Contacts of the strand formed by residues 81 - 89 (chain D) 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 MET 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D LEU* 4.2 4.5 - - + -
42D SER* 4.0 8.3 - - - -
43D PHE 3.7 12.3 - - - +
44D ARG* 4.3 7.2 - - + -
45D SER 4.1 2.2 - - - +
49D CYS* 3.5 8.0 - - - -
56D ILE* 3.4 26.0 - - + -
70D ILE* 4.2 7.6 - - + -
75D LEU* 3.8 21.3 - - + -
76D LEU 5.7 2.9 - - - +
79D GLN 4.8 1.1 - - - +
80D TYR* 1.3 76.6 - - - +
82D ALA* 1.3 58.9 + - - +
83D ILE* 3.8 24.3 + - + +
99D LEU 3.5 3.3 - - - +
101D LEU* 2.8 43.7 + - + +
103D PRO* 3.7 28.5 - - + -
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Residues in contact with ALA 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D SER* 3.3 8.0 - - - -
43D PHE* 3.2 64.7 + - + +
45D SER* 4.4 0.6 - - - -
49D CYS* 3.6 17.1 - - + +
81D MET* 1.3 73.5 - - - +
83D ILE* 1.3 59.9 + - - +
84D TRP* 3.9 5.9 - - + -
98D LYS* 4.6 10.1 - - + -
99D LEU 3.3 7.6 - - - +
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Residues in contact with ILE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 3.9 4.8 - - + +
13D CYS* 4.0 14.1 - - - -
22D LEU* 3.9 17.9 - - + -
24D CYS* 4.6 1.1 - - - -
40D LEU* 3.6 29.4 - - + -
41D LYS 3.7 7.4 - - - +
42D SER* 4.4 4.3 - - - -
70D ILE* 5.1 2.0 - - + -
81D MET* 3.8 19.3 - - + +
82D ALA* 1.3 80.7 - - - +
84D TRP* 1.3 68.6 + - - +
98D LYS* 3.6 0.3 - - - -
99D LEU* 2.8 40.9 + - + +
101D LEU* 3.6 44.0 - - + -
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Residues in contact with TRP 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.2 4.3 - - - -
40D LEU* 3.6 6.2 - - - +
41D LYS* 2.8 67.7 + - + +
42D SER* 3.9 12.1 - - - -
43D PHE* 3.4 42.4 - + - -
52D GLN* 5.9 1.6 - - - -
82D ALA 3.9 10.1 - - - -
83D ILE* 1.3 84.9 - - - +
85D VAL* 1.3 74.5 + - - +
86D GLN* 4.5 3.6 - - - +
95D GLU* 4.3 29.5 + - + +
96D SER* 3.5 24.5 - - - +
98D LYS* 3.7 33.0 - - + -
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D PRO* 4.3 12.1 - - + +
11D LEU* 4.3 9.6 - - + -
26D TRP* 4.0 51.6 - - + -
38D PHE* 4.3 19.7 - - + -
39D ILE 3.6 11.2 - - - +
40D LEU* 4.4 6.3 - - + +
84D TRP* 1.3 77.5 - - - +
86D GLN* 1.3 63.4 + - - +
87D ALA 4.3 0.4 + - - -
95D GLU* 3.4 3.1 - - - -
96D SER* 2.9 46.2 + - - +
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Residues in contact with GLN 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D PRO* 5.8 0.2 - - - -
37D SER 3.5 1.7 - - - +
38D PHE* 3.4 4.4 - - - -
39D ILE* 3.0 47.2 + - + +
41D LYS* 4.1 30.5 + - + +
84D TRP* 4.7 7.8 - - + +
85D VAL* 1.3 77.0 - - - +
87D ALA* 1.3 66.8 + - - +
88D GLU* 3.9 17.2 + - - +
93D SER* 5.1 10.2 + - - -
94D SER 3.4 11.9 - - - +
95D GLU* 3.7 25.8 + - + +
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Residues in contact with ALA 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PRO* 3.9 14.7 - - + +
6D ALA 5.0 0.4 - - - +
8D PRO* 4.6 7.6 - - + +
36D THR* 4.7 4.0 - - - +
37D SER 3.5 5.2 - - - +
38D PHE* 4.2 22.9 - - + -
85D VAL 4.3 0.4 + - - -
86D GLN* 1.3 74.1 - - - +
88D GLU* 1.3 59.9 + - - +
89D ASN 4.0 0.2 - - - -
92D GLY 3.9 1.0 - - - +
93D SER* 3.1 9.7 - - - -
94D SER* 2.9 46.6 + - - +
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Residues in contact with GLU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D PRO 4.3 1.6 - - - +
36D THR* 3.3 3.4 + - - -
37D SER* 3.0 48.0 + - - +
39D ILE* 5.7 7.5 - - + +
86D GLN* 3.9 16.3 + - - +
87D ALA* 1.3 70.5 - - - +
89D ASN* 1.3 66.5 + - - +
92D GLY 4.1 2.5 - - - -
93D SER* 4.3 12.1 - - - +
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Residues in contact with ASN 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D TYR 2.9 28.1 + - - -
5D PRO* 3.5 25.3 - - + +
32D THR* 3.7 17.7 + - - +
34D LEU* 3.7 21.9 - - - +
35D PRO 3.6 7.8 - - - +
36D THR* 3.6 23.7 - - - +
87D ALA 4.0 0.4 + - - -
88D GLU* 1.3 79.3 - - - +
90D MET* 1.3 65.1 + - - +
91D LEU 2.9 11.6 + - - +
92D GLY 3.0 16.4 + - - +
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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