Contacts of the strand formed by residues 89 - 94 (chain D) in PDB entry 4AP8
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 89 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78D THR* 4.2 3.1 - - - -
87D VAL* 3.2 11.2 - - - +
88D ILE* 1.3 84.9 - - - +
90D LEU* 1.3 64.6 + - - +
127D LEU* 3.6 28.4 - - - +
128D VAL 3.4 18.8 - - - -
129D PRO* 3.5 11.0 - - - -
169D ILE* 2.9 33.8 + - - +
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Residues in contact with LEU 90 (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 THR 5.5 0.7 - - - +
78D THR* 3.9 28.9 - - + +
79D ARG 4.9 4.7 - - - +
87D VAL* 4.5 4.0 - - + -
89D SER* 1.3 79.8 - - - +
91D GLU* 1.3 59.6 + - - +
92D TYR* 3.5 34.4 - - + +
126D GLY 3.4 1.7 - - - +
127D LEU* 3.4 0.5 - - - -
128D VAL* 2.6 39.5 + - - +
166D LYS* 4.1 15.5 - - + -
167D LYS 3.5 5.4 - - - +
168D GLU* 3.5 45.8 - - + +
169D ILE* 4.9 0.2 - - - -
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Residues in contact with GLU 91 (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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90D LEU* 1.3 73.1 - - - +
92D TYR* 1.3 66.2 + - - +
93D GLU* 4.2 8.6 + - + +
126D GLY* 3.3 16.1 - - - +
127D LEU* 3.8 28.1 - - + +
165D TRP 3.6 0.5 - - - +
166D LYS* 3.2 5.5 - - - -
167D LYS* 2.9 45.3 + - + +
169D ILE* 4.3 12.9 - - + +
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Residues in contact with TYR 92 (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 THR 5.6 1.2 + - - -
78D THR* 4.8 1.1 + - - -
90D LEU* 3.5 40.2 - - + +
91D GLU* 1.3 77.3 - - - +
93D GLU* 1.3 65.3 - - - +
123D HIS* 3.8 23.8 - + + -
124D ARG 3.8 15.7 - - - +
125D LEU* 3.8 6.7 - - + +
126D GLY* 3.0 29.4 + - - +
128D VAL* 3.9 21.3 - - + -
134D SER* 3.5 32.2 + - - -
159D LYS* 5.0 11.0 + - - -
164D ILE* 4.4 8.3 - - + -
165D TRP 3.1 15.7 - - - +
166D LYS* 3.6 22.8 - - + +
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Residues in contact with GLU 93 (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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165A TRP* 4.2 24.8 - - + -
167A LYS* 5.3 7.4 - - - +
91D GLU* 5.3 11.4 - - + +
92D TYR* 1.3 79.2 - - - +
94D ALA* 1.3 64.4 + - - +
125D LEU* 4.4 2.9 - - - -
164D ILE* 3.3 2.4 - - - -
165D TRP* 2.7 45.1 + - + +
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Residues in contact with ALA 94 (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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165A TRP* 3.8 18.5 + - - -
49D PHE* 5.1 0.4 - - + -
93D GLU* 1.3 76.8 - - - +
95D TYR* 1.3 62.4 + - - +
96D LEU* 3.4 21.0 + - + +
99D ALA* 4.4 4.5 - - + -
125D LEU* 4.1 15.2 - - + +
163D PRO 3.3 17.3 - - - +
164D ILE* 4.0 18.2 - - + -
165D TRP* 4.4 3.1 - - - -
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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