Contacts of the strand formed by residues 59 - 64 (chain C) in PDB entry 4Y1L
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 GLU 59 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ARG* 3.7 20.4 - - - -
44C ILE 3.7 3.4 - - - -
45C HIS* 3.7 22.8 + - + +
58C LEU* 1.3 72.9 - - - +
60C LEU* 1.3 62.8 + - - +
61C VAL* 4.0 19.8 - - + +
76C SER 3.3 5.0 - - - +
77C ILE* 3.4 3.5 - - - +
78C ASN* 2.7 65.5 + - + +
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ARG* 3.5 1.2 - - - -
44C ILE* 2.9 57.1 + - + +
46C THR* 3.5 32.3 - - + -
58C LEU* 4.2 19.5 - - + -
59C GLU* 1.3 77.6 - - - +
61C VAL* 1.3 62.1 + - - +
62C PHE* 3.7 22.0 + - + -
75C ILE* 4.6 3.4 - - + -
76C SER 3.4 3.6 - - - +
77C ILE* 4.1 16.4 - - + -
94C LEU* 3.6 31.0 - - + -
111C VAL* 5.4 6.1 - - + -
114C ILE* 5.0 7.4 - - + -
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Residues in contact with VAL 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.7 23.6 - - + -
41C VAL* 3.9 11.0 - - + -
42C PHE 3.4 13.5 - - - +
43C ARG* 4.4 7.9 - - + +
59C GLU* 4.0 25.8 - - + +
60C LEU* 1.3 73.0 - - - +
62C PHE* 1.3 59.8 + - - +
63C HIS 3.9 0.2 + - - -
74C GLY 3.3 10.7 - - - +
75C ILE* 3.4 2.1 - - - -
76C SER* 3.1 37.5 + - - +
78C ASN* 5.3 3.1 - - - +
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Residues in contact with PHE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C THR 4.0 0.3 - - - +
41C VAL* 3.4 5.3 - - - +
42C PHE* 2.9 73.8 + + + +
44C ILE* 4.2 6.5 - - + -
60C LEU* 3.9 31.6 - - + -
61C VAL* 1.3 73.4 - - - +
63C HIS* 1.3 60.0 + - - +
64C LEU* 4.1 4.5 - - + -
73C PRO* 4.5 12.1 - - + -
74C GLY 3.2 5.4 - - - -
75C ILE* 3.6 40.4 - - + -
94C LEU* 5.3 1.8 - - + -
107C VAL* 4.0 23.1 - - + -
110C LEU* 4.2 27.1 - - + -
111C VAL* 4.3 8.3 - - + -
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Residues in contact with HIS 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ASP* 2.4 38.0 + - + +
40C THR 3.6 6.1 - - - -
41C VAL* 3.4 29.6 - - + -
62C PHE* 1.3 73.4 - - - +
64C LEU* 1.3 68.1 + - - +
65C PRO* 3.2 22.2 - - + +
73C PRO* 3.2 10.0 - - - +
74C GLY* 2.5 49.4 + - - +
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Residues in contact with LEU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C VAL* 4.1 17.7 - - + -
15C GLU* 4.2 6.1 - - - +
16C LEU* 4.2 13.5 - - + -
39C GLY* 3.4 1.2 - - - -
40C THR* 2.8 40.4 + - - +
42C PHE* 3.8 27.8 - - + -
62C PHE* 4.7 2.5 - - + -
63C HIS* 1.3 81.4 - - - +
65C PRO* 1.3 69.1 - - - +
68C TYR* 3.7 51.8 - - + -
73C PRO* 3.8 9.2 - - + -
107C VAL* 4.3 9.6 - - + -
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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
------------------------------------------------------------
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