Contacts of the strand formed by residues 33 - 38 (chain B) in PDB entry 1CD0
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 VAL 33 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B LEU* 6.1 0.7 - - + -
23B CYS* 5.2 2.7 - - - -
28B ILE* 3.8 29.2 - - + +
31B ASN 3.9 7.6 - - - +
32B TYR* 1.3 75.5 - - - +
34B GLN* 1.3 73.9 + - - +
35B TRP* 4.0 10.1 - - - +
48B ILE* 4.5 2.6 - - - +
49B TYR* 4.0 1.0 - - - -
50B GLU 3.7 0.9 + - - -
51B ASP* 2.9 43.0 + - - +
66B ILE* 4.0 9.4 - - + -
71B ALA* 3.6 22.2 - - + -
88B CYS* 4.4 10.3 - - + -
89B GLN 3.2 8.7 - - - +
90B SER* 4.2 8.1 - - - +
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Residues in contact with GLN 34 (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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96A VAL* 4.1 9.9 - - + -
32B TYR* 3.4 12.8 + - - +
33B VAL* 1.3 79.0 - - - +
35B TRP* 1.3 66.2 + - - +
36B TYR* 3.5 29.6 - - + +
48B ILE 3.3 6.3 - - - +
49B TYR* 3.8 18.3 - - + +
50B GLU* 2.8 26.9 + - - +
87B TYR 3.8 0.6 - - - +
88B CYS* 3.1 7.1 - - - +
89B GLN* 2.7 59.4 + - - +
91B TYR* 3.2 31.6 + - - -
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Residues in contact with TRP 35 (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 GLN* 4.0 8.5 - - - -
21B ILE* 3.3 35.9 - - + -
22B SER 4.2 0.2 - - - -
23B CYS* 3.7 24.5 - - + -
33B VAL* 4.0 13.2 - - + +
34B GLN* 1.3 77.6 - - - +
36B TYR* 1.3 64.9 + - - +
47B VAL* 3.0 41.3 + - + -
48B ILE* 2.8 37.4 + - + +
51B ASP 4.9 4.8 + - - -
64B GLY* 5.0 0.4 - - - -
65B SER 5.4 0.2 + - - -
71B ALA* 3.5 26.9 - - + +
72B SER 3.9 10.3 + - - -
73B LEU* 3.5 40.2 - - + -
86B TYR* 4.6 5.8 - - + -
87B TYR 3.5 4.7 - - - -
88B CYS* 3.9 20.9 - - + -
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Residues in contact with TYR 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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36A TYR* 5.2 4.3 + - - -
89A GLN* 5.4 0.3 - - - -
96A VAL* 3.6 17.1 - - + +
98A PHE* 3.4 36.1 - + - -
34B GLN* 3.5 22.2 - - + +
35B TRP* 1.3 78.8 - - - +
37B GLN* 1.3 60.6 + - - +
44B PRO* 4.2 14.1 - - + -
45B ILE 3.4 2.0 - - - +
46B THR* 3.4 26.7 - - + -
47B VAL* 4.7 0.7 - - - -
85B ASP 3.5 1.0 - - - +
86B TYR* 3.2 11.8 - - - +
87B TYR* 2.8 51.0 + - + +
89B GLN* 2.8 42.6 + - + -
91B TYR* 5.3 0.3 + - - -
98B PHE* 3.9 21.8 - + - -
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Residues in contact with GLN 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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35B TRP 4.3 0.2 + - - -
36B TYR* 1.3 73.4 - - - +
38B GLN* 1.3 61.7 + - - +
39B ARG* 3.4 36.9 + - - +
43B ALA 4.4 0.2 - - - +
44B PRO* 3.3 1.0 - - - +
45B ILE* 2.6 60.2 + - - +
47B VAL* 3.7 20.5 - - + +
62B PHE* 4.0 16.8 - - - -
82B ASP* 4.2 8.1 + - - +
84B ALA* 3.9 9.6 - - + -
85B ASP 3.7 3.4 - - - -
86B TYR* 2.9 36.8 + - + +
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Residues in contact with GLN 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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38A GLN* 2.8 44.9 + - - -
87A TYR* 3.2 10.9 + - - -
37B GLN* 1.3 76.2 - - - +
39B ARG* 1.3 65.9 + - - +
40B PRO* 3.6 9.1 - - + +
41B GLY 5.6 1.2 - - - +
42B SER 3.1 27.9 + - - +
43B ALA 4.7 0.9 - - - -
44B PRO* 3.7 26.3 - - + +
84B ALA* 3.9 3.8 - - - -
85B ASP* 2.9 44.7 + - + +
87B TYR* 3.6 18.6 + - + -
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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