Contacts of the strand formed by residues 31 - 38 (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 SER 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A TYR* 3.6 32.3 + - - -
25A ILE 3.2 15.0 - - - -
26A THR* 4.4 2.5 - - - +
27A PHE* 4.4 2.0 - - - -
30A SER* 1.3 77.6 - - - +
32A CYS* 1.3 72.6 + - - +
132A TYR 5.2 0.3 + - - -
137A MET* 4.5 10.2 - - - +
168A SER* 5.7 0.3 + - - -
169A GLY* 4.1 16.3 + - - -
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Residues in contact with CYS 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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24A TYR* 4.0 9.7 - - - -
25A ILE* 3.0 37.8 + - + +
27A PHE* 4.2 4.7 - - + -
30A SER* 5.6 2.9 - - - -
31A SER* 1.3 83.7 - - - +
33A THR* 1.3 63.3 + - - +
44A THR* 4.0 0.7 - - - +
47A HIS* 5.1 1.8 - - - -
48A CYS* 2.0 54.1 - - + -
132A TYR* 4.6 1.4 - - - +
169A GLY 3.3 15.9 - - - +
171A SER* 3.5 12.1 - - - +
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Residues in contact with THR 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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22A ILE* 3.9 14.4 - - + -
23A ALA 3.5 10.5 - - - +
25A ILE* 4.0 3.1 - - - -
32A CYS* 1.3 75.0 - - - +
34A GLY* 1.3 63.8 + - - +
35A THR* 5.3 0.2 - - - +
44A THR* 2.8 23.5 + - - -
131A GLY* 3.7 14.4 - - - -
132A TYR* 3.0 20.5 + - + +
169A GLY 2.8 20.7 + - - -
171A SER 3.0 11.4 + - - +
172A GLY* 3.5 4.9 - - - -
173A SER* 3.5 34.3 + - - +
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Residues in contact with GLY 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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22A ILE* 3.6 2.1 - - - -
23A ALA* 2.8 37.7 + - - -
25A ILE* 4.1 5.5 - - - +
33A THR* 1.3 79.2 - - - +
35A THR* 1.3 62.5 + - - -
42A ILE* 3.7 16.2 - - - -
43A LEU 3.2 13.5 - - - -
44A THR* 4.3 0.9 - - - -
172A GLY 4.4 1.3 - - - -
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Residues in contact with THR 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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21A SER* 3.5 11.7 - - - +
22A ILE* 4.2 15.6 - - + +
33A THR* 5.3 0.2 - - - +
34A GLY* 1.3 75.1 + - - -
36A LEU* 1.3 75.1 + - - +
37A ILE* 3.4 2.9 + - - +
42A ILE* 3.4 4.4 - - - +
43A LEU* 2.9 34.5 + - - -
114A ARG* 3.7 22.9 - - + -
172A GLY 4.6 1.6 + - - -
173A SER* 5.1 0.5 - - - -
174A ALA* 3.7 26.3 + - + +
176A LEU* 5.4 1.6 - - + -
182A ILE* 4.1 17.7 - - + -
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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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21A SER* 2.9 24.4 + - - +
23A ALA* 4.6 2.5 - - + -
35A THR* 1.3 78.4 - - - +
37A ILE* 1.3 60.4 + - - +
38A ALA 3.9 9.4 - - - +
39A PRO 4.6 0.4 - - - +
40A ASN 5.1 0.7 - - - -
41A LYS 3.4 21.1 - - - +
42A ILE* 3.3 25.6 - - + -
63A VAL* 4.9 0.4 - - + -
65A PRO* 4.1 27.8 - - + -
103A THR* 5.4 1.1 - - + -
107A ILE* 4.2 17.9 - - + -
108A GLY* 4.4 8.5 - - - +
111A VAL* 4.7 2.5 - - + -
112A GLY 3.7 22.7 - - - +
113A TYR* 3.6 6.5 - - + -
114A ARG* 3.0 21.7 + - - +
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Residues in contact with ILE 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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35A THR 3.7 7.0 - - - +
36A LEU* 1.3 77.7 - - - +
38A ALA* 1.3 60.7 + - - +
41A LYS* 3.0 29.3 + - + +
43A LEU* 3.9 19.5 - - + +
100A VAL* 4.2 21.8 - - + -
113A TYR* 3.3 16.9 - - - -
114A ARG 3.7 13.4 - - - +
116A ILE* 4.3 8.5 - - + -
182A ILE* 3.7 27.6 - - + -
209A ILE* 3.9 27.4 - - + +
213A LYS* 3.4 27.7 + - + -
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Residues in contact with ALA 38 (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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36A LEU* 3.9 8.7 - - - +
37A ILE* 1.3 78.9 - - - +
39A PRO* 1.3 78.8 - - + +
40A ASN* 3.1 2.6 + - - +
41A LYS* 3.6 35.9 + - + +
108A GLY* 4.1 1.2 - - - -
113A TYR* 3.6 18.9 - - + +
213A LYS* 4.7 14.1 - - + +
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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