Contacts of the strand formed by residues 35 - 41 (chain A) in PDB entry 2B7T
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 35 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A SER 4.1 0.2 - - - +
27A GLN* 3.1 7.5 + - - +
28A THR* 2.8 52.2 + - + +
29A GLY* 4.0 15.0 - - - -
30A PRO* 4.6 7.0 - - + -
34A PRO* 1.3 74.1 - - - +
36A PHE* 1.3 66.8 + - - +
37A VAL* 3.8 18.4 - - + -
50A SER* 4.1 9.9 - - - -
51A GLY* 3.5 33.2 - - - +
52A PRO* 4.0 5.4 - - + -
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Residues in contact with PHE 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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24A LEU* 4.0 16.2 - - + -
25A LEU 4.4 4.0 - - - -
27A GLN* 3.2 43.5 - - + +
34A PRO* 3.7 9.4 - - + -
35A LEU* 1.3 74.7 - - - +
37A VAL* 1.3 65.5 + - - +
50A SER* 3.4 3.1 - - - -
51A GLY 2.9 34.0 + - - +
52A PRO 3.5 17.3 - - - -
53A THR* 3.5 20.0 - - - -
54A LYS* 3.5 48.5 - - + +
57A ALA* 3.3 2.3 - - + +
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.6 4.0 - - - +
25A LEU* 2.8 64.7 + - + +
26A SER 5.2 1.3 + - - +
28A THR* 6.3 0.4 - - + -
35A LEU* 3.8 12.3 - - + -
36A PHE* 1.3 79.3 - - - +
38A MET* 1.3 62.9 + - - +
48A GLU* 3.8 21.1 - - + +
49A GLY 3.4 9.6 - - - +
50A SER* 3.8 18.8 - - - +
57A ALA* 4.1 0.7 - - - -
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Residues in contact with MET 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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22A TYR* 3.5 31.2 - - + -
23A MET* 3.2 15.5 - - - +
24A LEU* 3.4 31.6 - - + -
37A VAL* 1.3 72.0 - - - +
39A SER* 1.3 60.2 - - - +
48A GLU* 3.3 4.6 - - - -
49A GLY 2.9 32.8 + - - -
54A LYS* 3.8 28.0 - - + +
57A ALA* 3.7 1.4 - - - +
58A LYS* 3.6 42.6 - - + +
61A ALA* 3.3 6.8 - - + +
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Residues in contact with SER 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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21A GLN 3.6 2.4 - - - +
22A TYR* 3.4 1.7 - - - -
23A MET* 2.9 45.6 + - - +
25A LEU* 4.1 15.0 - - - +
38A MET* 1.3 71.0 - - - +
40A VAL* 1.3 59.7 + - - +
46A VAL* 3.7 26.9 - - - +
47A PHE 3.4 5.2 - - - -
48A GLU* 3.5 20.2 - - - +
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Residues in contact with VAL 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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20A LEU* 3.7 21.3 - - + -
21A GLN 3.4 2.5 - - - +
22A TYR* 3.2 43.1 - - + -
38A MET* 4.0 0.6 - - + -
39A SER* 1.3 73.7 - - - +
41A GLU* 1.3 61.5 + - - +
42A VAL 4.0 0.9 + - - -
45A GLN 3.9 0.7 - - - +
46A VAL* 3.3 1.0 - - - -
47A PHE* 2.8 41.8 + - - +
61A ALA* 3.5 15.5 - - + +
62A ALA* 3.4 33.9 - - + +
65A ALA* 3.8 8.7 - - + +
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Residues in contact with GLU 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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20A LEU* 3.3 9.6 - - - -
21A GLN* 2.8 69.9 + - + +
40A VAL* 1.3 73.2 - - - +
42A VAL* 1.3 58.1 + - - +
43A ASN 2.9 13.5 + - - -
44A GLY* 2.8 31.7 + - - -
45A GLN 3.3 16.4 - - - +
46A VAL* 3.7 22.2 - - + +
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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