Contacts of the strand formed by residues 24 - 31 (chain A) in PDB entry 2P1E
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 ASN 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ARG* 3.0 13.2 + - - -
20A THR* 2.9 45.2 + - - +
21A LEU* 3.8 17.5 - - + +
23A ASP* 1.3 83.0 + - - +
25A PHE* 1.3 61.8 + - - +
43A ASN* 3.9 5.8 + - - +
80A ASP* 3.0 40.3 + - - +
81A HIS* 3.6 10.4 + - - -
209A GLY 3.4 5.0 - - - +
210A HIS* 3.2 23.8 + - - -
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Residues in contact with PHE 25 (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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2A ARG* 3.4 14.8 - - - -
17A VAL* 3.4 23.8 - - + -
18A VAL 3.5 2.0 - - - -
19A PRO* 4.2 10.1 - - + -
20A THR* 4.2 0.9 - - - -
24A ASN* 1.3 81.1 - - - +
26A SER* 1.3 62.1 + - - +
27A TYR* 3.3 39.6 - - + +
41A ASP* 4.2 12.3 - - - +
81A HIS* 5.3 0.5 + - - -
208A PRO 3.7 8.2 - - - +
209A GLY* 2.8 15.1 + - - +
210A HIS 3.5 19.1 - - - -
211A GLU* 3.4 48.2 - - + -
251A PRO* 4.0 17.3 - - + -
253A VAL* 3.7 18.6 - - + -
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Residues in contact with SER 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 2.8 33.4 + - - -
20A THR* 3.2 27.4 + - - +
25A PHE* 1.3 73.2 - - - +
27A TYR* 1.3 71.6 + - - +
40A VAL 3.3 9.4 - - - -
41A ASP 2.7 22.9 + - - -
42A VAL* 4.2 2.8 - - - -
43A ASN* 3.8 2.6 + - - -
49A ILE* 3.9 23.9 - - - +
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Residues in contact with TYR 27 (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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15A VAL* 4.0 6.3 - - + -
16A THR 3.3 14.8 - - - +
17A VAL* 3.7 22.9 - - + -
18A VAL* 4.6 3.1 - - - +
25A PHE* 3.3 26.2 - - + +
26A SER* 1.3 80.5 - - - +
28A LEU* 1.3 61.1 + - - +
29A ILE 4.1 0.4 - - - -
38A ALA 3.7 0.3 - - - +
39A ALA* 3.1 8.0 - - - +
40A VAL* 2.7 47.9 + - + +
41A ASP* 5.6 1.3 - - + -
49A ILE* 5.0 2.7 - - - +
161A PHE* 3.6 29.6 - + + -
207A PHE* 3.3 41.7 - + + -
208A PRO* 2.6 45.4 + - - +
209A GLY* 5.4 0.2 - - - -
253A VAL* 3.9 2.3 - - + +
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Residues in contact with LEU 28 (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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14A SER 3.8 0.2 - - - +
15A VAL* 3.5 2.6 - - - -
16A THR* 2.8 46.0 + - - +
18A VAL* 4.5 5.7 - - + +
27A TYR* 1.3 73.9 - - - +
29A ILE* 1.3 68.3 + - - +
30A ASN* 3.8 4.8 + - + +
37A LEU* 4.2 20.4 - - + -
38A ALA 3.4 18.8 - - - +
39A ALA* 4.5 0.9 - - - +
49A ILE* 4.1 17.7 - - + -
52A TYR* 3.8 24.0 - - + -
53A ILE* 3.7 39.7 - - + -
57A LEU* 4.6 2.7 - - + -
69A PHE* 4.1 9.4 - - + -
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Residues in contact with ILE 29 (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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13A PHE* 4.5 6.1 - - + -
14A SER 3.6 7.9 - - - +
15A VAL* 4.3 4.7 - - + +
27A TYR 4.1 0.2 - - - -
28A LEU* 1.3 74.4 - - - +
30A ASN* 1.3 63.3 + - - +
31A ASP 4.6 0.7 - - - +
36A THR 3.8 0.2 - - - +
37A LEU* 3.2 9.2 - - - +
38A ALA* 2.7 49.4 + - + +
40A VAL* 3.7 26.0 - - + -
73A LEU* 4.7 5.8 - - + -
126A VAL* 4.6 11.9 - - + -
129A LEU* 3.6 30.7 - - + -
131A VAL* 5.6 0.7 - - + -
148A VAL* 4.3 15.3 - - + -
161A PHE* 3.8 30.7 - - + -
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Residues in contact with ASN 30 (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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13A PHE* 3.2 7.7 - - - +
14A SER* 2.9 41.0 + - - +
16A THR* 6.0 1.3 - - - +
28A LEU* 3.8 5.1 + - + +
29A ILE* 1.3 74.7 - - - +
31A ASP* 1.3 70.9 + - - +
32A HIS* 3.3 25.1 + - + +
35A HIS* 5.5 0.2 + - - -
36A THR 3.7 2.9 - - - +
37A LEU* 3.6 19.2 - - + +
52A TYR* 5.9 0.2 + - - -
57A LEU* 4.1 19.7 - - + +
67A TYR* 4.0 25.3 + - - -
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Residues in contact with ASP 31 (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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12A ALA 3.4 10.5 - - - +
29A ILE* 4.1 1.2 - - - +
30A ASN* 1.3 69.2 - - - +
32A HIS* 1.3 58.4 + - - +
33A THR* 2.9 26.1 + - - +
34A THR* 2.7 22.9 + - - +
35A HIS* 2.8 31.5 + - - -
36A THR* 2.9 17.7 + - - +
126A VAL* 3.9 6.5 - - + +
127A GLY* 3.5 0.3 - - - -
128A ASP 2.9 21.3 + - - -
129A LEU* 3.7 35.2 - - + +
150A HIS* 4.1 0.7 - - - -
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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