Contacts of the strand formed by residues 30 - 37 (chain A) in PDB entry 2JFS
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 LEU 30 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.8 28.0 - - + +
26A ALA* 3.6 1.2 + - - -
27A ASP* 2.9 38.9 + - + +
28A GLY 3.5 0.2 - - - -
29A ILE* 1.3 77.5 - - - +
31A TYR* 1.3 68.9 + - - +
52A LEU* 4.2 11.4 - - + -
53A SER* 4.3 7.9 - - - +
56A PHE* 3.8 42.4 - - + -
65A LEU* 4.0 23.6 - - + -
93A ALA* 4.3 8.7 - - + -
94A VAL 3.5 17.3 - - - -
95A ALA* 4.5 5.4 - - + +
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Residues in contact with TYR 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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4A VAL* 3.5 32.7 - - + +
7A ALA* 3.6 24.5 - - + +
25A LEU* 3.3 6.1 - - - +
26A ALA* 3.6 32.3 - - + -
27A ASP 4.9 0.4 - - - -
28A GLY 2.9 29.7 + - - -
29A ILE* 3.5 16.8 - - - -
30A LEU* 1.3 75.6 - - - +
32A ALA* 1.3 63.9 + - - +
93A ALA* 3.3 1.7 - - - +
94A VAL 2.8 37.3 + - - -
96A VAL* 4.1 4.9 - - + -
182A ILE* 3.7 9.7 - - + +
228A VAL* 3.9 13.7 - - + -
230A ILE* 3.6 28.9 - - + -
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Residues in contact with ALA 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 CYS* 3.2 7.6 - - - +
25A LEU* 2.9 39.5 + - + +
31A TYR* 1.3 77.6 - - - +
33A VAL* 1.3 64.8 + - - +
49A LEU* 3.9 22.9 - - + -
52A LEU* 4.0 8.7 - - + -
91A LEU* 4.2 0.9 - - + -
92A THR 3.1 12.8 - - - +
93A ALA* 3.9 13.2 - - + -
182A ILE* 4.0 4.6 - - - +
228A VAL* 3.9 2.2 - - - +
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Residues in contact with VAL 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 ALA 3.5 9.9 - - - +
24A CYS* 4.3 4.9 - - + -
32A ALA* 1.3 78.3 - - - +
34A ALA* 1.3 69.3 + - - +
49A LEU* 4.5 0.9 - - - -
90A THR* 4.6 1.3 + - - -
91A LEU* 3.5 5.0 - - - +
92A THR* 2.9 31.1 + - - +
112A SER* 4.4 6.3 - - - +
182A ILE* 3.6 34.0 - - + +
183A SER* 4.1 3.4 - - - +
184A SER* 3.8 32.1 - - - +
226A THR* 4.4 12.1 - - + +
228A VAL* 3.7 19.5 - - + -
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Residues in contact with ALA 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 ASP* 3.3 3.1 - - - +
23A ALA 2.8 36.5 + - - +
33A VAL* 1.3 77.2 - - - +
35A ASP* 1.3 59.4 + - - +
36A GLY 3.8 0.2 - - - -
45A SER* 3.5 16.0 - - - +
48A ALA* 4.8 1.3 - - + -
49A LEU* 3.8 27.1 - - + +
89A THR* 3.5 10.3 - - + +
90A THR* 3.3 17.5 - - - +
91A LEU* 4.4 2.2 - - + -
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Residues in contact with ASP 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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22A ASP* 3.2 16.5 - - - +
34A ALA* 1.3 69.6 - - - +
36A GLY* 1.3 61.4 + - - +
37A PHE* 4.2 0.2 - - - -
89A THR* 3.3 4.1 + - - -
90A THR* 2.9 38.4 + - - +
111A ASP* 4.6 0.3 - - - +
112A SER* 3.6 9.8 + - - +
184A SER* 4.0 7.9 - - - -
185A ASP* 2.9 8.5 + - - +
1234A MN 2.1 35.0 + - - -
1235A MN 2.2 30.5 + - - -
1237A CAC 3.1 21.3 + - + +
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Residues in contact with GLY 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 GLN* 2.9 21.8 + - - +
35A ASP* 1.3 74.1 + - - +
37A PHE* 1.3 56.9 + - - -
41A GLY* 3.3 26.2 - - - -
45A SER* 3.8 1.2 - - - -
88A GLY 3.4 8.1 - - - -
89A THR* 3.4 7.0 + - - -
1234A MN 2.2 34.8 + - - -
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Residues in contact with PHE 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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21A GLN* 3.8 4.3 - - - -
35A ASP 4.2 3.6 - - - -
36A GLY* 1.3 75.6 - - - -
38A GLY* 1.3 67.7 + - - +
41A GLY* 3.2 7.6 - - - -
86A VAL* 4.3 17.9 - - + -
87A SER* 3.2 6.8 - - - -
88A GLY* 2.9 51.3 + - - -
89A THR* 3.4 21.5 - - - -
155A LEU* 3.5 30.1 - - + -
158A ALA* 3.7 20.6 - - + -
161A ILE* 4.1 5.6 - - + -
1237A CAC 3.5 23.3 - - + +
1239A GOL 3.8 27.4 - - - +
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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