Contacts of the strand formed by residues 41 - 44 (chain A) in PDB entry 1P3C
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 LYS 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.4 9.6 - - - +
37A ILE* 3.0 34.5 + - + -
38A ALA* 3.6 23.9 + - + -
40A ASN* 1.3 98.5 + - - +
42A ILE* 1.3 63.2 + - - +
83A TYR* 4.4 4.7 - - + -
100A VAL* 3.9 20.9 - - + -
101A ILE 3.3 1.8 - - - -
102A LYS* 3.9 27.4 - - + +
212A ALA 2.8 26.4 + - - +
213A LYS* 3.0 18.6 + - - -
215A GLN* 2.7 30.2 + - - -
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Residues in contact with ILE 42 (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 ALA* 4.4 6.1 - - + -
25A ILE* 4.5 16.8 - - + -
34A GLY* 3.7 22.7 - - - -
35A THR 3.4 3.4 - - - +
36A LEU* 3.3 46.2 - - + +
37A ILE* 4.5 0.9 - - - -
41A LYS* 1.3 75.0 - - - +
43A LEU* 1.3 64.9 + - - +
44A THR* 4.0 1.5 + - - -
63A VAL* 3.7 26.9 - - + -
99A ALA 3.8 0.3 - - - +
100A VAL* 3.1 8.4 - - - -
101A ILE* 2.9 45.3 + - + +
103A THR* 4.2 13.2 - - + -
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Residues in contact with LEU 43 (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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34A GLY* 3.2 5.9 - - - -
35A THR* 2.9 36.3 + - - +
37A ILE* 3.9 17.8 - - + +
42A ILE* 1.3 71.2 - - - +
44A THR* 1.3 67.3 + - - +
98A PHE* 4.4 5.6 - - + -
99A ALA 3.5 15.7 - - - +
100A VAL* 4.5 1.8 - - + +
116A ILE* 5.0 3.6 - - + -
172A GLY 3.9 4.4 - - - +
174A ALA* 5.6 3.1 - - + -
182A ILE* 4.1 28.0 - - + -
185A VAL* 3.8 26.7 - - + -
205A PHE* 4.0 17.7 - - + -
209A ILE* 3.8 24.9 - - + -
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Residues in contact with THR 44 (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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25A ILE* 3.7 14.4 - - + +
33A THR 2.8 21.7 + - - -
34A GLY* 4.3 0.4 - - - -
42A ILE* 4.6 0.9 - - + -
43A LEU* 1.3 78.5 - - - +
45A ASN* 1.3 77.5 + - - +
48A CYS* 3.8 11.0 - - + -
49A VAL* 4.2 8.3 - - + -
98A PHE* 3.3 8.1 - - - +
99A ALA* 3.0 31.1 + - + +
101A ILE* 3.8 29.4 - - + -
172A GLY* 3.7 13.8 - - - -
185A VAL* 4.5 3.3 - - - +
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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