Contacts of the strand formed by residues 31 - 38 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLU 3.5 1.9 - - - +
26A PHE* 3.5 3.6 - - - -
27A ARG* 2.9 50.5 + - - +
29A ASP* 3.3 19.2 + - - +
30A GLY* 1.3 76.3 - - - +
32A LEU* 1.3 62.3 + - - +
33A ARG* 4.1 18.5 + - + +
49A GLU* 3.5 29.9 + - + -
50A ALA* 3.4 12.6 - - - +
51A TYR* 3.6 39.3 + - + +
89C GLU* 4.2 17.0 + - - -
96C HIS* 5.8 1.6 - - - -
98C SER* 4.8 8.3 + - - -
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Residues in contact with LEU 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 PHE* 4.5 7.6 - - + -
25A GLU 3.3 17.3 - - - +
26A PHE* 3.8 30.5 - - + +
30A GLY 3.4 1.0 + - - -
31A LYS* 1.3 72.5 - - - +
33A ARG* 1.3 70.5 + - - +
48A LYS 4.0 0.3 - - - +
49A GLU* 3.2 4.5 - - - +
50A ALA* 2.8 40.2 + - + +
52A VAL* 4.3 16.2 - - + -
133A VAL* 4.5 6.7 - - + -
136A LEU* 3.9 33.9 - - + -
137A ILE* 4.0 28.1 - - + +
150B PHE* 5.5 2.5 - - + -
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Residues in contact with ARG 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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23A GLU 4.6 0.2 - - - -
24A PHE* 3.1 6.9 - - - +
25A GLU* 2.9 65.7 + - + +
27A ARG* 3.6 19.9 - - - +
31A LYS* 4.2 14.6 - - + +
32A LEU* 1.3 78.2 - - - +
34A TYR* 1.3 61.5 + - - +
47A ARG* 3.5 16.8 - - - +
48A LYS 3.4 5.4 - - - +
49A GLU* 3.1 29.8 + - + +
8C ARG* 3.0 50.1 - - - +
23C GLU* 4.4 1.6 + - - -
25C GLU* 5.6 1.0 + - - -
87C GLU* 3.8 2.2 + - - -
89C GLU* 4.9 0.2 - - - -
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Residues in contact with TYR 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 LEU* 3.3 29.6 - - + -
23A GLU 3.4 4.5 - - - -
24A PHE* 4.3 4.3 - - + -
32A LEU* 5.3 0.7 - - + -
33A ARG* 1.3 76.2 - - - +
35A ALA* 1.3 60.2 + - - +
36A ASN* 3.2 33.0 + - + +
46A ILE* 3.6 30.7 - - + -
47A ARG* 3.3 4.3 - - - +
48A LYS* 2.8 41.2 + - + +
133A VAL* 3.8 23.1 - - + -
134A PHE* 4.0 13.4 - + - -
137A ILE* 3.9 34.8 - - + -
143A ILE* 5.1 2.0 - - + -
145A PRO* 3.5 25.2 - - + +
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Residues in contact with ALA 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 PHE* 4.2 18.2 - - + +
22A LEU* 3.4 4.7 - - - +
23A GLU* 2.9 38.0 + - + +
34A TYR* 1.3 78.2 - - - +
36A ASN* 1.3 60.9 + - - +
45A MET* 4.3 4.0 - - - -
46A ILE 3.2 9.4 - - - +
47A ARG* 3.9 27.4 - - + +
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Residues in contact with ASN 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 PHE 3.4 9.5 - - - +
22A LEU* 4.3 14.3 - - - +
34A TYR* 3.2 33.9 + - + +
35A ALA* 1.3 74.9 - - - +
37A ASN* 1.3 71.4 + - - +
38A SER* 4.2 8.8 - - - -
44A VAL 3.5 5.0 - - - +
45A MET* 3.6 2.4 - - - -
46A ILE* 3.0 39.9 + - + +
134A PHE* 5.3 0.8 - - - -
145A PRO 4.0 16.0 + - - -
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Residues in contact with ASN 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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19A HIS* 3.3 21.0 + - - +
20A GLU* 3.3 6.9 - - - +
21A PHE* 2.8 57.5 + - + +
36A ASN* 1.3 73.3 - - - +
38A SER* 1.3 62.9 + - - +
43A ASP* 2.7 34.8 + - - +
44A VAL 4.1 1.1 - - - -
45A MET* 3.6 31.3 - - + +
19C HIS* 4.2 6.3 + - - -
21C PHE* 5.0 2.2 - - - -
37C ASN* 4.3 10.4 - - - +
45C MET* 5.7 0.2 - - - +
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Residues in contact with SER 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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19A HIS 5.6 0.2 - - - -
20A GLU* 2.5 30.8 + - - -
36A ASN* 4.0 10.7 - - - -
37A ASN* 1.3 75.3 - - - +
39A ASN* 1.3 57.9 + - - +
40A TYR* 3.2 25.4 + - - +
41A LYS* 5.5 3.7 - - - +
43A ASP* 3.5 16.5 + - - -
44A VAL* 3.7 11.3 + - - +
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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