Contacts of the strand formed by residues 111 - 116 (chain D) in PDB entry 4K81
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 MET 111 (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* 3.2 21.1 - - + +
80D CYS* 3.7 27.8 - - + -
93D ILE* 5.3 1.3 - - + -
97D ARG* 3.7 45.8 - - + -
100D ILE* 4.7 13.5 - - - -
109D VAL* 3.3 13.6 + - - +
110D PRO* 1.3 76.5 - - - +
112D VAL* 1.3 69.4 + - - +
137D TYR* 4.1 4.9 - - + -
139D ILE* 3.4 49.7 - - + +
140D PRO* 3.6 5.2 - - - +
159D LEU* 3.7 3.3 - - - +
162D GLU* 4.0 6.6 + - - +
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Residues in contact with VAL 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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78D PHE 3.1 5.7 + - - -
79D LEU* 3.7 14.0 - - + -
80D CYS* 2.9 28.5 + - - +
111D MET* 1.3 81.4 - - - +
113D LEU* 1.3 72.6 + - - +
114D VAL* 3.7 10.6 + - + +
139D ILE* 4.3 4.0 - - - -
140D PRO* 3.8 17.7 - - + +
142D ILE* 4.0 24.0 - - + -
155D ALA* 4.4 1.8 - - - +
158D THR* 4.1 7.6 - - + -
159D LEU* 3.6 35.4 - - + +
162D GLU* 4.1 7.0 - - + -
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Residues in contact with LEU 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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80D CYS* 3.5 18.6 - - + +
82D PHE* 3.9 24.9 - - + -
93D ILE* 3.6 29.6 - - + -
112D VAL* 1.3 72.7 - - - +
114D VAL* 1.3 60.5 + - - +
130D ALA* 3.5 26.7 - - + +
133D LEU* 4.1 16.4 - - + -
134D ALA* 4.1 10.3 - - + +
137D TYR* 5.7 0.2 - - + -
139D ILE* 4.0 13.2 - - + +
140D PRO 2.9 15.7 + - - +
141D TYR* 3.2 17.9 - - + -
142D ILE 2.9 27.5 + - - -
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Residues in contact with VAL 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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19D LEU* 3.8 17.7 - - + -
79D LEU* 3.7 33.2 - - + -
80D CYS 2.9 10.9 + - - +
81D VAL* 3.4 12.1 - - + -
82D PHE* 3.0 34.9 + - - +
112D VAL* 4.3 5.6 - - + +
113D LEU* 1.3 76.9 - - - +
115D GLY* 1.3 59.4 + - - +
142D ILE* 3.3 4.0 - - + +
144D THR* 3.3 35.2 - - + +
155D ALA* 3.9 18.6 - - + -
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Residues in contact with GLY 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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82D PHE* 3.8 15.7 - - - -
84D ILE* 4.1 7.4 - - - -
114D VAL* 1.3 69.8 - - - +
116D ASN* 1.3 56.8 + - - -
118D CYS* 4.4 1.4 - - - +
141D TYR* 3.6 23.3 - - - -
142D ILE 2.9 10.9 + - - -
143D GLU* 3.2 6.8 - - - +
144D THR* 2.6 33.3 + - - +
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Residues in contact with ASN 116 (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 2.8 25.2 + - - +
15D GLY* 3.6 15.0 + - - -
18D ALA* 5.6 0.2 - - - +
19D LEU* 3.7 9.4 - - + +
81D VAL* 4.0 12.6 - - + -
82D PHE 2.9 17.1 + - - +
83D ALA* 3.5 0.9 - - - +
84D ILE* 2.9 28.2 + - - +
115D GLY* 1.3 71.7 - - - +
117D LYS* 1.3 89.1 + - - +
118D CYS 3.2 2.7 - - - -
144D THR* 2.9 26.8 + - - +
146D ALA* 3.3 24.8 + - - +
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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