Contacts of the strand formed by residues 31 - 38 (chain C) in PDB entry 1P27
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 31 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLU* 5.0 12.3 + - - -
25C GLU 3.5 1.4 - - - +
26C PHE* 3.4 3.3 - - - -
27C ARG* 2.8 46.8 + - + +
29C ASP* 3.2 19.4 + - - +
30C GLY* 1.3 78.2 - - - +
32C LEU* 1.3 59.0 + - - +
33C ARG* 4.1 18.4 - - + +
49C GLU* 2.7 49.3 + - + +
50C ALA* 3.5 10.1 - - - +
51C TYR* 3.5 42.3 - - + -
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Residues in contact with LEU 32 (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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24C PHE* 4.4 9.4 - - + -
25C GLU 3.3 11.0 - - - +
26C PHE* 3.8 33.0 - - + +
30C GLY 3.4 0.8 + - - -
31C LYS* 1.3 73.1 - - - +
33C ARG* 1.3 73.5 + - - +
34C TYR* 5.0 0.9 - - + -
48C LYS 3.9 0.3 - - - +
49C GLU* 3.2 6.1 - - - +
50C ALA* 2.7 42.8 + - + +
52C VAL* 4.4 12.3 - - + -
133C VAL* 4.7 7.6 - - + -
136C LEU* 4.0 31.4 - - + -
137C ILE* 4.1 26.2 - - + -
150D PHE* 5.2 4.7 - - + -
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Residues in contact with ARG 33 (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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8A ARG* 3.5 16.5 - - - +
23A GLU* 3.0 30.9 + - - -
87A GLU* 3.5 9.1 + - - -
89A GLU* 5.3 0.7 - - - -
24C PHE* 3.1 7.4 - - - +
25C GLU* 2.9 57.2 + - + +
27C ARG* 3.8 22.0 - - - +
31C LYS* 4.1 17.7 - - + +
32C LEU* 1.3 79.1 - - - +
34C TYR* 1.3 61.9 + - - +
47C ARG* 3.3 24.7 - - - +
48C LYS 3.4 6.1 - - - +
49C GLU* 3.2 31.4 + - + +
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Residues in contact with TYR 34 (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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22C LEU* 3.4 30.8 - - + +
23C GLU 3.6 8.3 - - - -
24C PHE* 4.2 3.1 - - + -
32C LEU* 5.0 1.8 - - + -
33C ARG* 1.3 76.1 - - - +
35C ALA* 1.3 65.5 + - - +
36C ASN* 3.7 18.6 + - + +
46C ILE* 4.2 21.5 - - + -
47C ARG* 3.5 3.8 - - - +
48C LYS* 2.8 36.6 + - + +
133C VAL* 3.8 28.5 - - + -
134C PHE* 3.9 9.0 - + - -
137C ILE* 3.7 41.1 - - + -
145C PRO* 3.5 37.0 - - + +
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Residues in contact with ALA 35 (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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21C PHE* 4.1 19.9 - - + -
22C LEU* 3.4 2.9 - - - +
23C GLU* 2.9 40.9 + - + +
34C TYR* 1.3 78.8 - - - +
36C ASN* 1.3 63.9 + - - +
45C MET* 5.2 1.8 - - - -
46C ILE 3.2 10.5 - - - +
47C ARG* 4.3 22.7 - - + +
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Residues in contact with ASN 36 (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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21C PHE* 3.1 19.6 - - - +
22C LEU* 4.1 9.9 - - + +
34C TYR* 3.7 21.3 - - + +
35C ALA* 1.3 76.1 - - - +
37C ASN* 1.3 66.0 + - - +
38C SER* 4.3 10.1 + - - -
44C VAL 3.9 1.0 - - - +
45C MET* 3.7 3.0 - - - -
46C ILE* 2.9 45.5 + - + +
145C PRO 3.9 23.8 + - - -
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Residues in contact with ASN 37 (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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19A HIS* 4.6 9.2 - - + +
37A ASN* 4.3 10.7 - - - +
43A ASP* 5.5 1.4 - - - +
19C HIS* 3.9 7.9 + - - +
20C GLU* 3.4 12.5 - - - +
21C PHE* 3.0 58.1 + - + +
36C ASN* 1.3 71.7 + - - +
38C SER* 1.3 67.8 + - - +
39C ASN* 5.5 2.1 - - - +
44C VAL 3.5 7.6 - - - +
45C MET* 3.2 34.1 - - + +
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Residues in contact with SER 38 (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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19C HIS 4.9 2.0 - - - -
20C GLU* 4.0 16.5 + - - +
36C ASN* 4.3 13.0 + - - -
37C ASN* 1.3 79.7 + - - +
39C ASN* 1.3 67.4 + - - +
42C ASN* 2.7 20.4 - - - +
43C ASP* 3.7 10.9 - - - -
44C VAL* 3.4 13.8 + - - -
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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