Contacts of the strand formed by residues 93 - 100 (chain C) in PDB entry 3B94
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 GLY 93 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C GLN 3.7 1.4 + - - -
92C ASN* 1.3 75.8 - - - +
94C LEU* 1.3 61.1 + - - -
95C TYR* 3.6 5.7 - - - -
141C GLU* 3.8 7.9 - - - +
142C LEU 3.3 25.9 + - - +
169C LEU* 4.1 6.1 - - - -
171C ALA 3.0 13.5 - - - -
172C ASN* 3.5 9.4 - - - -
173C PRO* 5.4 1.1 - - - -
176C ILE* 5.3 2.7 - - - +
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Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B MET* 4.5 12.3 - - + -
98B TYR* 4.1 33.2 - - + -
168B ILE* 4.2 25.1 - - + -
93C GLY* 1.3 71.8 - - - -
95C TYR* 1.3 61.2 + - - +
139C THR* 3.0 32.5 - - + -
140C TYR* 3.3 20.4 - - - +
141C GLU* 4.3 5.4 - - + +
169C LEU* 3.6 3.8 - - - +
170C LEU* 2.8 45.7 + - + -
171C ALA* 2.6 20.3 + - + +
172C ASN* 4.6 0.2 - - - +
173C PRO* 5.3 0.8 - - - +
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Residues in contact with TYR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C CYS* 3.6 41.1 + - - +
79C VAL* 4.6 2.0 - - + -
89C ILE* 3.8 9.3 - - + +
91C GLN* 2.4 32.9 + - - +
92C ASN 4.5 0.3 + - - -
93C GLY 3.6 21.1 - - - -
94C LEU* 1.3 77.7 - - - +
96C LEU* 1.3 62.3 + - - +
97C ILE* 4.1 1.5 + - + -
138C GLY 3.9 0.3 - - - +
139C THR* 3.2 6.9 - - - +
140C TYR* 2.7 43.5 + - - +
142C LEU* 3.8 31.0 - - + -
167C ILE* 3.5 36.6 - - + -
168C ILE 3.3 13.9 - - - -
169C LEU* 3.9 14.7 - - + +
170C LEU* 4.6 1.3 - - - -
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 4.4 13.9 - - + -
139A THR* 3.5 36.8 - - + +
170A LEU* 4.1 14.8 - - + -
96B LEU* 4.6 2.9 - - + -
95C TYR* 1.3 74.5 - - - +
97C ILE* 1.3 79.6 + - - +
98C TYR* 4.1 2.6 + - + +
138C GLY* 3.6 8.5 - - - +
139C THR* 4.3 13.2 - - - +
167C ILE* 3.3 3.1 - - - -
168C ILE* 2.6 59.6 + - + +
170C LEU* 4.1 18.6 - - + +
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Residues in contact with ILE 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A THR* 5.4 0.2 - - - -
95C TYR* 4.8 2.0 - - + -
96C LEU* 1.3 82.5 - - - +
98C TYR* 1.3 66.1 + - - +
117C LEU* 4.0 14.8 - - + -
124C ILE* 4.8 2.5 - - + -
136C VAL* 3.3 2.9 - - + +
137C GLY* 3.1 17.3 - - - +
138C GLY 2.7 31.6 + - - +
140C TYR* 3.7 27.1 - - + -
142C LEU* 4.3 8.1 - - + -
148C ILE* 4.0 31.0 - - + -
165C TRP* 4.0 15.7 - - + -
166C GLY 3.3 10.5 - - - +
167C ILE* 3.8 20.4 - - + -
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Residues in contact with TYR 98 (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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94A LEU* 4.1 35.0 - - + -
139A THR* 3.7 35.9 - - + +
140A TYR* 5.2 0.2 - - - -
141A GLU* 4.9 8.5 - - + -
59C MET* 3.2 23.7 - - - +
60C ALA 3.9 5.7 + - - -
61C LYS* 4.2 14.7 - - + +
96C LEU* 4.2 6.3 - - + -
97C ILE* 1.3 75.4 - - - +
99C GLY* 1.3 59.3 + - - +
136C VAL* 3.2 13.5 - - - -
164C TYR* 4.0 26.5 - + - -
165C TRP* 2.9 8.0 - - - +
166C GLY* 2.6 68.0 + - - +
167C ILE* 3.6 10.3 - - - -
168C ILE* 4.6 0.4 - - + -
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Residues in contact with GLY 99 (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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139A THR 4.5 3.4 + - - +
98C TYR* 1.3 78.3 - - - +
100C GLN* 1.3 65.0 + - - +
135C ASN* 2.9 28.1 - - - +
136C VAL* 2.9 16.7 + - - -
164C TYR* 3.1 26.2 - - - -
165C TRP* 3.9 2.2 - - - -
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Residues in contact with GLN 100 (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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119A LYS* 4.7 14.3 + - - +
124A ILE* 4.2 22.2 - - - +
140A TYR* 4.2 18.9 - - + -
141A GLU 5.8 0.2 - - - +
99C GLY* 1.3 83.3 - - - +
101C VAL* 1.3 65.9 + - - +
102C ALA* 4.3 4.9 - - - +
103C PRO* 4.1 25.7 - - + +
134C GLN 4.7 6.9 + - - +
135C ASN* 4.1 15.3 - - + +
136C VAL* 4.8 2.9 - - - +
163C THR* 3.2 22.9 - - - +
164C TYR* 3.0 42.1 + - + +
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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