Contacts of the strand formed by residues 25 - 31 (chain A) in PDB entry 1AXC
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 GLU 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ILE* 4.5 1.7 - - - +
24A ASN* 1.3 90.8 + - + +
26A ALA* 1.3 64.0 + - - +
39A SER* 3.7 10.4 + - - -
70A VAL 3.4 7.2 - - - +
71A ASN* 4.8 9.1 + - - +
72A LEU* 4.8 0.9 - - - -
119A MET* 4.3 17.7 - - - +
121A LEU* 3.3 31.8 - - + +
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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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23A ILE* 4.3 0.2 - - + -
25A GLU* 1.3 77.3 - - - +
27A CYS* 1.3 60.2 + - - +
28A TRP* 3.5 7.9 - - - -
37A LEU* 4.1 14.8 - - + -
39A SER* 3.8 25.4 - - - +
70A VAL 2.9 29.4 + - - +
72A LEU* 4.0 22.0 - - + +
121A LEU* 3.6 9.0 - - - +
123A VAL* 5.5 2.5 - - - -
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Residues in contact with CYS 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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26A ALA* 1.3 72.4 - - - +
28A TRP* 1.3 61.3 + - - +
29A ASP* 3.6 30.3 + - - +
36A ASN 3.9 0.2 - - - +
37A LEU* 3.6 25.1 - - - +
38A GLN 4.5 6.3 + - - +
67A ALA* 3.8 14.8 - - - -
68A MET 3.5 6.3 - - - +
121A LEU* 4.0 3.2 - - + +
123A VAL* 4.0 24.0 - - + +
125A GLN* 4.4 9.1 - - - +
156B ARG* 3.7 15.3 - - - -
158B ILE* 3.7 17.9 - - + -
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Residues in contact with TRP 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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12A LEU* 4.7 18.2 - - + -
15A VAL* 4.9 5.6 - - + -
16A LEU* 4.5 8.1 - - + -
19A LEU* 5.1 2.0 - - + -
26A ALA 3.5 7.3 + - - -
27A CYS* 1.3 72.1 - - - +
29A ASP* 1.3 62.5 + - - +
30A ILE* 3.6 9.6 + - + +
35A VAL* 3.4 28.9 - - + -
36A ASN 3.8 4.0 - - - -
37A LEU* 3.4 21.1 - - + +
50A LEU* 4.2 20.2 - - + -
52A LEU* 5.0 1.3 - - + -
66A LEU 3.4 3.8 - - - +
68A MET* 3.0 49.3 + - + +
70A VAL* 3.4 27.3 - - + +
72A LEU* 3.3 35.4 - - + +
75A MET* 3.8 29.8 - - + -
90A LEU* 5.9 5.6 - - + -
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Residues in contact with ASP 29 (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 CYS* 3.6 12.4 - - - +
28A TRP* 1.3 70.3 - - - +
30A ILE* 1.3 62.7 + - - +
31A SER* 5.4 1.1 - - - -
34A GLY 3.7 1.7 - - - +
35A VAL* 3.6 1.7 - - - -
36A ASN* 2.8 57.1 + - + +
37A LEU* 5.1 1.6 - - - -
38A GLN 5.4 0.2 + - - -
66A LEU 3.2 4.8 - - - +
67A ALA* 3.7 6.4 - - - +
125A GLN* 4.5 6.1 + - - +
156B ARG* 2.9 44.0 + - - -
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Residues in contact with ILE 30 (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 PHE* 3.4 36.6 - - + -
28A TRP* 3.9 6.5 - - + +
29A ASP* 1.3 78.0 - - - +
31A SER* 1.3 61.3 + - - +
34A GLY 3.9 1.8 - - - +
35A VAL* 3.7 29.4 - - + -
60A TYR* 3.3 21.1 - - - +
62A CYS* 4.0 7.6 - - - -
65A ASN* 3.2 8.7 - - - +
66A LEU* 2.7 50.2 + - + +
68A MET* 3.6 33.2 - - + -
90A LEU* 6.3 0.4 - - + -
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Residues in contact with SER 31 (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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29A ASP* 5.3 1.6 - - - -
30A ILE* 1.3 77.2 - - - +
32A SER* 1.3 61.9 + - - +
33A SER* 3.7 17.5 + - - -
34A GLY 2.7 21.8 + - - -
36A ASN* 5.0 4.5 - - - -
60A TYR* 2.5 25.5 + - - -
62A CYS* 4.1 5.8 - - - -
65A ASN* 3.1 28.9 + - - +
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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