Contacts of the strand formed by residues 44 - 50 (chain L) in PDB entry 2CHS
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 GLN 44 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5J GLY* 3.6 17.6 - - - -
44J GLN* 4.7 7.1 - - - +
46J LEU* 5.2 4.5 - - - +
92J MET* 3.7 26.6 - - + +
94J THR* 2.7 35.5 + - - +
44K GLN* 4.8 5.0 - - - +
42L VAL* 3.4 13.6 - - - +
43L VAL* 1.3 84.1 - - + +
45L MET* 1.3 62.7 + - - +
46L LEU* 4.6 10.4 - - + +
71L VAL* 4.6 0.7 - - - -
72L PRO* 3.2 20.9 - - + +
94L THR* 3.0 39.8 + - - +
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Residues in contact with MET 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J MET* 4.1 2.4 - - - +
28L LEU* 4.2 24.2 - - + -
44L GLN* 1.3 75.0 - - - +
46L LEU* 1.3 71.4 + - - +
47L LEU* 4.2 10.3 - - + -
62L VAL* 4.2 15.0 - - + -
68L TRP* 3.7 34.8 - - + -
71L VAL* 4.2 6.3 - - + -
72L PRO 2.9 4.9 + - - +
73L VAL* 3.2 47.5 - - + -
74L THR 3.3 4.7 + - - -
91L VAL* 4.0 18.8 - - + -
92L MET 3.5 7.2 - - - +
93L MET* 4.2 13.0 - - + +
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Residues in contact with LEU 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J LEU* 4.1 18.6 - - + -
76J MET* 5.2 0.2 - - + -
92J MET* 4.8 7.0 - - + -
44K GLN* 5.3 4.0 - - - +
46K LEU* 3.9 38.1 - - + -
44L GLN* 4.6 13.9 - - + +
45L MET* 1.3 79.8 - - - +
47L LEU* 1.3 62.8 + - - +
74L THR* 3.4 25.6 - - + -
76L MET* 3.9 26.9 - - + -
91L VAL* 3.4 4.0 - - - +
92L MET* 2.9 47.7 + - + +
94L THR* 6.0 1.1 - - - +
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Residues in contact with LEU 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L THR* 4.1 25.4 - - + -
27L LEU* 6.2 0.4 - - + -
28L LEU* 5.3 2.5 - - + -
45L MET* 4.2 20.9 - - - -
46L LEU* 1.3 77.8 - - - +
48L SER* 1.3 61.0 + - - +
58L PRO* 4.3 12.3 - - + +
59L ALA* 3.7 33.4 - - + +
62L VAL* 4.8 2.5 - - + -
73L VAL* 4.5 10.8 - - + -
74L THR 3.0 6.6 + - - +
75L CYS* 3.1 16.3 - - - +
76L MET* 2.9 24.9 + - - +
89L ILE* 4.3 5.8 - - + -
90L ARG 3.4 7.4 - - - +
91L VAL* 4.1 21.3 - - + -
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Residues in contact with SER 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J MET* 5.6 0.2 - - - -
74K THR* 4.8 1.9 + - - -
75K CYS 4.6 2.2 + - - -
46L LEU 4.4 0.2 + - - -
47L LEU* 1.3 76.3 - - - +
49L ALA* 1.3 62.1 + - - +
58L PRO* 5.2 1.7 - - - +
76L MET* 3.2 34.7 - - - +
78L GLU* 4.0 18.0 + - - +
88L CYS 4.6 0.2 - - - -
89L ILE* 3.3 7.4 - - - +
90L ARG* 2.8 56.3 + - - +
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Residues in contact with ALA 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J MET* 3.7 35.4 - - + +
48L SER* 1.3 75.8 - - - +
50L THR* 1.3 68.5 + - - +
53L LEU* 4.1 16.2 - - + -
58L PRO* 4.4 10.1 - - + -
76L MET 3.2 5.9 + - - +
77L GLN* 3.7 8.3 - - - +
78L GLU* 3.0 22.1 + - - -
88L CYS 3.5 5.6 - - - -
89L ILE* 4.8 1.3 - - + -
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Residues in contact with THR 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J MET* 5.1 0.9 - - - +
57K PHE* 6.2 0.9 - - + -
49L ALA* 1.3 77.5 - - - +
51L PRO* 1.3 68.8 - - + +
52L ASP* 2.9 33.0 + - - -
53L LEU* 3.2 18.7 + - - +
78L GLU* 4.1 22.4 - - + -
79L MET 4.9 2.7 - - - +
80L ASP* 6.2 0.2 - - - -
85L LEU 3.6 21.3 - - - +
86L LYS* 5.0 2.0 - - + +
87L LYS* 3.1 3.2 + - - -
88L CYS* 3.1 30.0 + - + +
90L ARG* 4.1 6.7 - - - +
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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