Contacts of the strand formed by residues 61 - 66 (chain F) in PDB entry 4YHP
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 61 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36F GLN* 4.1 13.9 - - - -
46F VAL* 3.9 24.0 - - + -
47F VAL* 4.3 11.7 - - + -
53F ARG* 3.1 30.1 + - - +
57F ILE* 4.0 19.7 - - + -
58F PRO* 3.7 26.9 - - + +
59F GLU 3.0 1.5 - - - +
60F ARG* 1.3 101.9 - - + +
62F SER* 1.3 59.5 + - - +
72F LEU* 4.4 4.5 - - + -
73F THR 3.5 2.0 - - - -
74F ILE* 3.7 35.9 - - + -
81F ASP* 3.9 15.5 - - - -
85F TYR* 3.9 15.7 - + - -
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Residues in contact with SER 62 (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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47F VAL* 4.2 8.6 - - - +
51F SER 5.5 2.0 - - - -
53F ARG* 4.7 8.7 - - - +
59F GLU 4.8 3.8 - - - -
60F ARG 4.5 2.6 + - - -
61F PHE* 1.3 74.4 - - - +
63F GLY* 1.3 58.5 + - - +
72F LEU* 3.5 4.5 - - - +
73F THR* 2.7 54.0 + - - +
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Residues in contact with GLY 63 (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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34F TRP* 5.1 1.8 - - - -
47F VAL* 4.2 11.0 - - - +
50F ASP 3.1 19.9 + - - -
51F SER* 3.2 21.7 + - - +
62F SER* 1.3 77.9 - - - +
64F SER* 1.3 63.6 + - - -
71F THR 3.3 9.2 - - - -
72F LEU* 4.6 2.0 - - - -
73F THR* 5.7 0.2 - - - -
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Residues in contact with SER 64 (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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34F TRP* 5.4 0.9 + - - +
50F ASP* 3.4 6.9 + - - +
51F SER* 5.2 0.9 - - - -
63F GLY* 1.3 75.2 - - - -
65F ASN* 1.3 60.5 + - - +
69F THR 4.9 0.7 - - - -
70F ALA* 3.3 2.8 - - - +
71F THR* 2.6 56.0 + - - +
73F THR* 5.4 1.2 + - - -
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Residues in contact with ASN 65 (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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27F ILE 3.0 11.7 + - - +
28F GLY* 3.2 21.2 + - - +
30F ILE 2.7 30.5 + - - -
32F VAL* 3.4 8.2 - - + +
50F ASP* 3.2 34.8 + - + +
64F SER* 1.3 78.5 - - - +
66F SER* 1.3 72.8 + - - +
69F THR 3.7 4.2 - - - +
70F ALA* 3.6 22.8 + - + +
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Residues in contact with SER 66 (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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28F GLY* 4.0 7.4 - - - -
65F ASN* 1.3 80.7 + - - +
67F GLY* 1.3 61.6 + - - +
68F ASN 3.0 0.7 + - - -
69F THR* 2.9 31.4 + - - +
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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