Contacts of the strand formed by residues 194 - 203 (chain A) in PDB entry 1B70
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 PHE 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A TYR* 3.7 35.7 - + + +
187A MET* 3.9 10.5 - - + -
190A HIS* 5.2 0.2 - - + -
191A THR 3.8 6.3 - - - -
192A PRO* 3.7 15.0 - - + -
193A PRO* 1.3 74.7 - - - +
195A ARG* 1.3 67.3 - - - +
196A ILE* 3.9 10.8 - - + -
222A LEU* 3.6 37.5 - - + -
223A VAL* 3.2 8.0 - - - +
224A VAL* 2.9 50.2 + - + +
307A TYR* 3.5 24.9 - + - -
479B PHE* 3.5 7.4 - - - -
481B PRO* 4.7 4.5 - - + -
485B ASN* 3.8 19.3 - - + +
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Residues in contact with ARG 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU 3.4 25.6 + - - -
118A GLY* 3.5 26.0 + - - +
119A TYR* 3.8 25.1 - - + -
120A GLN* 3.0 21.6 + - - +
194A PHE* 1.3 81.0 - - - +
196A ILE* 1.3 66.2 + - - +
222A LEU 3.4 5.2 - - - -
223A VAL* 3.6 14.6 - - + -
477B PRO* 3.4 30.5 + - - +
478B ALA* 4.2 0.8 - - - +
479B PHE* 3.5 50.8 + - + +
481B PRO* 5.3 7.3 - - - +
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Residues in contact with ILE 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A TYR* 3.3 12.3 - - - -
120A GLN* 3.3 16.4 - - + +
122A VAL* 3.9 8.3 - - + -
182A MET 5.2 2.5 - - - +
183A GLN* 5.2 2.2 - - - -
186A TYR* 3.7 62.6 - - + +
194A PHE* 3.9 7.6 - - + -
195A ARG* 1.3 80.6 - - - +
197A VAL* 1.3 63.3 + - - +
198A VAL* 4.2 18.8 - - + -
221A GLY* 3.5 0.7 - - - -
222A LEU* 2.7 58.1 + - + +
488B VAL* 5.1 1.1 - - + -
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 5.0 10.8 - - + -
114A PHE* 4.2 22.2 - - + -
119A TYR* 4.3 13.2 - - + +
120A GLN 3.0 7.1 + - - +
121A ALA* 3.4 24.4 - - + +
122A VAL* 3.2 21.8 + - - +
196A ILE* 1.3 77.8 - - - +
198A VAL* 1.3 62.7 + - - +
199A PRO* 3.6 1.6 - - + +
219A LEU* 3.6 32.3 - - + -
220A GLU 3.1 17.7 - - - +
221A GLY* 4.4 3.8 - - - -
315A PHE* 4.7 3.1 - - + -
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Residues in contact with VAL 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A VAL* 3.0 22.7 - - + +
123A GLU* 4.1 3.6 - - - -
124A GLY 4.3 2.5 - - - +
176A ARG* 5.1 1.1 - - - +
179A THR* 3.9 11.3 + - + +
182A MET* 3.6 36.3 - - + -
183A GLN 5.6 0.4 - - - +
196A ILE* 4.2 20.2 - - + -
197A VAL* 1.3 81.6 - - - +
199A PRO* 1.3 72.4 - - - +
218A GLN 3.7 1.0 - - - +
219A LEU* 3.4 2.7 - - - -
220A GLU* 2.5 54.1 + - + +
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Residues in contact with PRO 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLU* 3.6 25.8 - - + +
111A VAL* 4.8 3.1 - - + -
121A ALA* 4.6 1.8 - - + -
122A VAL 3.9 11.7 - - - +
123A GLU* 4.3 16.4 - - + +
176A ARG* 4.7 1.2 + - - -
179A THR* 4.4 0.4 - - - -
197A VAL* 3.6 13.0 - - + +
198A VAL* 1.3 102.1 - - - +
200A GLY* 1.3 58.0 + - - +
218A GLN 3.5 8.1 - - - +
219A LEU* 3.6 17.5 - - + -
319A VAL* 6.4 0.4 - - + -
492B TYR* 3.9 32.8 - - + +
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Residues in contact with GLY 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLU* 4.8 3.4 + - - -
123A GLU* 5.1 4.7 - - - -
176A ARG* 3.5 14.8 - - - -
179A THR* 3.9 11.5 - - - +
199A PRO* 1.3 78.0 - - - +
201A ARG* 1.3 64.7 + - - -
202A VAL* 3.6 0.5 + - - +
217A HIS* 3.4 8.1 - - - +
218A GLN 3.1 30.3 + - - +
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Residues in contact with ARG 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLU* 3.5 18.5 + - - +
176A ARG* 2.7 32.2 + - - +
200A GLY* 1.3 71.0 - - - -
202A VAL* 1.3 57.1 + - - +
203A PHE* 3.5 23.7 - - + -
215A VAL* 3.3 23.1 - - + -
216A PHE 3.3 8.1 - - - +
217A HIS* 3.5 26.5 + - + +
336A PHE* 3.3 30.1 - - - -
511B TYR* 4.7 8.7 - - - -
512B THR 3.6 7.9 + - - +
514B SER* 3.3 26.8 + - - -
545B ARG* 3.3 26.1 - - - +
572B GLU* 4.6 2.4 + - - -
573B VAL 5.2 1.4 + - - -
574B GLY* 4.6 8.7 - - - -
575B ARG 4.7 0.8 - - - +
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Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ARG* 3.8 11.2 - - - +
177A THR 4.0 5.8 - - - +
178A HIS* 3.4 38.4 - - - +
179A THR* 3.7 16.4 - - + +
200A GLY 4.1 2.2 - - - +
201A ARG* 1.3 78.1 - - - +
203A PHE* 1.3 72.5 + - - +
214A ALA 3.6 0.3 - - - +
215A VAL* 3.6 0.9 - - - +
216A PHE* 2.6 74.4 + - + +
217A HIS 4.7 0.2 - - - +
218A GLN* 4.1 12.6 - - + +
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Residues in contact with PHE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLU* 3.6 40.2 - - + -
150A ASP 4.5 0.7 - - - +
151A THR* 5.3 0.9 - - - -
152A PHE* 4.0 12.3 - - + -
175A LEU* 3.4 53.5 - - + +
176A ARG* 3.0 20.9 + - + +
177A THR* 3.6 17.4 + - - -
201A ARG* 3.5 37.9 - - + -
202A VAL* 1.3 78.2 - - - +
204A ARG* 1.3 61.7 + - - +
214A ALA 3.2 5.6 - - - +
215A VAL* 3.8 24.2 - - + -
216A PHE* 5.0 0.9 - - - -
514B SER* 4.2 17.7 - - - -
515B PHE* 5.3 4.3 - + + -
577B PHE* 5.6 0.4 - + - -
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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