Contacts of the strand formed by residues 30 - 35 (chain A) in PDB entry 6PAI
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 ASN 30 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL 3.8 0.4 - - - +
20A THR* 2.9 24.6 + - - -
21A GLY 2.7 26.9 + - - +
23A PHE* 2.8 28.8 + - + +
24A THR* 2.9 36.4 + - - +
28A ASP* 3.4 4.3 - - - +
29A LEU* 1.3 75.8 - - - +
31A LEU* 1.3 58.3 + - - +
32A LEU* 3.7 18.5 - - + +
41A ILE* 4.1 2.2 - - - +
42A TYR 2.7 21.2 + - - +
43A VAL* 3.2 16.4 - - - +
44A VAL* 5.0 2.0 - - - -
317A LEU* 5.7 0.2 - - - -
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Residues in contact with LEU 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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18A CYS* 4.3 16.8 - - + -
19A VAL 3.6 9.4 - - - +
20A THR* 5.0 0.2 - - - -
29A LEU 4.2 0.8 + - - -
30A ASN* 1.3 73.2 - - - +
32A LEU* 1.3 63.6 + - - +
33A ILE* 4.0 20.9 - - + -
40A GLU 3.8 1.0 - - - +
41A ILE* 3.7 0.3 - - - -
42A TYR* 2.8 43.5 + - + +
44A VAL* 4.9 2.3 - - + +
49A LEU* 4.1 29.4 - - + -
315A THR* 3.8 22.4 - - - +
317A LEU* 3.9 23.8 - - + -
323A PHE* 4.0 21.5 - - + -
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Residues in contact with LEU 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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18A CYS* 3.1 6.4 - - - +
19A VAL* 2.8 54.1 + - + +
23A PHE* 4.4 19.3 - - + -
30A ASN* 3.7 23.8 - - + +
31A LEU* 1.3 80.1 - - - +
33A ILE* 1.3 61.3 + - - +
39A LEU* 4.3 11.0 - - + -
40A GLU 3.3 9.4 - - - +
41A ILE* 3.7 20.6 - - + -
64A MET* 3.6 2.8 - - - +
66A LEU* 4.4 6.1 - - + -
77A LEU* 3.6 42.0 - - + -
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Residues in contact with ILE 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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15A VAL* 3.8 35.7 - - + -
17A GLY 3.6 2.2 - - - -
18A CYS* 4.3 0.7 - - + +
31A LEU* 4.0 24.2 - - + -
32A LEU* 1.3 78.2 - - - +
34A ALA* 1.3 66.4 + - - +
35A LYS* 3.9 13.6 + - + -
38A ARG 3.7 1.2 - - - +
39A LEU* 3.3 7.6 - - - -
40A GLU* 2.8 48.2 + - + +
42A TYR* 4.4 22.4 - - + -
49A LEU* 5.8 2.0 - - + -
64A MET* 4.5 0.2 - - - -
323A PHE* 4.1 24.7 - - + -
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Residues in contact with ALA 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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15A VAL* 3.7 4.9 - - - +
16A ASN* 2.9 32.3 + - + -
17A GLY* 2.7 26.3 + - - +
33A ILE* 1.3 72.2 - - - +
35A LYS* 1.3 60.9 + - - +
36A ASN 3.8 1.6 - - - +
38A ARG 3.6 4.9 - - - -
61A ILE* 4.2 26.2 - - + +
64A MET* 3.9 20.6 - - + +
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Residues in contact with LYS 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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12A PRO* 3.7 27.1 + - - +
13A THR* 4.1 20.3 + - - +
14A ALA 3.4 22.7 - - - +
15A VAL* 4.4 10.5 - - + -
16A ASN* 4.0 0.2 - - - -
33A ILE* 3.9 12.5 + - + +
34A ALA* 1.3 73.3 - - - +
36A ASN* 1.3 58.7 + - - +
37A THR 2.8 16.8 + - - -
38A ARG* 2.9 32.9 + - + +
40A GLU* 3.7 36.4 + - + +
353A PHE* 6.1 3.4 - - - +
354A THR 5.6 2.2 + - - -
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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