Contacts of the strand formed by residues 17 - 25 (chain C) in PDB entry 1PU5
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 ALA 17 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ASN* 4.6 0.7 - - - +
15C ASP* 4.1 1.4 - - - +
16C PRO* 1.3 76.1 - - + +
18C VAL* 1.3 66.9 + - - +
42C SER 3.3 6.1 - - - +
43C THR* 3.9 17.5 - - - +
47C LEU* 4.5 13.7 - - + -
145C LEU* 4.7 8.3 - - + -
152C LEU* 2.8 21.8 + - + +
153C GLY* 3.4 20.5 - - - -
154C CYS 4.5 1.6 + - - -
155C ILE* 6.0 0.7 - - - +
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Residues in contact with VAL 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ASN* 3.4 22.7 - - + +
11C ASP 5.2 0.2 - - - +
12C GLU* 4.1 18.4 - - + +
15C ASP* 3.3 22.9 - - + +
16C PRO 4.7 2.2 - - - +
17C ALA* 1.3 81.5 - - - +
19C ILE* 1.3 64.8 + - - +
20C ARG* 3.5 42.4 - - - +
41C GLY* 3.2 2.3 - - - -
42C SER* 2.8 41.6 + - - +
155C ILE* 5.8 0.7 - - - -
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Residues in contact with ILE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TRP* 3.3 28.0 - - + -
9C ASN* 2.9 29.0 + - - +
18C VAL* 1.3 74.5 - - - +
20C ARG* 1.3 65.5 + - - +
21C SER 3.4 26.2 - - - +
22C LEU* 4.1 12.6 - - + -
39C VAL* 4.0 18.8 - - + -
40C VAL 3.6 1.3 - - - +
41C GLY* 4.1 11.4 - - - -
155C ILE* 3.8 30.1 - - + -
901C EPE 5.2 1.2 - - - -
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Residues in contact with ARG 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TRP* 3.6 12.2 - - - -
9C ASN* 6.0 0.8 - - - +
12C GLU* 6.1 2.8 - - - +
18C VAL* 3.5 21.9 - - - +
19C ILE* 1.3 79.9 + - - +
21C SER* 1.3 60.3 + - - +
40C VAL* 2.6 33.5 + - + +
41C GLY* 4.6 3.4 - - - -
42C SER* 3.5 24.9 + - - +
115C THR* 6.1 0.9 - - + -
901C EPE 4.8 8.8 - - - -
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Residues in contact with SER 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 4.6 5.2 - - - +
7C TRP* 3.7 7.2 - - - -
19C ILE* 3.4 4.7 - - - +
20C ARG* 1.3 79.3 - - - +
22C LEU* 1.3 63.4 + - - +
23C THR* 5.8 4.0 - - - -
38C SER* 5.6 1.2 + - - -
39C VAL* 3.3 2.8 - - - -
40C VAL* 2.9 51.8 + - - +
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PHE* 3.7 28.2 - - + -
7C TRP* 3.3 43.4 + - + +
19C ILE* 4.1 10.3 - - + -
21C SER* 1.3 77.4 - - - +
23C THR* 1.3 67.7 + - - +
24C LEU* 5.7 0.2 - - + -
37C LEU* 3.6 23.3 - - + -
38C SER 3.3 18.4 - - - +
39C VAL* 3.7 14.4 - - + -
155C ILE* 5.5 4.5 - - + -
157C ILE* 3.9 24.5 - - + -
901C EPE 5.3 0.5 + - - -
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Residues in contact with THR 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PHE* 4.1 4.9 - - - -
21C SER* 5.8 2.9 - - - -
22C LEU* 1.3 82.6 - - - +
24C LEU* 1.3 61.8 + - - +
25C GLU* 4.6 8.3 + - - -
36C THR 4.2 1.7 + - - -
37C LEU* 3.4 11.0 - - - +
38C SER* 2.6 51.7 + - - +
120C LYS* 4.0 20.5 - - - +
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PHE* 3.6 55.6 - - + +
22C LEU* 6.5 0.2 - - + -
23C THR* 1.3 77.5 - - - +
25C GLU* 1.3 62.9 + - - +
26C PRO 3.9 7.4 - - - +
27C ASP* 4.9 2.1 - - - +
29C ILE* 3.7 28.5 - - + -
35C VAL* 3.0 37.0 - - + -
36C THR 3.4 4.5 - - - +
37C LEU* 4.5 15.3 - - + -
157C ILE* 5.4 1.8 - - + -
159C ALA* 4.7 4.9 - - + -
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Residues in contact with GLU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C THR* 4.6 6.7 + - - -
24C LEU* 1.3 82.8 - - - +
26C PRO* 1.3 73.7 - - + +
29C ILE* 5.3 0.4 - - - -
35C VAL* 3.3 8.6 - - - +
36C THR* 2.7 47.6 + - - +
120C LYS* 2.8 42.9 + - - +
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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