Contacts of the strand formed by residues 37 - 44 (chain B) in PDB entry 1CD9
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 SER 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B THR* 1.3 76.0 + - - +
38B PHE* 1.3 64.6 + - - +
39B ILE* 4.8 10.9 - - - +
86B GLN 3.4 1.7 - - - +
87B ALA* 3.4 2.8 - - - -
88B GLU* 2.7 63.3 + - - +
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Residues in contact with PHE 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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6B ALA 5.7 0.4 - - - -
8B PRO* 4.5 5.4 - - + -
26B TRP* 3.8 35.4 - + + -
28B PRO* 3.5 34.8 - - + -
36B THR* 4.3 29.8 - - + -
37B SER* 1.3 75.7 - - - +
39B ILE* 1.3 65.2 + - - +
60B VAL* 3.9 0.7 - - - +
61B ALA* 3.1 36.9 + - + +
62B LYS 6.2 0.2 - - - -
65B GLN 5.2 2.9 - - - -
66B ASN* 4.5 10.5 - - - -
85B VAL* 4.4 9.6 - - + -
86B GLN 3.2 4.7 - - - +
87B ALA* 3.8 27.4 - - + -
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Residues in contact with ILE 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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37B SER* 4.8 11.4 - - - +
38B PHE* 1.3 80.1 - - - +
40B LEU* 1.3 66.4 + - - +
41B LYS* 3.3 19.2 + - + +
58B ASP* 3.6 36.6 - - + +
59B CYS 3.5 7.4 - - - +
60B VAL* 3.7 19.5 - - + -
85B VAL* 4.5 2.9 - - - -
86B GLN* 3.0 48.7 + - + +
88B GLU* 5.6 7.2 - - + +
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Residues in contact with LEU 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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11B LEU* 4.3 4.3 - - + -
24B CYS* 3.7 33.7 - - + -
26B TRP* 4.1 19.2 - - + -
38B PHE 4.2 0.4 - - - -
39B ILE* 1.3 69.3 - - - +
41B LYS* 1.3 60.5 + - - +
42B SER* 5.4 0.7 + - - -
57B PRO 4.8 0.5 - - - +
58B ASP* 3.6 2.9 - - - -
59B CYS* 2.7 46.2 + - + +
68B CYS* 4.1 23.3 - - + +
70B ILE* 4.2 24.4 - - + +
83B ILE* 3.6 25.6 - - + -
84B TRP 3.7 12.3 - - - +
85B VAL* 4.2 7.1 - - + +
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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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39B ILE* 3.3 22.3 + - + +
40B LEU* 1.3 72.8 - - - +
42B SER* 1.3 63.7 + - - +
58B ASP* 3.4 35.9 + - - +
83B ILE* 3.6 2.0 - - - +
84B TRP* 2.8 69.1 + - + +
86B GLN* 3.8 28.7 - - - +
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Residues in contact with SER 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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40B LEU 5.4 0.7 + - - -
41B LYS* 1.3 77.3 - - - +
43B PHE* 1.3 64.4 + - - +
55B THR* 4.0 4.7 - - - +
56B ILE* 3.1 50.7 + - - +
57B PRO 5.2 1.4 + - - -
58B ASP* 5.0 0.6 + - - -
70B ILE* 4.0 8.5 - - - +
81B MET* 3.7 18.3 - - - +
82B ALA 2.9 20.9 - - - -
83B ILE* 4.0 7.6 - - - -
84B TRP* 4.0 5.8 - - - -
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Residues in contact with PHE 43 (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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42B SER* 1.3 76.6 - - - +
44B ARG* 1.3 81.9 + - - +
45B SER* 4.0 4.3 - - - -
49B CYS 4.8 6.3 - - - -
51B TYR 3.7 8.1 - - - -
52B GLN* 3.6 49.8 - - + -
53B GLY 3.9 13.5 - - - +
54B ASP 3.2 15.7 - - - +
55B THR* 4.1 7.2 - - - +
56B ILE* 4.0 6.7 - - - -
81B MET* 3.4 2.1 - - - +
82B ALA* 2.9 45.8 + - + -
84B TRP* 3.4 41.1 - + - -
98B LYS* 4.5 9.6 - - + -
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Residues in contact with ARG 44 (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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116A THR* 5.7 3.0 - - - +
120A GLN* 5.9 2.5 - - - +
43B PHE* 1.3 75.1 - - - +
45B SER* 1.3 61.1 + - - +
53B GLY* 2.9 28.9 + - - -
54B ASP* 2.7 34.7 + - - +
56B ILE* 3.9 17.2 - - + +
73B LYS 5.0 3.4 + - - -
74B ASN* 3.5 29.3 + - - +
75B LEU 4.6 3.6 + - - -
76B LEU* 3.8 46.4 - - + +
79B GLN* 5.8 0.9 - - + -
80B TYR 4.1 7.0 - - - +
81B MET* 4.2 4.7 - - + -
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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