Contacts of the strand formed by residues 35 - 41 (chain B) in PDB entry 5T5W
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 TYR 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B PRO* 5.0 2.7 - - + -
23B TRP* 3.4 44.2 - + + -
25B PRO* 3.9 24.9 - - + +
34B THR* 1.3 86.5 - - - +
36B PHE* 1.3 64.0 + - - +
37B VAL* 5.4 0.2 - - + -
54B CYS 3.4 6.6 - - - +
56B GLY* 2.9 25.6 + - - -
57B THR* 2.9 29.7 + - + +
58B LYS* 4.3 10.1 - - - -
59B GLU 3.5 20.0 - - - -
60B LEU* 5.9 0.7 - - + -
80B VAL* 4.5 7.6 - - + -
81B ARG 3.8 5.2 - - - +
82B THR* 3.4 33.7 - - + +
83B VAL* 4.4 2.2 - - - -
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Residues in contact with PHE 36 (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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35B TYR* 1.3 81.9 - - - +
37B VAL* 1.3 62.2 + - - +
50B GLU* 6.2 6.1 - - + -
54B CYS 4.3 0.7 - - - -
55B ALA* 3.9 15.7 - - + -
56B GLY* 3.4 23.6 - - - -
80B VAL* 3.2 6.8 - - - +
81B ARG* 3.0 47.8 + - + +
83B VAL* 3.9 24.2 - - + +
88B LYS* 3.9 19.3 - - - -
91B TRP* 3.4 18.0 - + + -
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Residues in contact with VAL 37 (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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21B LEU* 4.1 9.9 - - + -
23B TRP* 3.6 36.6 - - + -
35B TYR* 5.4 0.4 - - + -
36B PHE* 1.3 82.0 - - - +
38B ALA* 1.3 61.2 + - - +
50B GLU* 3.6 5.7 - - - +
51B VAL* 3.0 41.0 + - + +
54B CYS* 3.4 34.9 + - + +
57B THR* 5.9 0.2 - - + -
62B CYS* 3.7 7.4 - - + -
64B MET* 5.3 1.8 - - - -
79B ARG 3.3 4.9 - - - +
80B VAL* 3.7 14.1 - - + -
91B TRP* 4.6 1.8 - - - -
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Residues in contact with ALA 38 (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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21B LEU* 5.1 0.5 - - - +
37B VAL* 1.3 75.9 - - - +
39B TYR* 1.3 63.1 + - - +
48B TRP* 3.9 8.7 - - + -
49B ARG 3.1 21.8 - - - +
50B GLU* 4.3 6.7 - - + +
51B VAL* 4.7 1.8 - - - +
64B MET* 4.1 6.7 - - - +
78B GLY* 3.2 5.0 - - - -
79B ARG* 2.8 54.1 + - + +
91B TRP* 4.4 7.4 - - + -
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Residues in contact with TYR 39 (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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38B ALA* 1.3 77.8 - - - +
40B GLN* 1.3 65.4 + - - +
41B SER* 5.0 10.3 - - - -
47B ARG 4.1 0.3 - - - +
48B TRP* 3.3 9.4 - - - -
49B ARG* 2.9 87.6 + - + +
50B GLU 4.7 3.4 - - - -
51B VAL* 4.9 4.0 - - + -
64B MET* 3.6 20.0 - - + -
67B LEU* 3.5 33.2 - - + +
68B LYS* 4.5 1.0 + - + +
69B LYS* 3.4 32.4 + - - +
70B GLN* 3.5 20.6 + - + -
76B PHE* 4.8 11.0 - + + -
77B LYS 3.4 10.1 - - - +
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Residues in contact with GLN 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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39B TYR* 1.3 75.8 - - - +
41B SER* 1.3 66.3 + - - +
44B THR 4.6 1.8 - - - +
45B ARG* 4.7 6.1 - - - +
47B ARG 3.6 17.7 - - - +
48B TRP* 3.5 31.8 - - + +
76B PHE* 3.2 8.1 - - - +
77B LYS* 3.0 31.3 + - + +
96B TYR* 4.9 3.1 - - + +
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Residues in contact with SER 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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39B TYR* 4.6 11.7 - - - -
40B GLN* 1.3 75.7 - - - +
42B SER* 1.3 66.9 + - - +
43B PRO* 3.2 18.4 - - - +
44B THR* 3.1 44.0 + - - +
45B ARG* 3.4 5.0 + - - -
49B ARG* 6.1 1.1 - - - -
69B LYS 5.7 3.1 - - - -
71B ASP* 4.1 23.2 + - - +
74B ASN* 5.0 0.7 - - - +
75B LYS 4.7 1.4 + - - -
76B PHE* 4.2 8.9 - - - +
96B TYR* 5.5 1.3 + - - -
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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