Contacts of the strand formed by residues 38 - 44 (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 PHE 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D PRO* 4.7 5.2 - - + -
26D TRP* 3.7 36.3 - + + -
28D PRO* 3.5 36.6 - - + -
36D THR* 4.3 24.2 - - + -
37D SER* 1.3 77.5 - - - +
39D ILE* 1.3 64.6 + - - +
40D LEU 4.2 0.2 - - - -
60D VAL* 3.9 0.7 - - - +
61D ALA* 3.1 32.7 + - + +
63D LYS 6.2 0.4 - - - -
65D GLN 5.8 0.9 - - - -
66D ASN* 3.5 17.0 - - - -
85D VAL* 4.3 9.4 - - + -
86D GLN 3.4 3.1 - - - +
87D ALA* 4.2 24.0 - - + -
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Residues in contact with ILE 39 (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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37D SER* 4.9 11.0 - - - +
38D PHE* 1.3 79.9 - - - +
40D LEU* 1.3 62.8 + - - +
41D LYS* 3.2 20.0 + - + +
58D ASP* 3.4 43.3 - - + +
59D CYS 3.5 6.3 - - - +
60D VAL* 3.8 22.0 - - + -
85D VAL* 4.4 2.5 - - - -
86D GLN* 3.0 44.2 + - + +
88D GLU* 5.7 8.3 - - + +
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Residues in contact with LEU 40 (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* 4.6 4.3 - - + -
24D CYS* 3.6 34.8 - - + -
26D TRP* 4.6 11.3 - - + -
38D PHE 4.2 0.6 - - - -
39D ILE* 1.3 68.5 - - - +
41D LYS* 1.3 59.8 + - - +
42D SER* 4.7 1.2 + - - -
57D PRO 4.5 1.2 - - - +
58D ASP* 3.5 3.3 - - - -
59D CYS* 2.8 47.3 + - + +
68D CYS* 3.8 27.1 - - + +
70D ILE* 4.2 22.6 - - + +
83D ILE* 3.6 28.3 - - + -
84D TRP 3.6 14.4 - - - +
85D VAL* 4.4 10.9 - - + +
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Residues in contact with LYS 41 (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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39D ILE* 3.2 23.9 + - + +
40D LEU* 1.3 73.6 - - - +
42D SER* 1.3 66.0 + - - +
58D ASP* 3.3 35.1 + - - +
83D ILE* 3.7 2.4 - - - +
84D TRP* 2.8 69.8 + - + +
86D GLN* 4.1 29.5 + - + +
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Residues in contact with SER 42 (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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40D LEU 4.7 1.2 + - - -
41D LYS* 1.3 81.1 - - - +
43D PHE* 1.3 64.5 + - - +
55D THR* 3.8 4.7 - - - +
56D ILE* 2.8 58.9 + - - +
57D PRO 4.6 2.1 + - - -
58D ASP* 4.9 0.4 + - - -
70D ILE* 3.8 11.7 - - - +
81D MET* 4.0 9.6 - - - -
82D ALA 3.3 16.8 - - - -
83D ILE* 4.2 7.2 - - - -
84D TRP* 3.9 6.4 - - - -
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Residues in contact with PHE 43 (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* 1.3 76.7 - - - +
44D ARG* 1.3 76.8 + - - +
45D SER* 3.8 7.2 - - - -
49D CYS 4.7 9.6 - - - -
51D TYR 3.7 7.9 - - - -
52D GLN* 3.6 47.6 - - + -
53D GLY 3.6 13.7 - - - +
54D ASP 3.2 12.3 - - - +
55D THR* 3.9 9.4 - - - +
56D ILE* 3.9 6.5 - - - -
81D MET* 3.7 1.9 - - - +
82D ALA* 3.2 40.0 + - + +
84D TRP* 3.4 40.8 - + + -
98D LYS* 4.5 11.7 - - + -
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Residues in contact with ARG 44 (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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43D PHE* 1.3 75.1 - - - +
45D SER* 1.3 60.1 + - - +
51D TYR* 5.2 0.7 - - - -
53D GLY* 3.0 28.3 + - - -
54D ASP* 2.8 36.7 + - + +
56D ILE* 3.8 14.9 - - + +
73D LYS 4.5 4.9 + - - -
74D ASN* 3.4 32.6 + - - +
75D LEU 4.7 2.2 + - - -
76D LEU* 3.9 43.8 - - + +
79D GLN* 6.5 0.2 - - + -
80D TYR 5.0 1.3 - - - +
81D MET* 4.3 8.5 - - + -
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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