Contacts of the strand formed by residues 36 - 42 (chain B) in PDB entry 3T0E
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 PHE 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TYR 4.3 0.2 - - - +
14A LEU* 2.9 20.2 - - - +
15A ASN* 3.0 28.8 + - + +
16A PRO* 5.6 0.7 - - + -
70A LEU* 4.1 17.0 - - + -
74A THR* 3.3 33.4 - - + +
79A TYR* 3.7 27.4 - + + -
80A THR 3.5 11.7 - - - -
81A PRO* 4.0 10.1 - - + -
82A ILE* 5.2 0.2 - - - -
34B PRO* 3.8 21.1 - - + -
35B ARG* 1.3 80.6 - - - +
37B LEU* 1.3 61.2 + - - +
61B TYR* 3.1 24.9 - + - -
62B HIS* 3.7 4.0 - - - -
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.9 22.4 - - + -
13A TYR 3.8 9.0 - - - +
14A LEU* 4.2 12.6 - - + -
70A LEU* 3.9 8.9 - - - +
82A ILE* 5.0 5.2 - - + -
113A THR* 3.8 22.7 - - - +
114A PRO* 5.0 2.2 - - + -
115A PRO* 4.7 7.2 - - + -
145A PHE* 4.4 7.4 - - + -
36B PHE* 1.3 75.9 - - - +
38B GLU* 1.3 82.8 + - - +
39B GLN* 3.9 11.0 - - + +
61B TYR* 3.6 6.9 - - - -
62B HIS* 3.0 63.8 + - - +
63B GLN* 4.9 0.7 - - - +
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Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 2.9 28.3 - - - +
13A TYR 3.0 14.3 + - - +
66A ASP* 3.4 30.5 - - + +
69A ASN* 3.7 18.3 - - + +
70A LEU* 3.4 28.9 + - + +
73A MET* 3.8 7.3 - - - +
37B LEU* 1.3 75.7 - - - +
39B GLN* 1.3 78.4 + - - +
40B VAL* 4.2 6.6 - - + +
59B TYR* 4.8 0.2 - - - +
60B PHE 2.6 27.6 + - - +
61B TYR* 5.4 0.7 - - - -
66B TYR* 3.3 19.8 + - - -
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Residues in contact with GLN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA* 6.4 0.9 - - + -
11A GLU 3.5 4.7 - - - +
12A PHE* 3.7 20.6 - - + -
139A PRO* 4.8 1.6 - - - +
143A HIS* 3.4 27.6 + - - +
145A PHE* 3.5 21.2 - - + -
37B LEU* 3.9 11.1 - - + +
38B GLU* 1.3 83.6 + - - +
40B VAL* 1.3 60.8 + - - +
41B LYS* 3.6 27.1 + - + -
59B TYR* 3.4 0.7 - - - -
60B PHE* 2.6 52.7 + - + +
62B HIS 3.0 25.1 + - - +
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLN 3.7 0.7 - - - +
10A ALA* 3.4 1.6 - - - -
11A GLU* 2.7 50.3 + - + +
66A ASP* 3.4 23.1 - - - +
69A ASN* 5.0 1.6 - - - +
8B GLN* 3.8 14.1 - - + -
38B GLU* 4.2 7.9 - - - +
39B GLN* 1.3 76.7 - - - +
41B LYS* 1.3 62.1 + - - +
42B HIS* 3.6 30.5 - - + +
58B ARG 4.2 10.3 - - - +
59B TYR* 3.6 27.4 - - + -
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Residues in contact with LYS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 4.4 19.9 - - + +
9A GLN 3.7 2.9 - - - -
10A ALA* 3.6 18.8 - - + -
139A PRO* 3.4 26.0 - - + +
140A ARG 3.0 27.9 + - - -
143A HIS* 3.5 30.1 + - + +
39B GLN* 3.6 17.3 - - + +
40B VAL* 1.3 74.5 - - - +
42B HIS* 1.3 62.6 + - - +
43B GLU* 3.3 15.2 + - + +
58B ARG* 2.9 34.5 + - - +
60B PHE* 3.7 24.7 - - + -
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Residues in contact with HIS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE 3.8 0.5 - - - +
8A ILE* 3.3 3.5 - - - +
9A GLN* 2.8 79.3 + - + +
11A GLU* 3.7 3.4 + - - -
6B GLU* 3.6 20.0 - - + +
7B GLY 3.9 3.6 - - - -
8B GLN* 2.7 43.9 + - + -
40B VAL* 3.6 11.7 - - + +
41B LYS* 1.3 71.2 - - - +
43B GLU* 1.3 61.9 + - - +
55B PHE* 4.8 3.4 - - + -
56B LEU 3.6 6.3 - - - +
57B ASP* 3.2 26.3 + - - +
107B TYR* 4.0 18.6 + - + +
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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