Contacts of the strand formed by residues 30 - 35 (chain A) in PDB entry 2A1A
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 GLY 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ILE* 4.8 0.4 - - - -
27A ALA* 2.7 39.9 + - - +
28A GLU 3.1 4.2 + - - -
29A MET* 1.3 81.5 - - - +
31A ALA* 1.3 58.2 + - - -
32A TYR* 4.2 2.8 + - - -
44A MET* 4.4 9.9 - - - -
45A ILE 3.2 12.1 - - - -
47A LEU* 3.7 15.0 - - - -
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Residues in contact with ALA 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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23A VAL* 4.1 18.6 - - + -
25A GLN 3.3 8.5 - - - +
26A ILE* 4.2 13.9 - - + +
30A GLY* 1.3 72.2 - - - -
32A TYR* 1.3 63.7 + - - +
33A VAL* 3.7 4.9 + - + +
44A MET* 3.3 2.5 - - - +
45A ILE* 2.7 48.6 + - + +
47A LEU* 4.7 8.0 - - + +
62A ILE* 4.9 11.7 - - + -
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Residues in contact with TYR 32 (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 VAL* 3.7 0.7 - - - +
24A GLN* 2.7 37.4 + - + +
25A GLN* 2.7 47.7 + - + +
27A ALA* 3.9 24.1 - - + +
30A GLY 4.5 1.6 - - - -
31A ALA* 1.3 72.2 - - - +
33A VAL* 1.3 56.2 + - - +
42A GLU* 5.3 5.8 - - + +
43A GLY 3.5 5.6 - - - +
44A MET* 3.7 29.6 - - + -
489B PHE* 3.5 31.4 - + - -
492B SER* 3.1 28.1 + - - -
493B LYS* 4.0 19.3 + - - -
496B THR* 5.5 1.7 + - - -
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Residues in contact with VAL 33 (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 VAL* 3.7 21.5 - - + -
22A ASN 3.3 9.0 - - - +
23A VAL* 3.8 23.6 - - + -
24A GLN* 4.3 2.9 - - - +
31A ALA 3.8 6.3 - - - +
32A TYR* 1.3 79.5 - - - +
34A LYS* 1.3 62.2 + - - +
35A LEU* 4.3 1.1 - - + -
42A GLU* 3.5 7.3 - - - +
43A GLY* 2.8 38.9 + - - +
45A ILE* 3.7 27.4 - - + -
84A LEU* 3.6 30.7 - - + -
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Residues in contact with LYS 34 (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 VAL* 3.2 4.7 - - - -
22A ASN* 2.9 36.0 + - + +
24A GLN* 3.0 49.9 + - + +
33A VAL* 1.3 74.1 - - - +
35A LEU* 1.3 64.7 + - - +
36A LEU* 3.3 2.0 + - + +
40A ASN* 3.4 45.6 - - + +
41A ILE 3.5 3.8 - - - -
42A GLU* 4.4 19.1 - - + -
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Residues in contact with LEU 35 (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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13A PRO* 3.7 30.7 - - + -
19A VAL* 4.0 18.2 - - + -
20A MET 3.9 5.6 - - - +
21A VAL* 3.8 9.9 - - + -
33A VAL* 4.3 0.9 - - + -
34A LYS* 1.3 71.7 - - - +
36A LEU* 1.3 64.5 + - - +
37A GLU 3.2 2.1 + - - +
38A TYR* 3.2 26.7 + - + -
40A ASN* 3.1 22.2 + - - -
41A ILE* 2.9 27.4 + - + +
42A GLU 4.5 0.7 - - - -
43A GLY* 4.3 11.4 - - - +
82A ILE* 4.0 13.5 - - + -
84A LEU* 3.7 27.8 - - + -
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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