Contacts of the strand formed by residues 66 - 72 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208E SER* 3.4 34.8 - - - +
210E ILE* 4.0 16.8 - - + -
21F HIS* 4.0 26.2 - - + -
22F VAL 3.4 5.8 - - - +
23F MET* 4.0 15.3 - - + -
56F HIS* 5.1 0.9 - - - -
58F MET 5.1 0.9 - - - +
59F ILE* 5.5 1.6 - - - +
60F HIS 5.2 1.6 + - - -
63F GLU* 3.1 32.0 + - + +
64F PRO 3.2 2.5 - - - +
65F HIS* 1.3 102.0 - - + +
67F LEU* 1.3 66.0 + - - +
68F LEU* 3.5 16.6 + - + +
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Residues in contact with LEU 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F HIS* 3.2 6.1 - - - +
22F VAL* 2.8 38.2 + - + +
24F LEU* 3.9 32.1 - - + -
32F VAL* 4.3 26.7 - - + -
38F MET* 4.6 4.7 - - - -
43F TRP* 4.6 5.8 - - + -
46F LEU* 4.4 9.9 - - + -
48F VAL* 4.0 17.3 - - + -
56F HIS* 4.1 22.0 - - + +
64F PRO 4.4 7.4 - - - +
66F ILE* 1.3 76.3 - - - +
68F LEU* 1.3 60.4 + - - +
69F PHE* 3.5 27.1 - - + -
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Residues in contact with LEU 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E ILE* 3.9 19.3 - - + -
214E PHE* 3.8 31.6 - - + -
12F TYR* 4.2 2.0 - - - +
20F ARG 4.0 1.3 - - - -
21F HIS* 3.9 17.5 - - + -
56F HIS* 3.2 15.1 + - - -
57F TYR* 3.1 40.6 + - + +
58F MET* 3.8 31.0 - - + +
60F HIS* 4.1 18.6 - - + +
66F ILE* 3.5 24.5 - - + +
67F LEU* 1.3 74.5 - - - +
69F PHE* 1.3 62.7 + - - +
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Residues in contact with PHE 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F TYR* 3.2 4.7 - - - +
20F ARG 2.8 37.0 + - - +
22F VAL* 3.8 23.3 - - + -
43F TRP* 3.6 52.5 - + + -
48F VAL* 4.5 4.3 - - + -
50F GLN* 3.9 23.1 - - - +
54F TRP* 4.0 17.5 - - + -
55F VAL 3.4 5.2 - - - -
56F HIS* 3.7 25.4 - - + -
57F TYR* 3.3 7.2 - - - -
67F LEU* 3.5 40.6 - - + -
68F LEU* 1.3 74.3 - - - +
70F ARG* 1.3 62.2 + - - +
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Residues in contact with ARG 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E THR* 4.3 27.9 + - - +
17F PHE* 3.3 59.0 - - + -
18F GLU 3.2 6.7 - - - -
19F TYR* 3.7 9.8 + - + -
54F TRP* 3.7 3.3 - - - -
55F VAL* 2.9 42.3 + - - +
57F TYR* 3.2 45.3 - - + +
69F PHE* 1.3 78.5 - - - +
71F ARG* 1.3 63.7 + - - +
72F PRO* 5.8 0.2 - - - -
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Residues in contact with ARG 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F PHE* 3.6 4.5 - - - -
18F GLU* 2.7 75.1 + - + +
51F SER* 2.7 30.1 + - - -
52F GLN 3.1 22.0 + - - -
53F GLY* 3.5 18.4 - - - +
54F TRP* 3.0 40.6 - - + +
70F ARG* 1.3 77.0 - - - +
72F PRO* 1.4 82.9 - - + +
92G ASP 3.6 14.3 + - - -
93G SER* 3.7 19.9 + - - +
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Residues in contact with PRO 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F GLU 4.0 3.4 - - - +
17F PHE* 3.5 27.6 - - + -
18F GLU* 5.0 0.5 - - - +
53F GLY 4.7 4.3 - - - +
55F VAL* 5.2 6.3 - - + -
70F ARG 4.8 0.7 - - - +
71F ARG* 1.4 107.6 - - + +
73F LEU* 1.3 68.5 + - - +
74F PRO* 4.9 0.2 - - - +
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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