Contacts of the strand formed by residues 145 - 151 (chain C) in PDB entry 1YLK
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 SER 145 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C ARG 3.6 1.4 + - - -
82C GLU* 3.4 26.4 + - - -
83C ILE 2.8 32.4 + - - -
143C HIS* 3.4 6.1 - - - +
144C THR* 1.3 82.2 + - - +
146C LEU* 1.3 59.7 + - - +
147C ARG* 3.6 24.1 + - - +
2D THR* 5.0 11.8 + - - +
4D THR* 4.2 8.4 + - - -
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Residues in contact with LEU 146 (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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83C ILE* 3.4 33.9 - - + +
85C LEU* 4.3 2.7 - - + -
131C LEU* 3.9 38.3 - - + +
134C ILE* 3.9 33.4 - - + -
135C GLU* 4.0 17.9 - - + +
143C HIS* 3.7 19.0 - - + +
145C SER* 1.3 75.7 + - - +
147C ARG* 1.3 70.1 + - - +
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Residues in contact with ARG 147 (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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83C ILE 3.1 8.7 + - - +
84C ILE* 3.5 5.1 - - - -
85C LEU* 3.0 24.8 + - - +
131C LEU* 4.1 5.8 - - - +
145C SER* 3.6 19.3 + - - +
146C LEU* 1.3 80.9 - - - +
148C GLY* 1.3 59.5 + - - +
149C PHE* 3.6 14.8 - - + -
160C GLU* 2.9 41.8 + - - +
2D THR* 4.1 3.0 + - - +
4D THR* 3.6 20.3 - - + +
5D ASP* 2.8 30.5 + - - -
8D LEU* 3.4 22.7 - - - +
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Residues in contact with GLY 148 (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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85C LEU* 3.5 7.0 - - - -
127C VAL* 3.6 23.1 - - - -
131C LEU* 3.9 15.4 - - - +
147C ARG* 1.3 74.4 - - - +
149C PHE* 1.3 63.5 + - - -
160C GLU* 3.4 10.0 + - - +
161C VAL* 2.8 26.6 + - - +
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Residues in contact with PHE 149 (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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84C ILE* 3.9 19.5 - - + -
85C LEU 2.8 16.2 + - - +
86C LEU* 4.0 12.3 - - + -
87C HIS* 2.9 26.6 + - - -
127C VAL* 3.8 7.2 - - - +
147C ARG* 3.6 42.2 - - + -
148C GLY* 1.3 72.7 - - - -
150C VAL* 1.3 63.6 - - - +
151C PHE 4.0 0.2 - - - -
158C LEU* 4.1 15.3 - - + -
159C ASN 3.4 7.0 - - - +
160C GLU* 3.5 37.2 - - + -
161C VAL* 4.4 1.1 - - - +
4D THR* 4.2 6.5 - - + -
8D LEU* 3.5 45.5 - - + -
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Residues in contact with VAL 150 (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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87C HIS* 3.4 5.4 - - + -
88C HIS* 3.7 6.1 - - - -
89C THR* 3.6 38.6 - - + +
123C ALA* 4.1 13.5 - - + +
124C VAL* 4.0 19.7 - - + -
127C VAL* 3.9 11.7 - - + -
149C PHE* 1.3 76.3 - - - +
151C PHE* 1.3 60.8 + - - +
152C ASP 3.7 1.4 + - - -
158C LEU* 3.6 2.1 - - - -
159C ASN* 2.8 49.2 + - + +
161C VAL* 3.8 19.7 - - + -
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Residues in contact with PHE 151 (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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39C ARG 4.1 8.3 - - - -
40C LEU* 3.6 38.6 - - + -
45C MET* 3.8 31.2 - - + -
86C LEU* 5.2 1.1 - - + -
87C HIS 2.9 16.9 + - - +
88C HIS* 3.2 5.3 - - + +
89C THR 3.0 24.8 + - - -
150C VAL* 1.3 71.4 - - - +
152C ASP* 1.3 63.8 + - - +
153C VAL* 3.4 19.0 + - + -
156C GLY* 3.2 42.2 - - - -
157C LYS 3.5 5.4 - - - -
158C LEU* 3.5 17.8 - - + +
14D TYR* 3.9 12.3 - + - -
18D PHE* 4.1 15.0 - + - -
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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