Contacts of the strand formed by residues 27 - 32 (chain A) in PDB entry 1ADN
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 PHE 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ARG* 3.1 41.7 - - + -
15A SER* 2.9 26.7 - - - -
16A VAL* 4.0 18.6 - - + -
21A PRO* 5.6 0.2 - - + -
23A ALA* 5.3 0.2 - - + -
24A ASP* 2.7 60.7 + - + +
25A GLY 3.9 0.2 - - - -
26A GLU* 1.5 63.3 - - - +
28A VAL* 1.5 59.8 + - - +
29A PHE* 5.5 0.4 - - + -
39A ARG* 4.2 2.1 - - - +
40A PRO* 2.8 48.6 - - + +
54A PHE* 4.8 15.0 - + + -
55A TYR 3.1 18.6 - - - +
56A ALA* 3.4 7.1 + - - +
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Residues in contact with VAL 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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26A GLU 3.7 9.6 - - - +
27A PHE* 1.5 65.0 - - - +
29A PHE* 1.5 59.2 + - - +
37A PHE* 4.7 6.3 - - + -
38A CYS 3.8 9.0 - - - +
39A ARG* 5.1 8.7 - - + +
40A PRO* 5.1 0.2 - - - -
54A PHE* 3.2 6.1 - - - +
55A TYR* 2.8 79.1 + - + +
57A ASN 3.4 12.1 - - - +
58A ALA* 3.2 38.8 - - + +
61A ALA* 4.2 1.1 - - + -
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Residues in contact with PHE 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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13A TRP* 4.5 9.2 - + - -
16A VAL* 4.4 22.9 - - + -
27A PHE* 5.5 1.3 - - + -
28A VAL* 1.5 58.0 - - - +
30A ALA* 1.5 58.4 + - - +
31A VAL* 3.2 31.9 - - + -
36A ILE* 3.7 8.5 - - + +
37A PHE* 3.3 2.2 - - - -
38A CYS* 2.9 68.5 + - + -
39A ARG 4.7 1.3 - - - -
40A PRO* 4.5 10.5 - - + -
42A CYS* 4.2 17.0 - - + -
46A HIS* 5.0 15.0 - + + -
47A ALA 5.5 0.7 - - - -
52A VAL* 3.1 26.7 - - + -
53A SER 3.3 4.5 - - - -
54A PHE* 3.8 20.4 - - + -
55A TYR* 4.4 1.3 - - - -
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Residues in contact with ALA 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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29A PHE* 1.5 55.0 - - - +
31A VAL* 1.5 59.8 + - - +
32A ARG* 3.7 2.4 + - - +
36A ILE 3.6 5.4 - - - -
37A PHE* 4.0 0.9 - - + -
51A ASN 3.4 4.9 - - - +
52A VAL* 3.2 4.4 - - - -
53A SER* 2.6 39.9 + - - +
55A TYR* 3.0 32.1 - - + +
66A PHE* 3.3 26.5 - - + -
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Residues in contact with VAL 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 PHE* 3.2 27.3 - - + -
30A ALA* 1.5 54.3 - - - +
32A ARG* 1.5 57.0 + - - +
33A THR* 3.1 12.7 + - + -
34A THR* 4.1 4.7 - - - +
35A GLY 3.2 15.4 + - - -
36A ILE* 3.2 26.3 + - + +
46A HIS* 6.2 0.4 - - + -
47A ALA* 2.9 41.7 - - + +
48A LEU 4.5 2.5 - - - +
51A ASN* 3.0 19.5 - - - +
52A VAL* 3.7 16.0 - - + +
66A PHE* 4.1 1.3 - - - -
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Residues in contact with ARG 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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30A ALA 3.7 3.0 + - - +
31A VAL* 1.5 51.9 - - - +
33A THR* 1.5 54.9 + - - -
34A THR 3.8 0.2 - - - -
35A GLY* 4.0 6.0 + - - -
51A ASN* 2.8 28.9 + - - +
66A PHE* 4.0 33.4 - - - -
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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