Contacts of the strand formed by residues 17 - 23 (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 PHE 17 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13F ASP* 3.3 5.4 - - - +
14F ASP* 3.2 31.6 + - - +
16F GLU* 1.3 88.2 - - + +
18F GLU* 1.3 67.0 - - - +
19F TYR* 3.5 28.7 - - + -
70F ARG* 3.3 55.6 - - + -
71F ARG 3.5 3.8 - - - +
72F PRO* 3.5 36.1 - - + -
73F LEU* 3.8 6.7 - - - +
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Residues in contact with GLU 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F LYS* 3.7 23.7 + - + +
12F TYR 3.5 8.5 - - - +
13F ASP* 3.9 6.3 - - + +
17F PHE* 1.3 76.2 - - - +
19F TYR* 1.3 63.1 + - - +
54F TRP* 3.6 17.9 - - + -
70F ARG* 3.2 3.6 - - - -
71F ARG* 2.7 77.3 + - + +
72F PRO 5.0 0.3 - - - +
73F LEU* 3.7 15.3 - - + +
94G ILE 4.7 2.5 - - - +
95G PRO* 4.5 8.9 - - - +
96G PRO* 3.8 24.7 - - + +
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Residues in contact with TYR 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E THR 4.3 4.7 + - - -
241E PHE 4.3 0.9 + - - -
242E PRO* 3.5 32.5 - - + +
243E LYS* 5.5 0.7 - - - +
11F LYS* 3.3 6.8 - - - +
12F TYR* 2.7 63.6 + + + +
13F ASP* 4.1 3.8 - - - -
14F ASP* 2.6 34.6 + - - -
17F PHE* 3.5 26.8 - - + -
18F GLU* 1.3 77.8 - - - +
20F ARG* 1.3 63.2 + - - +
54F TRP* 3.8 6.3 - - - -
57F TYR* 3.4 40.4 - + - -
69F PHE 3.2 6.7 - - - +
70F ARG* 3.7 23.0 + - + -
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Residues in contact with ARG 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F TYR* 4.7 14.4 - - - +
9F SER* 3.5 32.2 + - - +
10F ASP 3.8 6.5 - - - +
11F LYS* 3.6 27.1 - - + +
12F TYR* 3.7 12.0 + - - -
19F TYR* 1.3 77.1 - - - +
21F HIS* 1.3 70.6 + - - +
22F VAL* 4.1 11.2 - - + +
49F GLN 5.4 0.9 + - - -
50F GLN* 3.1 38.9 - - - +
54F TRP* 3.8 7.1 - - + +
68F LEU* 4.0 0.2 - - - -
69F PHE* 2.8 33.8 + - + +
92G ASP* 2.7 40.2 + - - -
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Residues in contact with HIS 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E ASP* 3.5 29.7 + - - -
208E SER* 4.7 2.9 - - - -
210E ILE* 5.1 2.4 - - + +
211E ASP* 3.2 30.9 + - + +
214E PHE* 4.9 1.7 - + - -
7F TYR* 5.0 1.2 - + - -
9F SER* 2.8 59.5 + - - -
12F TYR* 2.8 30.3 + + - +
20F ARG* 1.3 75.3 - - - +
22F VAL* 1.3 66.7 + - - +
23F MET* 4.4 8.9 + - + -
66F ILE* 4.0 17.9 - - + -
67F LEU 3.2 12.3 - - - +
68F LEU* 3.9 16.7 - - + +
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Residues in contact with VAL 22 (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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6F ILE* 3.2 33.7 - - + -
7F TYR 3.3 6.1 - - - +
8F TYR* 3.4 28.9 - - + -
20F ARG* 4.1 9.2 - - - -
21F HIS* 1.3 79.3 - - - +
23F MET* 1.3 63.8 + - - +
24F LEU* 3.7 8.6 + - + -
48F VAL* 4.5 8.3 - - + -
50F GLN* 4.9 1.3 - - - +
65F HIS 3.6 1.4 - - - +
66F ILE* 3.4 1.9 - - - -
67F LEU* 2.8 39.3 + - + +
69F PHE* 3.8 28.3 - - + -
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Residues in contact with MET 23 (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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207E ASP* 3.2 40.8 - - + +
208E SER* 5.4 0.4 - - - -
5F GLN 4.7 0.5 - - - +
6F ILE* 3.6 5.0 - - - +
7F TYR* 2.8 67.9 + - + +
21F HIS* 4.6 3.8 - - + -
22F VAL* 1.3 73.9 - - - +
24F LEU* 1.3 63.9 + - - +
25F PRO* 4.3 0.2 - - - +
65F HIS* 3.8 15.3 - - + +
66F ILE* 4.0 29.4 - - + -
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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