Contacts of the strand formed by residues 16 - 22 (chain A) in PDB entry 3IU3
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 VAL 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A VAL* 3.5 39.5 - - + -
10A ALA* 5.0 3.4 - - + -
15A SER* 1.3 79.0 - - - +
17A LYS* 1.3 69.2 + - - +
18A MET* 4.4 7.6 - - + -
79A MET 3.6 2.1 - - - +
80A GLU* 3.2 4.5 - - - -
81A LEU* 2.7 47.7 + - + +
84A LEU* 3.5 22.2 - - + -
111A LEU* 4.0 17.5 - - + -
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Residues in contact with LYS 17 (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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8A VAL* 5.9 0.9 - - - +
16A VAL* 1.3 81.2 - - - +
18A MET* 1.3 60.6 + - - +
69A THR* 4.5 8.5 + - - -
78A TYR* 3.7 43.9 - - + -
79A MET 3.4 9.6 - - - +
80A GLU* 3.4 32.7 + - + +
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Residues in contact with MET 18 (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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5A SER* 3.6 13.9 - - - +
8A VAL* 4.6 7.9 - - + -
16A VAL* 4.1 15.7 - - + -
17A LYS* 1.3 75.4 - - - +
19A SER* 1.3 62.9 + - - +
34A TRP* 4.0 16.2 - - + -
78A TYR* 3.4 6.2 - - - +
79A MET* 3.0 51.2 + - + +
81A LEU* 4.9 0.9 - - + -
92A TYR* 3.7 43.7 - - + -
109A THR* 4.1 26.0 - - + +
111A LEU* 4.2 20.9 - - + -
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Residues in contact with SER 19 (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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3A GLN 5.0 0.9 + - - -
4A GLN* 3.3 7.4 + - - +
5A SER* 3.2 39.7 + - - -
18A MET* 1.3 77.2 - - - +
20A CYS* 1.3 64.8 + - - +
21A LYS* 4.9 2.3 + - - +
34A TRP* 4.1 4.9 - - - -
76A THR* 3.7 18.5 - - - +
77A ALA 3.4 5.2 - - - -
78A TYR* 3.8 17.7 - - - -
109A THR* 4.8 0.2 + - - -
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Residues in contact with CYS 20 (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* 4.4 12.3 - - - -
3A GLN 3.4 6.1 - - - -
4A GLN* 4.2 1.8 - - + +
19A SER* 1.3 78.2 - - - +
21A LYS* 1.3 60.8 + - - +
22A ALA* 3.4 4.1 + - - +
27A PHE* 5.1 0.5 - - - -
32A MET* 4.2 17.3 - - - -
34A TRP* 3.8 8.7 - - + -
76A THR* 3.8 1.8 - - - -
77A ALA* 2.9 33.7 + - + +
94A CYS* 2.0 52.7 - - + -
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Residues in contact with LYS 21 (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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1A GLN 3.3 4.9 - - - +
2A LEU* 4.7 0.9 - - - -
3A GLN* 2.7 46.4 + - + +
19A SER* 4.9 2.0 + - - +
20A CYS* 1.3 71.9 - - - +
22A ALA* 1.3 78.5 + - - +
23A SER* 4.6 10.9 + - - -
74A ALA 3.5 16.9 + - - -
75A SER* 3.6 5.8 - - - +
76A THR* 3.3 23.0 - - + +
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Residues in contact with ALA 22 (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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1A GLN 3.3 5.4 - - - -
2A LEU* 4.9 3.4 - - + -
20A CYS* 3.4 3.7 + - - +
21A LYS* 1.3 88.2 + - - +
23A SER* 1.3 65.3 + - - +
25A TYR* 3.4 31.9 - - + +
27A PHE* 3.5 22.9 - - + -
32A MET* 4.9 2.5 - - + -
75A SER* 2.7 29.8 + - - +
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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