - + +
50B PHE* 5.7 1.1 - - + -
52B TRP* 3.6 24.1 - - + -
65B LEU* 4.4 5.6 - - + -
66B HIS 3.3 4.0 - - - -
67B VAL* 4.1 16.8 - - + -
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Residues in contact with VAL 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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25B SER* 4.6 2.7 - - - +
26B ALA* 1.3 79.8 - - - +
28B PHE* 1.3 66.1 + - - +
30B GLY* 4.6 10.1 - - - +
31B VAL 3.5 14.6 - - - +
32B LYS* 3.7 31.4 - - + -
64B GLU 4.2 2.6 - - - +
65B LEU* 3.6 4.3 - - - +
66B HIS* 2.8 49.0 + - + +
68B VAL* 6.4 1.3 - - + -
202B FMT 4.8 2.1 + - - +
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Residues in contact with PHE 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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2B LEU* 3.7 19.3 - - + -
27B VAL* 1.3 75.2 - - - +
29B ALA* 1.3 80.4 + - + +
30B GLY 3.2 2.0 - - - -
31B VAL 2.9 22.2 + - - -
52B TRP* 3.1 42.8 + + + +
54B LEU* 3.6 31.4 - - + -
57B ILE* 4.4 13.9 - - + -
59B LEU* 4.5 9.4 - - + -
63B SER* 4.8 5.4 - - - -
64B GLU 4.1 4.5 - - - -
65B LEU* 3.8 11.7 - - + -
88B LEU* 3.4 33.0 - - + -
202B FMT 3.7 23.3 - - - -
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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