Contacts of the strand formed by residues 22 - 28 (chain A) 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 ALA 22 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 4.2 19.1 - - + -
20A SER* 3.8 3.0 - - - -
21A ASP* 1.3 76.2 - - - +
23A TYR* 1.3 59.5 + - - +
37A VAL* 4.2 1.6 - - - -
38A ILE* 3.0 32.7 + - - +
41A SER 5.4 1.1 + - - +
44A PRO* 4.3 8.9 - - + +
46A TRP* 3.2 18.2 + - + -
69A VAL* 4.1 17.7 - - + -
70A LYS 3.2 9.6 - - - +
81A LEU* 4.5 3.4 - - + -
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Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA* 1.3 74.5 - - - +
24A CYS* 1.2 71.0 + - - +
25A SER* 4.4 4.5 - - - -
34A ARG* 2.9 49.1 + - + -
35A THR* 3.9 8.5 - - - +
36A LYS 3.5 16.2 - - - +
37A VAL* 3.8 17.7 - - + -
46A TRP* 3.6 12.6 - - - +
69A VAL* 3.5 4.2 - - - +
70A LYS* 3.0 71.1 + - + +
71A ASP 4.6 0.4 - - - -
72A HIS* 3.0 41.7 - + + -
74A THR 5.0 0.2 - - - -
75A MET 4.7 4.9 + - - -
78A ASN* 4.7 1.6 + - - -
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Residues in contact with CYS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 3.4 34.7 - - + +
23A TYR* 1.2 79.1 - - - +
25A SER* 1.1 69.7 + - - +
26A ALA* 4.0 0.7 + - - +
33A LYS 4.0 0.2 - - - +
34A ARG* 3.5 4.0 - - - -
35A THR* 3.1 44.5 + - + +
46A TRP* 4.4 12.1 - - + -
50A PHE* 5.6 0.3 - - - -
67A VAL* 4.3 4.5 - - - -
68A VAL 3.3 9.6 - - - -
69A VAL* 4.4 4.9 - - + +
117A LEU* 4.0 21.8 - - - -
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Residues in contact with SER 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 4.4 2.0 - - - -
24A CYS* 1.1 76.3 - - - +
26A ALA* 1.3 60.8 + - - +
27A VAL* 4.7 1.7 - - - +
32A LYS* 3.3 33.9 + - - +
33A LYS 3.7 3.6 - - - -
34A ARG* 3.5 24.5 + - - -
66A HIS 3.6 1.0 - - - +
67A VAL* 3.2 5.0 - - - +
68A VAL* 2.7 52.7 + - - +
70A LYS* 4.9 4.5 - - - -
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 5.8 0.2 - - + -
6A ILE* 4.3 15.7 - - + -
24A CYS 4.0 1.0 + - - +
25A SER* 1.3 74.8 + - - +
27A VAL* 1.3 60.2 + - - +
31A VAL 3.7 1.4 - - - +
32A LYS* 3.3 2.1 - - - -
33A LYS* 2.7 42.6 + - + +
50A PHE* 5.2 3.6 - - + -
52A TRP* 3.8 24.2 - - + -
65A LEU* 4.4 4.3 - - + -
66A HIS 3.3 6.3 - - - +
67A VAL* 4.1 14.4 - - + -
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER* 4.7 1.8 - - - +
26A ALA* 1.3 77.6 - - - +
28A PHE* 1.3 67.9 + - - +
30A GLY* 4.7 3.1 - - - +
31A VAL 3.5 12.8 - - - +
32A LYS* 3.6 38.1 - - + -
64A GLU 4.5 1.6 - - - +
65A LEU* 3.9 3.3 - - - +
66A HIS* 3.0 46.1 + - + +
201A FMT 4.8 1.2 + - - -
29F ALA 3.6 21.5 - - - +
30F GLY* 4.7 5.4 - - - +
31F VAL* 5.9 2.5 - - + -
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Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 3.8 13.9 - - + -
27A VAL* 1.3 75.3 - - - +
29A ALA* 1.3 76.9 + - + +
30A GLY 3.1 2.9 - - - +
31A VAL 2.7 28.6 + - - -
52A TRP* 3.0 35.9 + + + +
54A LEU* 3.3 28.9 - - + -
57A ILE* 5.8 4.0 - - + -
59A LEU* 3.5 24.9 - - + -
63A SER* 4.3 5.2 - - - -
64A GLU 3.4 24.9 - - - -
65A LEU* 3.8 11.9 - - + -
88A LEU* 3.4 21.8 - - + -
201A FMT 3.2 28.7 - - - -
56F GLY 5.5 1.8 - - - -
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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