Contacts of the strand formed by residues 90 - 96 (chain C) in PDB entry 6ZGI
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 VAL 90 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C PHE* 3.7 30.9 - - + -
89C GLY* 1.3 78.6 - - - +
91C TYR* 1.3 74.6 + - - +
92C PHE* 4.0 10.5 + - + +
106C PHE* 6.3 0.2 - - + -
192C PHE 3.8 0.7 - - - +
193C VAL* 3.4 5.9 - - - +
194C PHE* 2.9 41.0 + - + +
238C PHE* 3.8 24.9 - - + -
267C VAL* 4.1 13.5 - - + -
268C GLY 3.7 6.1 - - - +
269C TYR* 4.2 16.6 - - + -
270C LEU* 4.0 5.1 - - - +
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Residues in contact with TYR 91 (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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31C SER* 6.0 0.4 - - - -
34C ARG* 3.9 17.6 - - + +
35C GLY* 3.6 28.7 - - - -
56C LEU* 3.9 26.2 - - + -
62C VAL* 5.4 5.4 - - + -
90C VAL* 1.3 73.6 - - - +
92C PHE* 1.3 59.7 + - - +
93C ALA* 3.6 25.8 - - + +
191C GLU* 3.0 45.3 + - + +
192C PHE 3.6 10.8 - - - -
193C VAL* 4.0 9.0 - - + -
216C LEU* 4.9 9.6 - - + +
223C LEU* 4.8 2.2 - - + -
266C TYR* 4.9 2.7 - - + -
267C VAL* 3.6 4.8 - - - -
268C GLY* 2.9 42.9 + - - +
270C LEU* 4.2 14.7 - - + +
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Residues in contact with PHE 92 (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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90C VAL* 3.9 5.1 - - + -
91C TYR* 1.3 75.8 - - - +
93C ALA* 1.3 61.6 + - - +
94C SER* 4.0 22.0 - - - -
101C ILE* 4.2 14.8 - - + -
104C TRP* 3.7 42.0 - + - -
190C ARG 3.7 0.3 - - - +
191C GLU* 3.5 2.3 - - - +
192C PHE* 2.9 46.3 + + + +
194C PHE* 4.2 17.5 - + + -
238C PHE* 4.8 7.9 - + - -
240C THR* 3.9 13.2 - - + -
265C TYR* 3.5 39.5 - + + -
266C TYR 3.6 1.8 - - - -
267C VAL* 4.2 15.5 - - + -
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Residues in contact with ALA 93 (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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91C TYR* 3.6 30.2 - - + +
92C PHE* 1.3 76.3 - - - +
94C SER* 1.3 60.9 + - - +
189C LEU* 4.4 2.0 - - + -
190C ARG 3.5 4.0 - - - -
191C GLU* 4.4 6.5 - - + +
216C LEU* 4.1 21.5 - - + -
265C TYR* 3.2 7.3 - - - +
266C TYR* 2.9 41.1 + - + +
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Residues in contact with SER 94 (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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92C PHE* 4.0 17.5 - - - -
93C ALA* 1.3 76.5 - - - +
95C THR* 1.3 62.3 + - - +
96C GLU* 3.7 13.5 + - - +
101C ILE* 3.4 27.0 - - - +
188C ASN 3.4 2.4 - - - +
189C LEU* 3.3 6.8 - - - +
190C ARG* 2.9 46.5 + - - +
192C PHE* 5.8 1.6 - - - -
264C ALA 3.6 4.7 - - - -
265C TYR* 4.6 1.1 - - - -
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Residues in contact with THR 95 (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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94C SER* 1.3 73.7 - - - +
96C GLU* 1.3 59.1 + - - +
186C PHE* 4.0 26.5 - - - -
188C ASN 3.5 4.3 - - - -
189C LEU* 3.8 20.2 - - + -
210C ILE* 4.2 12.6 - - + -
212C LEU* 4.8 7.9 - - + -
216C LEU* 4.9 3.8 - - + -
217C PRO* 5.0 3.6 - - + -
263C ALA* 3.9 2.1 - - - -
264C ALA* 2.9 48.5 + - - +
266C TYR* 3.8 21.3 + - + +
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Residues in contact with GLU 96 (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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94C SER* 3.7 9.8 + - - +
95C THR* 1.3 73.2 - - - +
97C LYS* 1.3 61.1 + - - +
98C SER 4.4 2.7 - - - +
99C ASN* 3.5 8.0 - - - +
100C ILE* 2.8 15.2 + - + +
101C ILE* 2.3 62.8 + - + +
186C PHE* 4.1 7.8 - - - -
187C LYS 3.2 5.0 + - - -
188C ASN* 2.9 38.9 + - - +
190C ARG* 3.5 34.0 + - + +
263C ALA* 4.2 7.6 - - + -
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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