Contacts of the strand formed by residues 110 - 115 (chain D) in PDB entry 2YIN
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 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78D PHE* 3.5 17.9 - - + +
80D ILE* 4.1 23.3 - - + -
98D TYR* 4.0 15.9 - - + -
101D VAL* 3.7 24.0 - - + -
102D ARG* 3.9 26.9 - - - +
108D THR 4.1 6.1 - - - +
109D PRO* 1.3 81.8 - - - +
111D ILE* 1.3 74.1 + - - +
149D ILE* 4.2 9.4 - - + +
150D GLY 4.8 0.8 + - - +
151D ALA* 3.3 22.5 - - + +
152D VAL* 2.8 33.2 + - - +
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Residues in contact with ILE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D VAL* 4.4 7.4 - - + -
78D PHE 2.8 8.9 + - - +
79D LEU* 3.5 22.0 - - + -
80D ILE* 2.8 28.4 + - - +
110D ILE* 1.3 80.6 - - - +
112D LEU* 1.3 69.5 + - - +
113D VAL* 3.7 5.1 + - + +
152D VAL* 5.0 2.5 - - + -
153D LYS* 3.6 20.4 - - + +
155D LEU* 4.1 18.2 - - + -
168D VAL 4.4 2.2 - - - +
171D GLU* 3.6 13.5 - - + +
172D ALA* 3.2 43.3 - - + +
175D ALA* 4.5 8.7 - - + -
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Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ILE* 3.4 31.0 - - + +
82D PHE* 4.0 18.2 - - + -
93D VAL* 3.9 16.6 - - + -
111D ILE* 1.3 75.1 - - - +
113D VAL* 1.3 63.0 - - - +
142D GLY 3.5 24.7 - - - +
145D MET* 3.9 17.9 - - + -
146D ALA* 3.9 9.0 - - + +
149D ILE* 3.9 9.4 - - + -
151D ALA* 4.1 10.6 - - + +
153D LYS 2.8 16.4 + - - +
154D TYR* 3.4 16.7 - - + -
155D LEU 2.9 26.0 + - - -
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Residues in contact with VAL 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 4.3 12.1 - - + -
79D LEU* 4.0 18.6 - - + -
80D ILE 2.5 19.5 + - - +
81D CYS* 3.1 17.8 - - + +
82D PHE* 2.9 34.5 + - - +
111D ILE* 4.1 4.9 - - + +
112D LEU* 1.3 80.0 - - - +
114D GLY* 1.3 61.4 + - - +
115D THR 4.8 0.7 - - - +
155D LEU* 3.3 7.4 - - + +
157D CYS* 3.8 28.7 - - - -
168D VAL* 4.0 28.3 - - + -
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Residues in contact with GLY 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D PHE* 3.5 23.0 - - - -
84D LEU* 3.9 11.1 - - - +
112D LEU 4.3 0.4 + - - -
113D VAL* 1.3 72.7 - - - +
115D THR* 1.3 62.6 + - - +
154D TYR* 4.5 2.8 - - - -
155D LEU 2.9 13.3 + - - -
156D GLU* 3.4 5.0 - - - +
157D CYS* 2.9 32.6 + - - +
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Residues in contact with THR 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D VAL* 2.9 46.9 - - - +
15D GLY 4.4 9.0 - - - +
19D LEU* 4.7 17.9 - - + +
81D CYS* 4.0 7.8 - - - +
82D PHE 2.8 13.2 + - - -
83D SER* 4.0 4.3 - - - -
84D LEU* 3.1 20.0 + - - +
113D VAL* 4.8 2.9 - - - +
114D GLY* 1.3 74.3 - - - -
116D LYS* 1.3 87.6 + - + +
117D LEU 3.0 4.1 + - - -
157D CYS* 3.5 7.0 - - - +
159D ALA* 5.6 2.9 - - + +
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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