Contacts of the strand formed by residues 32 - 37 (chain A) in PDB entry 3DOY
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 ARG 32 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLN* 4.2 12.6 - - - +
12A PHE 3.4 15.0 - - - +
13A PHE* 3.6 37.6 - - + +
17A ILE* 3.6 4.7 - - - +
30A VAL* 4.0 0.3 - - - +
31A ASP* 1.3 78.3 + - - +
33A ILE* 1.3 70.8 + - - +
34A THR 4.1 0.7 - - - -
44A ALA* 3.0 6.2 - - - +
45A TYR* 3.0 67.1 + - + -
114D THR* 3.8 8.7 + - - -
115D PRO 2.9 26.9 + - - -
116D GLY 3.3 6.8 + - - -
117D ASP* 3.0 25.3 + - - +
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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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10A SER 3.9 9.0 - - - +
11A GLN* 3.3 11.3 + - - +
12A PHE* 2.9 45.7 + - + +
17A ILE* 4.1 13.9 - - + -
30A VAL* 4.6 3.6 - - + -
32A ARG* 1.3 78.7 - - - +
34A THR* 1.3 62.1 + - - +
35A GLU 3.8 14.1 - - - +
36A LEU* 4.3 2.7 - - + -
42A ILE* 3.8 15.0 - - + -
43A VAL 3.7 10.8 - - - +
44A ALA* 3.8 10.1 - - + -
80A PHE* 3.4 53.4 - - + -
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Residues in contact with THR 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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10A SER* 3.4 9.7 - - - +
11A GLN* 3.5 28.9 - - - +
32A ARG* 4.1 0.4 - - + -
33A ILE* 1.3 74.0 - - - +
35A GLU* 1.3 61.4 + - - +
43A VAL* 2.8 38.6 + - - +
44A ALA* 4.2 0.9 - - - +
45A TYR* 4.0 16.8 - - + -
118A ARG* 3.9 24.6 + - - +
120A GLU* 4.8 2.1 + - - -
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Residues in contact with GLU 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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10A SER* 3.2 10.7 + - - -
33A ILE* 3.8 0.7 - - - +
34A THR* 1.3 82.2 + - - +
36A LEU* 1.3 62.8 + - - +
41A LYS* 3.0 30.7 + - - +
42A ILE* 3.4 4.3 - - - +
43A VAL* 2.8 65.6 + - + +
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Residues in contact with LEU 36 (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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8A LEU* 3.5 31.9 - - + -
9A GLN 4.0 12.6 - - - +
10A SER* 3.4 29.6 + - - +
12A PHE* 4.2 13.7 - - + -
33A ILE* 4.3 2.5 - - + -
35A GLU* 1.3 77.1 - - - +
37A GLN* 1.3 69.3 + - - +
38A ALA 4.0 7.9 - - - +
41A LYS 3.6 2.2 - - - -
42A ILE* 3.6 27.8 - - + -
80A PHE* 4.6 2.5 - - + -
81A LEU* 3.3 32.5 - - + -
84A THR* 3.6 11.2 - - + -
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Residues in contact with GLN 37 (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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10A SER* 5.0 3.6 + - - -
36A LEU* 1.3 83.0 + - - +
38A ALA* 1.3 70.3 + - - +
39A ASN 3.3 0.5 + - - -
40A GLN* 2.9 33.3 + - + +
41A LYS* 2.7 46.4 + - + +
81A LEU* 3.6 2.8 - - - +
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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