Contacts of the strand formed by residues 32 - 39 (chain A) in PDB entry 1EBF
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 THR 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LYS 2.7 18.3 + - - -
5A VAL* 3.4 11.5 - - + +
6A VAL* 2.7 35.2 + - - +
29A SER 5.6 0.2 + - - -
30A THR 3.8 3.8 + - - -
31A ILE* 1.3 71.9 - - - +
33A TYR* 1.3 60.7 + - - +
34A ASN* 3.5 29.4 - - - +
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Residues in contact with TYR 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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6A VAL* 3.3 19.1 - - + -
8A VAL* 4.0 13.0 - - + -
24A LEU* 4.0 22.2 - - + +
27A MET* 4.6 14.6 - - + -
29A SER* 4.0 15.0 + - - -
31A ILE* 3.3 36.0 + - + +
32A THR* 1.3 74.3 - - - +
34A ASN* 1.3 65.0 + - - +
35A LEU 3.8 1.6 + - - -
349A LEU* 6.1 0.2 - - + -
352A VAL* 3.7 27.6 - - + -
353A ILE* 3.7 24.3 - - + +
356A ALA* 3.1 37.3 - - + +
357A GLN* 5.7 0.2 + - - -
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Residues in contact with ASN 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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5A VAL* 3.5 29.1 - - - +
6A VAL 2.7 10.1 + - - -
7A ASN* 3.2 20.4 - - - +
8A VAL* 2.6 32.6 + - - -
32A THR* 3.5 18.6 - - - +
33A TYR* 1.3 72.6 - - - +
35A LEU* 1.3 58.9 + - - +
36A VAL* 3.4 3.7 + - + +
50A PHE 4.8 2.8 + - - +
52A PRO* 2.9 43.2 - - + +
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Residues in contact with LEU 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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8A VAL* 3.4 8.3 - - - +
10A VAL* 3.5 32.8 - - + -
21A LEU* 4.1 11.0 - - + -
24A LEU* 4.2 13.2 - - + +
25A LEU* 4.3 28.5 - - + -
33A TYR 3.8 3.6 + - - -
34A ASN* 1.3 69.5 - - - +
36A VAL* 1.3 59.0 + - - +
37A LEU 3.5 11.4 - - - +
38A LEU* 4.3 19.1 - - + -
52A PRO* 3.8 5.8 - - - +
53A LEU* 3.0 54.7 + - + +
55A VAL* 4.7 7.6 - - + -
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Residues in contact with VAL 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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7A ASN* 3.7 29.4 - - + +
8A VAL 2.8 23.7 + - - +
9A ALA* 4.2 3.1 - - + -
34A ASN* 3.7 11.7 - - + +
35A LEU* 1.3 77.7 - - - +
37A LEU* 1.3 60.8 + - - +
46A ILE* 3.6 2.3 - - - +
47A SER* 3.0 34.7 + - - +
50A PHE* 3.9 31.0 - - + +
51A SER 4.5 1.6 - - - +
53A LEU* 3.9 5.6 - - - -
79A HIS* 5.8 0.9 + - - -
80A LEU* 4.1 25.9 - - + +
87A VAL* 5.3 0.7 - - + -
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Residues in contact with LEU 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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8A VAL 3.7 1.2 + - - -
9A ALA* 3.8 25.8 - - + -
10A VAL* 3.0 41.3 + - - +
11A ILE* 3.8 18.8 - - + -
35A LEU* 3.5 9.5 - - - +
36A VAL* 1.3 83.7 - - + +
38A LEU* 1.3 61.2 + - - +
39A ALA* 4.0 7.2 - - + +
44A SER* 3.7 9.9 - - - +
45A LEU 3.4 7.9 - - - +
46A ILE* 3.2 33.2 - - + -
53A LEU* 3.7 3.5 - - - +
76A LEU* 4.0 30.3 - - + -
80A LEU* 5.3 2.9 - - + -
89A LEU* 4.8 0.4 - - + -
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Residues in contact with LEU 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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10A VAL* 3.6 8.3 - - + -
13A ALA* 4.3 15.3 - - + -
21A LEU* 3.7 34.8 - - + -
35A LEU* 4.3 8.1 - - + -
37A LEU* 1.3 73.0 - - - +
39A ALA* 1.3 61.2 + - - +
44A SER* 3.3 2.8 - - - -
45A LEU* 2.7 60.5 + - + -
53A LEU* 4.3 4.0 - - + -
59A TRP* 3.6 42.4 - - + -
63A LEU* 3.7 15.0 - - + +
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Residues in contact with ALA 39 (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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10A VAL 3.0 13.6 + - - +
11A ILE* 3.6 12.0 - - + -
12A GLY* 2.9 30.5 + - - -
37A LEU* 4.0 15.0 - - + -
38A LEU* 1.3 77.8 - - - +
40A GLU* 1.3 60.1 + - - +
44A SER* 3.5 21.5 - - - +
70A THR* 4.1 15.9 - - + -
76A LEU* 6.1 1.1 - - + -
2109A NAD 3.9 1.8 + - - -
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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