Contacts of the strand formed by residues 88 - 94 (chain D) in PDB entry 2G9H
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 TYR 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D LYS* 4.0 16.6 - - + +
63D ASP* 2.6 37.5 + - - -
84D LEU 5.7 0.7 - - - -
85D SER* 3.2 3.2 + - - -
86D GLY* 3.2 34.9 + - - -
87D GLN* 1.3 84.2 - - - +
89D LEU* 1.3 68.3 + - - +
90D ASN* 5.2 1.6 - - - +
116D ASN* 3.1 32.1 - - - +
117D LYS* 4.1 14.8 - - + -
118D LYS* 3.3 21.4 + - - +
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Residues in contact with LEU 89 (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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88D TYR* 1.3 82.1 - - - +
90D ASN* 1.3 64.2 + - - +
91D SER* 3.3 16.3 + - - +
93D ARG* 3.9 27.1 - - + -
115D THR 4.0 8.5 - - - +
116D ASN* 2.7 23.8 + - - +
117D LYS 4.2 4.3 - - - +
118D LYS* 3.7 23.3 - - + +
203D SER* 3.7 17.0 - - - +
204D GLU* 3.3 39.0 - - + +
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Residues in contact with ASN 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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88D TYR 5.2 1.6 - - - +
89D LEU* 1.3 74.0 - - - +
91D SER* 1.3 62.4 + - - +
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Residues in contact with SER 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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89D LEU* 3.3 19.6 - - - +
90D ASN* 1.3 79.5 - - - +
92D ALA* 1.3 72.8 + - - +
93D ARG 3.6 0.2 + - - -
116D ASN* 4.2 6.7 - - - -
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Residues in contact with ALA 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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91D SER* 1.3 81.5 + - - +
93D ARG* 1.3 59.7 + - - +
94D LYS* 3.9 3.6 + - - +
111D ASP* 6.0 1.8 - - - +
114D SER* 3.8 20.2 - - - +
115D THR* 3.4 17.7 - - - -
116D ASN* 3.9 9.4 - - + +
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Residues in contact with ARG 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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76B ASP* 2.9 35.4 + - - -
89D LEU* 3.9 15.9 - - + -
91D SER 3.6 0.4 + - - -
92D ALA* 1.3 71.2 - - - +
94D LYS* 1.3 69.3 + - - +
95D ILE* 3.3 9.3 + - + +
96D PRO* 3.5 21.6 - - - +
114D SER* 3.0 22.5 - - - -
115D THR* 2.7 20.5 + - + +
203D SER 2.8 34.6 + - - -
204D GLU* 3.5 31.4 + - + +
206D PHE* 3.0 25.1 + - - -
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Residues in contact with LYS 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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69B GLU* 2.7 26.1 + - + +
92D ALA 3.9 3.4 + - - +
93D ARG* 1.3 77.3 + - - +
95D ILE* 1.3 64.8 + - - +
96D PRO* 3.2 11.4 - - - +
109D SER* 3.5 26.4 + - - +
110D THR* 3.6 27.8 - - - +
111D ASP* 3.4 28.1 + - - +
113D ILE 3.7 5.6 - - - -
114D SER* 3.8 3.4 - - - -
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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