Contacts of the strand formed by residues 22 - 28 (chain A) in PDB entry 2AA0
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 ILE 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ASN 3.3 9.6 + - - +
21A PRO* 1.3 78.4 - - - +
23A LEU* 1.3 58.6 + - - +
68A GLY* 2.6 41.3 + - - +
69A GLY* 3.9 7.4 - - - +
103A LEU* 3.8 8.7 - - - +
125A GLY* 3.5 8.3 - - - -
126A VAL* 3.5 7.4 - - - -
127A CYS* 3.4 35.4 - - + +
140A THR* 3.9 17.5 - - + -
142A LEU* 4.1 9.6 - - + -
145A CYS* 4.1 9.4 - - - -
1001A MTP 3.7 44.4 - - + +
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Residues in contact with LEU 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 ILE* 1.3 72.5 - - - +
24A ASP* 1.3 66.5 + - - +
25A LEU* 4.0 8.5 - - + +
65A SER* 4.0 22.2 - - - +
66A LEU 3.6 27.4 - - - +
67A PRO* 4.6 0.2 - - + -
99A ARG* 3.3 37.0 - - + +
102A VAL* 4.2 22.4 - - + +
103A LEU* 4.2 24.8 - - + +
106A LEU* 5.3 2.2 - - + -
124A THR* 5.2 0.4 - - + -
125A GLY 3.0 13.6 + - - +
126A VAL* 3.4 8.1 - - - +
127A CYS 3.0 19.9 + - - -
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Residues in contact with ASP 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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22A ILE* 3.7 0.9 + - - +
23A LEU* 1.3 73.0 - - - +
25A LEU* 1.3 61.2 + - - +
26A VAL* 3.8 7.6 - - + -
64A THR 3.3 4.0 - - - +
65A SER* 3.5 2.9 - - - -
66A LEU* 2.8 45.9 + - + +
67A PRO 4.3 1.6 - - - +
68A GLY* 3.6 10.0 - - - -
127A CYS* 3.2 14.9 - - - +
129A VAL* 4.1 15.7 - - + -
354A PHE* 3.4 18.2 - - - -
1001A MTP 2.6 46.5 + - - -
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Residues in contact with LEU 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 LEU* 4.0 14.8 - - + +
24A ASP* 1.3 75.9 - - - +
26A VAL* 1.3 62.3 + - - +
55A TYR* 4.5 18.4 - - + +
58A LEU* 3.7 30.1 - - + +
59A ASP* 5.9 2.5 - - - +
63A PRO* 4.4 12.8 - - + -
64A THR 3.6 3.1 - - - +
65A SER* 3.4 26.0 - - - +
99A ARG* 5.1 5.8 - - - +
126A VAL* 3.7 27.8 - - + -
127A CYS 2.8 12.5 + - - +
128A ALA* 3.7 2.0 - - - -
129A VAL 2.9 24.5 + - - +
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Residues in contact with VAL 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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24A ASP* 4.6 7.9 - - + -
25A LEU* 1.3 74.7 - - - +
27A ALA* 1.3 69.0 + - - +
62A ASN 4.3 0.7 - - - +
63A PRO* 3.4 0.7 - - - +
64A THR* 2.8 49.6 + - - +
66A LEU* 4.4 18.2 - - + -
129A VAL* 3.5 31.2 - - + +
131A ILE* 3.7 25.4 - - + -
352A VAL* 6.2 3.4 - - + -
353A GLY* 6.2 2.9 - - - -
354A PHE* 6.0 1.8 - - + -
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Residues in contact with ALA 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 LEU 4.0 0.2 + - - -
26A VAL* 1.3 82.9 - - - +
28A GLU* 1.3 65.4 + - - +
29A VAL* 3.7 3.2 + - - +
58A LEU* 4.1 22.4 - - + -
61A PHE* 3.8 21.3 - - + +
62A ASN 4.3 2.0 - - - +
63A PRO* 4.0 11.0 - - + -
129A VAL 3.2 7.1 + - - +
130A LEU* 3.7 4.0 - - - +
131A ILE* 3.0 24.9 + - - -
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Residues in contact with GLU 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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27A ALA* 1.3 73.4 - - - +
29A VAL* 1.3 64.7 - - - +
61A PHE* 4.0 17.2 + - - +
131A ILE* 3.3 35.7 - - + +
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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