Contacts of the strand formed by residues 16 - 22 (chain A) in PDB entry 2I6A
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 LEU 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASN* 2.8 14.8 + - + +
15A PRO* 1.3 80.8 - - - +
17A LEU* 1.3 53.6 + - - +
18A ASP* 4.6 0.2 - - - +
63A GLY 2.6 36.3 + - - +
64A GLY* 4.0 8.5 - - - +
99A LEU* 3.3 10.4 - - - +
121A GLY* 3.5 24.0 - - - +
122A THR 4.0 6.1 - - - +
123A CYS* 4.0 14.1 - - + +
136A ALA* 4.0 18.4 - - + -
138A LEU* 3.7 33.0 - - + -
141A ALA* 3.8 13.7 - - + -
500A 5I5 4.0 23.1 - - + +
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Residues in contact with LEU 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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16A LEU* 1.3 71.7 - - - +
18A ASP* 1.3 65.3 + - - +
19A ILE* 3.4 3.3 + - + +
60A TYR* 3.8 26.9 - - + -
61A HIS 3.1 42.8 - - - +
62A ALA* 3.7 4.3 - - + +
95A PHE* 3.5 46.9 - - + +
98A ILE* 4.7 14.8 - - + -
99A LEU* 4.0 12.5 - - + +
121A GLY 3.0 14.5 + - - +
122A THR* 3.4 13.1 - - + +
123A CYS 3.2 17.3 + - - -
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Residues in contact with ASP 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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16A LEU* 4.5 0.7 - - - +
17A LEU* 1.3 72.6 - - - +
19A ILE* 1.3 60.7 - - - +
20A SER 3.8 0.8 + - - +
59A GLU 3.2 6.6 - - - +
60A TYR* 3.4 2.8 - - - -
61A HIS* 2.7 38.7 + - - +
63A GLY* 3.2 9.8 - - - -
123A CYS* 3.3 12.8 - - + +
125A ALA* 5.6 5.8 - - + -
332A ARG* 2.6 47.2 + - - +
500A 5I5 2.6 43.6 + - - -
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Residues in contact with ILE 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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17A LEU* 3.9 7.9 - - + +
18A ASP* 1.3 73.6 - - - +
20A SER* 1.3 59.6 + - - +
49A PHE* 5.3 8.3 - - + -
52A LEU* 3.5 23.7 - - + +
53A VAL* 4.3 15.7 - - + -
58A VAL* 2.9 25.6 - - + -
59A GLU 3.5 3.1 - - - -
60A TYR* 3.6 27.8 - - + -
95A PHE* 4.4 7.2 - - + -
122A THR* 3.8 27.8 - - + +
123A CYS 2.7 13.2 + - - +
124A ALA* 3.3 5.5 - - + -
125A ALA 2.9 21.8 + - - +
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Residues in contact with SER 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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18A ASP 3.8 0.6 - - - -
19A ILE* 1.3 75.9 - - - +
21A ALA* 1.3 61.2 + - - +
57A LYS 4.0 1.0 - - - +
58A VAL* 3.1 3.2 - - - +
59A GLU* 2.7 49.8 + - - +
61A HIS* 4.5 9.7 - - - -
125A ALA* 3.5 25.1 - - - -
127A ILE* 4.9 6.7 - - - -
132A ARG* 4.6 8.5 - - - -
332A ARG* 5.1 6.7 + - - -
334A THR* 4.7 8.1 + - - -
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Residues in contact with ALA 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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19A ILE 4.3 0.4 + - - -
20A SER* 1.3 78.9 - - - +
22A VAL* 1.3 65.0 + - - +
23A VAL* 3.6 2.3 + - - +
52A LEU* 4.0 15.6 - - + +
56A PHE* 4.0 18.4 - - + -
57A LYS 3.7 11.7 - - - +
58A VAL* 3.7 19.7 - - + +
125A ALA 3.3 5.1 + - - +
126A CYS* 3.8 3.1 - - - -
127A ILE* 2.9 28.3 + - - +
334A THR* 5.8 2.2 - - - -
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Residues in contact with VAL 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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21A ALA* 1.3 74.2 - - - +
23A VAL* 1.3 66.2 + - - +
56A PHE* 3.1 21.1 - - - +
57A LYS 5.0 2.3 + - - +
127A ILE* 3.4 26.9 - - + +
128A THR* 4.8 4.0 - - - -
129A GLY 5.0 4.9 - - - +
334A THR* 4.6 21.3 - - + -
289D GLN* 4.8 14.1 - - - +
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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