Contacts of the strand formed by residues 59 - 64 (chain B) in PDB entry 4CY1
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 TRP 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PHE* 3.4 9.4 - - - -
54B SER* 2.8 37.6 + - - +
56B ASN* 4.2 9.0 - - - +
57B GLY 3.5 0.7 - - - -
58B GLU* 1.3 106.6 - - + +
60B LEU* 1.3 60.3 + - - +
71B ILE* 4.0 17.3 - - + -
72B TRP 3.4 21.1 - - - +
73B GLY* 4.3 10.1 - - - -
74B ALA* 3.8 4.9 - - - -
78B LYS 5.4 0.2 - - - -
80B GLU* 3.7 40.2 - - + -
95B TRP* 3.8 27.1 - + + -
99B SER 5.3 3.1 - - - -
116B VAL* 5.8 3.7 - - + +
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Residues in contact with LEU 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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41B LEU* 4.2 14.4 - - + -
51B VAL* 4.1 6.5 - - + -
52B LYS 3.5 29.6 - - - +
53B PHE* 3.7 20.4 - - + +
59B TRP* 1.3 75.1 - - - +
61B ALA* 1.3 64.5 + - - +
71B ILE* 3.4 3.8 - - - +
72B TRP* 2.8 53.6 + - + +
73B GLY 5.0 0.7 - - - +
74B ALA* 4.2 4.5 - - - +
95B TRP* 4.3 2.5 - - - -
308B ALA* 4.9 0.2 - - + -
317B ALA* 3.6 28.3 - - + -
327B ILE* 3.7 29.8 - - + -
329B LEU* 4.4 5.8 - - + -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B SER 3.9 0.2 - - - +
51B VAL* 3.2 5.9 - - - +
52B LYS* 2.8 32.7 + - + +
60B LEU* 1.3 75.3 - - - +
62B SER* 1.3 60.0 + - - +
69B ILE* 4.7 1.1 - - + -
70B LYS 3.4 4.7 - - - -
71B ILE* 3.9 12.3 - - + -
93B VAL* 4.4 13.1 - - + +
95B TRP* 3.6 30.8 - - + +
102B LEU* 4.0 13.5 - - + -
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Residues in contact with SER 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B HIS* 2.8 26.9 + - - -
48B VAL* 4.5 2.0 - - - -
50B SER 3.3 4.9 - - - -
51B VAL* 3.8 9.0 - - - -
60B LEU* 5.6 0.2 - - - -
61B ALA* 1.3 75.1 - - - +
63B SER* 1.3 60.3 + - - +
69B ILE* 3.2 7.6 - - - +
70B LYS* 2.8 32.8 + - - +
72B TRP* 2.9 20.6 + - - -
93B VAL* 4.4 3.1 - - - -
327B ILE* 3.5 25.1 - - - -
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Residues in contact with SER 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B HIS* 4.4 0.7 - - - -
48B VAL* 3.3 10.6 - - - +
49B SER* 2.8 38.5 + - - -
50B SER* 2.9 24.2 + - - -
62B SER* 1.3 73.1 - - - +
64B SER* 1.3 61.6 + - - +
68B LEU 3.6 6.7 - - - -
69B ILE* 4.7 2.0 - - - -
90B ILE* 3.5 27.4 - - - -
92B ASP 3.8 4.5 - - - -
93B VAL* 3.8 15.0 - - - +
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Residues in contact with SER 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B HIS* 3.2 21.1 - - - -
46B LYS 3.2 9.5 + - - -
47B ALA 2.8 21.3 + - - -
48B VAL* 4.1 1.1 - - - -
49B SER* 3.6 4.6 + - - -
63B SER* 1.3 78.2 - - - +
65B ALA* 1.3 61.6 + - - +
66B ASP* 3.0 32.5 + - - -
67B LYS* 3.1 9.5 + - - -
68B LEU 3.3 5.5 + - - -
90B ILE* 3.1 26.6 + - - +
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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