Contacts of the strand formed by residues 56 - 62 (chain B) in PDB entry 1YF9
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 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B GLU* 3.8 30.3 - - + +
44B PHE 3.5 2.9 - - - +
45B LYS* 2.9 32.6 + - + +
54B ASP 4.9 1.6 + - - -
55B GLY* 1.3 74.8 - - - -
57B TRP* 1.3 63.5 + - - +
78B ASN* 3.1 18.2 + - - -
155B ALA* 2.8 17.3 + - - +
157B PRO* 3.9 32.2 - - + +
160B ALA* 3.7 15.7 - - + +
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Residues in contact with TRP 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLU* 3.6 6.8 - - - +
44B PHE* 2.9 53.7 + + + +
46B GLY* 3.8 10.5 - - - -
52B TYR* 3.7 36.3 - + + -
55B GLY* 3.7 24.5 - - - -
56B THR* 1.3 75.7 - - - +
58B MET* 1.3 61.6 + - - +
59B LEU* 4.1 0.4 - - + -
76B PHE* 3.6 29.8 - + + -
78B ASN* 3.3 36.1 - - - +
79B ARG 2.9 21.1 + - - -
80B ILE* 3.6 21.5 - - + +
119B LEU* 4.4 4.3 - - + -
150B HIS* 6.2 0.4 - - - -
151B VAL* 3.9 13.9 - - + -
155B ALA* 3.6 18.8 - - + +
160B ALA* 3.8 5.6 - - - -
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Residues in contact with MET 58 (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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32B TYR* 3.6 42.6 - - + +
41B TRP* 3.8 18.8 - - + -
42B VAL 3.7 17.5 - - - -
43B GLU* 4.4 13.2 - - + +
57B TRP* 1.3 71.2 - - - +
59B LEU* 1.3 61.9 + - - +
75B GLY 3.8 0.2 - - - +
76B PHE* 3.8 2.6 - - - -
77B CYS* 2.8 30.3 + - + +
78B ASN* 3.0 7.3 + - - -
160B ALA* 3.4 36.0 - - + +
161B LEU* 4.3 4.9 - - + +
163B SER* 3.4 9.6 - - - +
164B ILE* 3.6 25.1 - - + -
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Residues in contact with LEU 59 (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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41B TRP* 3.1 8.0 - - - -
42B VAL* 2.8 40.6 + - + +
44B PHE* 3.7 23.6 - - + -
57B TRP* 4.9 0.2 - - + -
58B MET* 1.3 74.3 - - - +
60B HIS* 1.3 60.8 + - - +
61B VAL* 3.5 12.3 + - + +
74B ILE* 4.1 11.4 - - + -
75B GLY 3.3 5.8 - - - +
76B PHE* 3.7 49.1 - - + -
77B CYS* 4.2 1.6 - - - -
111B PHE* 3.7 23.8 - - + -
115B LEU* 3.5 26.2 - - + -
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Residues in contact with HIS 60 (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 GLU* 2.6 41.8 + - + +
40B PHE 4.0 1.1 - - - -
41B TRP* 3.5 27.1 - + - +
59B LEU* 1.3 69.6 - - - +
61B VAL* 1.3 61.8 + - - +
62B GLN* 3.4 27.9 + - + +
73B SER 3.6 2.3 - - - +
74B ILE* 3.5 4.2 - - - -
75B GLY* 2.7 37.6 + - - +
77B CYS* 3.6 19.5 - - - -
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Residues in contact with VAL 61 (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 3.9 0.2 - - - +
39B GLU* 3.4 3.3 - - - -
40B PHE* 2.9 64.4 + - + +
42B VAL* 3.9 13.7 - - + -
59B LEU* 3.9 11.9 - - + +
60B HIS* 1.3 76.7 - - - +
62B GLN* 1.3 64.9 + - - +
63B LEU* 4.4 13.2 - - + -
72B PRO* 4.4 2.9 - - + -
73B SER 3.5 2.7 - - - +
74B ILE* 4.0 21.8 - - + -
107B LEU* 5.1 2.2 - - + -
111B PHE* 3.8 31.9 - - + -
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Residues in contact with GLN 62 (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 3.1 9.8 + - - +
39B GLU* 4.2 14.3 + - + +
60B HIS* 3.4 34.3 + - + +
61B VAL* 1.3 79.7 - - - +
63B LEU* 1.3 65.2 + - - +
64B PRO* 3.8 1.9 - - - +
72B PRO* 3.2 7.8 - - - +
73B SER* 3.0 49.9 + - - +
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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