Contacts of the strand formed by residues 37 - 42 (chain A) in PDB entry 1BLJ
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 SER 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.0 23.3 - - - +
33A ASN* 3.3 16.3 - - - +
34A LYS 2.6 37.5 + - - -
36A GLY* 1.3 77.3 - - - +
38A PHE* 1.4 61.9 + - - +
54A VAL* 3.9 0.2 - - - -
55A LYS* 3.7 16.5 + - - +
107A THR* 3.8 2.3 + - - -
108A LEU* 3.0 28.0 - - - -
110A CYS 3.6 9.2 - - - -
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Residues in contact with PHE 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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13A LYS 3.3 14.3 - - - +
14A TRP* 3.8 11.3 - - + -
28A LEU* 3.8 0.9 - - - -
36A GLY* 2.9 25.8 + - - +
37A SER* 1.4 79.5 - - - +
39A LEU* 1.4 62.4 + - - +
40A ILE* 5.6 0.2 - - + -
52A LEU* 3.3 31.4 - - + -
53A SER 3.3 6.7 - - - +
54A VAL* 2.9 42.8 - - + -
92A VAL* 5.8 1.3 - - + -
95A TYR* 4.8 1.3 - + - -
102A LEU* 3.4 21.5 - - + -
104A GLN 3.3 18.6 - - - -
106A LEU* 2.9 41.1 - - + -
109A PRO* 4.2 7.2 - - - +
110A CYS* 3.1 17.8 - - - -
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Residues in contact with LEU 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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13A LYS* 3.5 11.4 - - + +
14A TRP 3.7 0.2 - - - -
16A PHE* 3.3 38.8 - - + -
19A ILE* 4.2 2.7 - - + -
24A ALA* 3.2 45.3 - - + +
27A GLN* 4.5 6.3 - - + +
28A LEU* 3.9 2.7 - - + -
38A PHE* 1.4 71.3 - - - +
40A ILE* 1.4 60.7 + - - +
41A ARG* 3.8 2.8 + - + +
52A LEU* 2.8 18.9 - - - +
53A SER* 3.0 31.5 + - - +
110A CYS* 3.0 35.7 - - - -
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Residues in contact with ILE 40 (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 LYS 4.1 0.8 + - - -
14A TRP* 2.8 35.6 + - + +
15A PHE* 3.5 15.0 - - + -
16A PHE* 2.7 27.4 - - - +
38A PHE* 5.6 0.2 - - + -
39A LEU* 1.4 71.6 - - - +
41A ARG* 1.4 55.6 + - - +
50A PHE* 3.4 4.8 - - + -
51A SER 3.1 15.7 - - - +
52A LEU* 3.5 23.3 - - + -
69A ILE* 3.3 23.3 - - + -
88A LEU* 3.4 31.9 - - + -
91A LEU* 3.8 18.2 - - + -
92A VAL* 4.4 2.9 - - + -
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Residues in contact with ARG 41 (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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16A PHE* 4.3 0.9 - - - -
17A ARG 3.0 23.3 - - - +
18A THR* 3.3 16.9 + - - +
19A ILE* 2.8 42.2 + - + +
20A SER* 4.2 6.3 - - - +
21A ARG* 4.2 16.3 - - + +
24A ALA* 4.9 5.2 - - + -
39A LEU* 3.7 3.4 - - + -
40A ILE* 1.4 76.7 - - - +
42A GLU* 1.4 74.1 + - - +
43A SER* 4.1 7.9 - - - +
44A GLU* 4.3 8.7 + - - +
50A PHE* 3.4 1.3 - - - -
51A SER* 2.7 60.1 + - - -
53A SER* 4.7 11.2 - - - +
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Residues in contact with GLU 42 (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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17A ARG* 3.4 32.2 - - - +
18A THR* 3.3 35.8 - - + +
41A ARG* 1.4 97.9 + - - +
43A SER* 1.4 66.4 + - - +
44A GLU* 4.5 3.3 - - - -
46A ASN* 2.9 24.3 + - - +
49A ALA 3.9 0.4 - - - -
50A PHE* 3.5 28.3 - - + -
51A SER* 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