Contacts of the strand formed by residues 66 - 72 (chain D) in PDB entry 4YC6
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 ILE 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208C SER* 3.4 34.8 - - - +
210C ILE* 4.0 17.3 - - + -
21D HIS* 4.0 26.5 - - + -
22D VAL 3.4 5.8 - - - +
23D MET* 4.0 15.5 - - + -
56D HIS* 5.1 0.9 - - - -
58D MET 5.1 0.9 - - - +
59D ILE* 5.5 1.2 - - - +
60D HIS* 5.2 2.0 + - + -
63D GLU* 3.2 32.6 + - + +
64D PRO 3.2 2.2 - - - +
65D HIS* 1.3 101.9 - - + +
67D LEU* 1.3 64.7 + - - +
68D LEU* 3.5 15.7 - - + +
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Residues in contact with LEU 67 (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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21D HIS* 3.2 6.2 - - - +
22D VAL* 2.8 36.0 + - + +
24D LEU* 3.9 34.8 - - + -
32D VAL* 4.3 27.8 - - + -
38D MET* 4.6 4.7 - - - -
43D TRP* 4.6 5.8 - - + -
46D LEU* 4.4 9.2 - - + -
48D VAL* 4.0 18.2 - - + -
56D HIS* 4.2 22.0 - - + +
64D PRO 4.4 5.2 - - - +
66D ILE* 1.3 76.8 - - - +
68D LEU* 1.3 59.3 + - - +
69D PHE* 3.5 26.2 - - + -
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Residues in contact with LEU 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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210C ILE* 3.9 20.2 - - + -
214C PHE* 3.7 32.1 - - + -
12D TYR* 4.3 1.6 - - - +
20D ARG 4.0 1.3 - - - -
21D HIS* 4.0 16.8 - - + -
56D HIS* 3.2 14.8 + - - -
57D TYR* 3.1 40.5 + - + +
58D MET* 3.8 30.7 - - + +
60D HIS* 4.1 18.8 - - + +
66D ILE* 3.5 24.7 - - + +
67D LEU* 1.3 75.0 - - - +
69D PHE* 1.3 61.0 + - - +
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Residues in contact with PHE 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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19D TYR* 3.2 4.5 - - - +
20D ARG 2.8 36.6 + - - +
22D VAL* 3.9 24.9 - - + -
43D TRP* 3.6 52.0 - + + -
48D VAL* 4.5 3.8 - - + -
50D GLN* 3.9 16.6 - - - +
54D TRP* 3.9 25.1 - - + -
55D VAL 3.4 5.4 - - - -
56D HIS* 3.7 25.6 - + + -
57D TYR* 3.3 7.1 - - - -
67D LEU* 3.5 40.6 - - + -
68D LEU* 1.3 74.7 - - - +
70D ARG* 1.3 62.9 + - - +
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Residues in contact with ARG 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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240C THR* 4.2 31.3 + - - +
17D PHE* 3.3 59.8 - - + -
18D GLU 3.1 7.2 - - - -
19D TYR* 3.7 9.4 + - + -
54D TRP* 3.6 3.3 - - - -
55D VAL* 2.8 42.1 + - - +
57D TYR* 3.2 44.0 - - + +
69D PHE* 1.3 79.0 - - - +
71D ARG* 1.3 60.3 + - - +
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Residues in contact with ARG 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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92A ASP 3.6 12.7 + - - -
93A SER* 3.7 18.6 + - - +
94A ILE 4.7 1.2 + - - -
95A PRO* 5.2 1.0 - - - +
17D PHE* 3.7 4.0 - - - -
18D GLU* 2.7 77.0 + - + +
51D SER* 2.7 30.9 + - - -
52D GLN 3.1 21.6 + - - -
53D GLY* 3.5 18.3 - - - +
54D TRP* 3.0 39.8 - - + +
70D ARG* 1.3 77.5 - - - +
72D PRO* 1.4 81.9 - - + +
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Residues in contact with PRO 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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95A PRO* 6.1 0.2 - - - +
16D GLU 4.0 2.9 - - - +
17D PHE* 3.6 27.6 - - + -
18D GLU* 5.0 0.2 - - - +
53D GLY 4.7 4.3 - - - +
55D VAL* 5.3 6.1 - - + -
70D ARG 4.8 0.7 - - - +
71D ARG* 1.4 108.2 - - + +
73D LEU* 1.3 69.0 + - - +
74D PRO* 4.8 0.3 - - - +
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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