Contacts of the strand formed by residues 67 - 72 (chain D) in PDB entry 4CDC
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 GLY 67 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62D ILE* 3.2 11.1 - - - +
63D ILE* 2.7 34.8 + - - +
66D GLN* 1.3 82.1 - - - +
68D PHE* 1.3 56.5 + - - -
78D PHE* 5.2 1.6 - - - -
79D ALA 3.3 15.3 - - - -
80D PHE* 4.0 2.0 - - - -
81D PHE* 3.3 18.8 - - - -
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Residues in contact with PHE 68 (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* 3.5 38.6 - - + -
15D TRP* 4.8 6.7 - + - -
17D PHE* 3.7 22.9 - + - -
44D LEU* 6.2 0.2 - - + -
60D PHE* 5.6 0.7 - - + -
61D THR 3.3 12.8 - - - +
63D ILE* 3.6 8.9 - - - +
67D GLY* 1.3 74.4 - - - +
69D GLU* 1.3 61.7 + - - +
70D ILE* 3.6 33.9 - - + -
77D TRP* 4.7 3.8 - - + -
78D PHE* 3.2 22.3 - - - -
79D ALA* 3.2 24.1 + - + -
81D PHE* 4.0 13.0 - + - -
97D THR* 3.6 30.7 - - + -
113D PHE* 4.4 7.0 - + - -
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Residues in contact with GLU 69 (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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60D PHE* 3.2 3.8 - - - +
61D THR* 3.0 34.9 + - + +
63D ILE* 3.7 13.2 - - + +
68D PHE* 1.3 74.1 - - - +
70D ILE* 1.3 67.5 + - - +
71D VAL* 4.4 9.6 - - + +
76D LYS* 4.1 9.3 + - - +
77D TRP 3.2 17.0 - - - +
78D PHE* 4.5 4.3 - - + -
280E TYR* 2.6 34.8 + - - +
285E LYS* 2.9 26.0 + - - +
321E TYR* 2.6 31.4 + - - -
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Residues in contact with ILE 70 (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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17D PHE* 3.7 26.5 - - + -
42D VAL* 4.4 4.0 - - + -
44D LEU* 4.0 20.9 - - + -
50D ALA* 3.9 18.6 - - + -
59D HIS 3.5 9.4 - - - +
60D PHE* 3.9 12.6 - - + -
68D PHE* 3.6 28.5 - - + -
69D GLU* 1.3 78.8 - - - +
71D VAL* 1.3 66.0 + - - +
72D LEU* 3.9 19.5 - - + -
75D TYR 3.7 0.7 - - - +
76D LYS* 3.2 5.4 - - - +
77D TRP* 2.8 44.6 + - + +
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Residues in contact with VAL 71 (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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58D GLY* 3.3 3.5 - - - -
59D HIS* 2.8 40.7 + - + +
69D GLU* 4.4 13.7 - - + +
70D ILE* 1.3 77.7 - - - +
72D LEU* 1.3 63.5 + - - +
74D ASP* 5.6 1.6 - - - -
75D TYR 3.4 7.9 - - - +
76D LYS* 4.0 25.8 - - + +
105D VAL* 4.4 20.0 - - + -
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Residues in contact with LEU 72 (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 VAL* 6.2 0.4 - - + -
42D VAL* 3.9 39.0 - - + -
50D ALA* 3.9 4.7 - - + +
51D TYR* 4.2 11.0 - - - -
52D ASP* 4.2 9.0 - - + +
56D ASN* 3.6 32.8 - - + +
57D SER 3.7 4.3 - - - +
58D GLY* 3.7 20.4 - - - +
70D ILE* 3.9 13.2 - - + -
71D VAL* 1.3 77.7 - - - +
73D ASN* 1.3 80.1 + - + +
74D ASP 3.3 1.3 - - - -
75D TYR* 2.9 25.9 + - - +
77D TRP* 4.5 8.7 + - - +
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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