Contacts of the strand formed by residues 47 - 53 (chain A) in PDB entry 1IPA
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 LEU 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ILE* 4.4 9.9 - - + -
37A ILE* 4.0 18.6 - - + -
40A ALA* 5.1 2.7 - - + -
41A LEU* 3.5 33.7 - - + +
45A ILE* 3.8 14.2 + - + +
46A GLU* 1.3 83.6 - - - +
48A GLU* 1.3 65.1 + - - +
49A GLN 4.8 0.7 - - - +
68A LEU* 4.6 11.7 - - + -
74A LEU* 4.1 20.1 - - + +
98A ALA* 4.0 20.9 - - + -
99A LEU 3.5 3.4 - - - +
100A ALA* 3.8 18.6 - - + -
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Residues in contact with GLU 48 (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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28A ARG* 2.5 52.2 + - - -
46A GLU* 6.1 0.7 - - + -
47A LEU* 1.3 79.3 - - - +
49A GLN* 1.3 66.3 + - + +
74A LEU* 3.5 9.9 - - - +
75A ALA* 3.3 17.8 + - - +
99A LEU* 2.9 26.6 + - + +
101A ARG* 3.8 21.8 + - + +
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Residues in contact with GLN 49 (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 ARG* 2.5 47.3 + - - +
14A LEU* 3.5 21.0 - - - +
47A LEU* 5.1 0.2 - - - +
48A GLU* 1.3 81.5 - - - +
50A ALA* 1.3 59.6 + - - +
51A LEU* 3.7 12.7 - - + +
74A LEU* 3.5 8.3 - - - +
75A ALA* 2.9 27.7 - - + +
77A LEU* 4.0 15.7 - - + +
98A ALA* 3.4 4.3 - - - +
99A LEU* 2.8 44.7 + - + +
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Residues in contact with ALA 50 (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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47A LEU* 6.2 1.6 - - + -
49A GLN* 1.3 75.6 - - - +
51A LEU* 1.3 65.5 + - - +
52A VAL* 4.4 2.0 - - + +
68A LEU* 4.4 13.0 - - + -
74A LEU* 4.3 4.0 - - + +
75A ALA 3.0 6.9 + - - -
76A LEU* 3.2 24.3 - - + +
77A LEU* 2.9 23.4 + - - +
96A LEU* 4.3 18.4 - - + -
97A ILE 3.6 4.9 - - - +
98A ALA* 4.3 7.4 - - + +
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Residues in contact with LEU 51 (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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11A ILE* 4.5 5.6 - - + -
14A LEU* 4.1 16.2 - - + -
30A LEU* 6.4 0.9 - - + -
49A GLN* 3.7 29.2 - - + +
50A ALA* 1.3 80.0 - - - +
52A VAL* 1.3 60.2 + - - +
77A LEU* 3.4 13.7 - - + +
79A VAL* 3.9 25.8 - - + -
83A VAL* 4.7 0.4 - - + -
84A LEU* 4.3 17.0 - - + -
87A LEU* 4.1 26.7 - - + -
95A GLY 4.3 0.7 - - - -
96A LEU* 3.2 20.3 - - - +
97A ILE* 2.8 33.9 + - + +
98A ALA* 5.6 0.9 - - - -
99A LEU* 5.7 1.6 - - + +
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Residues in contact with VAL 52 (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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50A ALA* 4.4 6.3 - - + +
51A LEU* 1.3 81.5 - - - +
53A TRP* 1.3 70.5 + - - +
56A GLY* 5.7 0.4 - - - -
57A LEU* 3.3 31.2 - - + -
65A TYR* 4.0 30.5 - - + +
76A LEU* 5.3 2.5 - - + -
77A LEU 2.7 14.3 + - - +
78A GLU* 3.5 8.3 - - + -
79A VAL* 2.6 34.1 + - - +
84A LEU* 4.8 1.6 - - - -
95A GLY 3.3 2.9 - - - -
96A LEU* 3.8 15.3 - - + -
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Residues in contact with TRP 53 (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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52A VAL* 1.3 81.9 - - - +
54A GLU* 1.3 100.7 + - + +
55A GLY* 3.0 29.2 + - - -
56A GLY* 2.9 39.1 + - - +
78A GLU* 5.1 0.5 - - - +
79A VAL 3.4 8.1 - - - -
80A SER 3.5 3.1 - - - -
81A GLU* 2.9 56.1 - - + -
84A LEU* 3.8 11.5 - - + +
95A GLY* 2.9 28.6 + - - +
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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