Contacts of the strand formed by residues 222 - 228 (chain A) in PDB entry 1V9P
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 ARG 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ILE* 4.2 6.1 - - + -
156A PRO* 6.2 2.0 - - - +
157A THR* 5.0 14.6 - - + +
175A VAL* 3.3 2.3 - - - +
176A TYR* 2.5 69.6 + - + +
178A PRO* 4.2 18.8 - - + -
220A GLY 3.5 6.4 + - - +
221A LEU* 1.3 79.8 + - - +
223A ALA* 1.3 57.7 + - - +
255A GLU* 3.7 29.5 + - - +
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Residues in contact with ALA 223 (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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155A ILE* 4.1 13.3 - - + +
157A THR* 3.9 2.4 + - - +
158A ILE* 4.2 18.6 - - + -
174A GLU 3.1 13.0 - - - +
175A VAL* 3.3 19.5 - - + -
176A TYR* 4.2 4.0 - - - -
222A ARG* 1.3 76.5 - - - +
224A THR* 1.3 61.0 + - - +
225A PHE* 4.3 8.7 - - + -
253A PRO* 2.9 26.3 - - - +
255A GLU* 3.9 7.2 + - - -
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Residues in contact with THR 224 (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 VAL* 3.8 29.8 - - + -
173A GLY* 3.2 0.5 - - - -
174A GLU* 2.6 46.6 + - + +
176A TYR* 4.4 6.0 - - + -
223A ALA* 1.3 75.3 - - - +
225A PHE* 1.3 59.2 + - - +
226A TYR* 5.0 3.8 - - + -
253A PRO 3.0 5.2 - - - -
254A VAL* 3.1 5.9 - - - -
255A GLU* 2.7 34.9 + - - -
256A HIS* 3.0 27.7 + - + +
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Residues in contact with PHE 225 (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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124A VAL* 3.5 31.2 - - + -
126A LEU* 3.7 31.2 - - + -
158A ILE* 4.5 10.5 - - + -
171A VAL* 4.4 9.0 - - + -
172A ARG* 3.5 7.2 - - - +
173A GLY* 3.1 27.8 - - - -
223A ALA* 4.3 18.8 - - + -
224A THR* 1.3 76.6 + - - +
226A TYR* 1.3 61.5 + - - +
244A LEU* 4.2 0.5 - - - +
247A LEU* 3.4 22.8 - - + +
252A PHE* 4.0 22.2 - + + -
253A PRO* 2.8 42.0 + - + +
254A VAL* 3.8 21.7 - - - +
256A HIS* 4.5 1.1 - - - -
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Residues in contact with TYR 226 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A MET* 6.0 0.7 - - - +
116A GLU* 3.6 16.6 - - - +
119A VAL* 5.8 0.4 - - + -
123A SER* 4.5 5.9 + - - -
172A ARG* 3.1 12.1 + - + +
173A GLY* 3.4 34.3 + - - -
174A GLU* 3.8 14.7 - - + +
224A THR* 4.7 4.9 - - + -
225A PHE* 1.3 76.7 - - - +
227A ALA* 1.3 78.9 + - + +
240A GLN* 3.8 11.2 + - - +
243A LEU* 2.9 17.2 - - - +
244A LEU* 3.7 11.3 - - + +
247A LEU* 3.5 11.4 - - - -
256A HIS* 4.0 8.5 - + - +
291A LYS* 4.9 3.9 - - - -
700A AMP 3.6 62.6 + + - -
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Residues in contact with ALA 227 (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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171A VAL* 3.4 1.6 - - - +
172A ARG* 2.7 45.4 + - + +
226A TYR* 1.3 93.7 - - + +
228A LEU* 1.3 77.8 + - - +
240A GLN* 6.2 0.4 - - - +
243A LEU* 3.8 5.2 - - - -
247A LEU* 3.8 2.8 - - - +
291A LYS* 5.2 7.6 - - - +
298A TRP* 6.3 3.6 - - + -
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Residues in contact with LEU 228 (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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169A LEU* 4.2 7.0 - - + -
170A GLU 3.3 5.4 - - - +
171A VAL* 4.1 16.4 - - + -
172A ARG* 3.8 10.3 + - - -
227A ALA* 1.3 90.7 - - - +
229A GLY* 1.3 62.1 + - - +
231A GLY 4.1 7.2 - - - +
232A LEU* 3.9 45.2 - - + +
235A SER* 4.3 3.1 - - - +
237A LEU* 4.1 13.9 - - + -
243A LEU* 4.1 14.7 - - + +
246A TRP* 4.0 20.4 - - + -
247A LEU* 3.8 26.0 - - + -
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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