Contacts of the strand formed by residues 230 - 237 (chain A) in PDB entry 3V50
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 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A LEU* 4.5 9.2 - - + -
212A VAL* 4.1 22.7 - - + -
228A GLY 3.8 2.4 + - - -
229A TRP* 1.3 70.6 - - - +
231A ILE* 1.3 65.8 + - - +
232A ALA* 3.8 24.7 - - + -
249A LEU* 3.7 9.9 - - + -
250A LEU* 3.3 29.3 - - - +
251A GLY 2.8 9.5 + - - +
255A ASN* 3.6 23.9 - - + +
256A LYS 3.4 23.6 - - - +
257A ALA* 3.6 37.5 - - + -
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Residues in contact with ILE 231 (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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212A VAL* 4.5 3.1 - - - +
218A GLY* 4.5 3.8 - - - +
221A ILE* 3.8 20.2 - - + -
222A ARG* 2.9 65.1 + - + +
225A LEU* 3.8 15.0 - - + -
229A TRP 3.8 1.5 + - - +
230A PHE* 1.3 81.9 - - - +
232A ALA* 1.3 74.5 + - - +
233A ASP* 4.2 12.6 - - + +
248A ALA* 4.0 8.3 - - + -
249A LEU 3.4 13.7 - - - +
250A LEU* 4.4 5.8 - - + -
302A MA4 3.8 28.7 - - + -
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Residues in contact with ALA 232 (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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208A LEU 4.7 0.4 - - - +
211A MET* 3.6 15.5 - - + -
212A VAL* 3.7 26.7 - - + +
222A ARG* 5.0 0.7 - - - +
230A PHE* 3.8 16.4 - - + -
231A ILE* 1.3 75.8 - - - +
233A ASP* 1.3 67.4 + - - +
248A ALA* 3.2 2.4 - - - +
249A LEU* 2.8 43.1 + - + +
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Residues in contact with ASP 233 (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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127A ILE* 5.0 1.2 - - - +
211A MET* 3.1 24.2 + - - +
214A ASP* 2.6 41.5 - - - +
217A ALA* 3.9 0.9 - - - +
218A GLY* 3.4 23.4 - - - -
221A ILE* 4.2 11.4 - - - +
222A ARG* 5.6 0.5 + - - -
231A ILE* 4.2 9.7 - - + +
232A ALA* 1.3 79.0 - - - +
234A LYS* 1.3 67.4 + - - +
235A THR* 3.8 12.0 - - - +
246A ILE* 4.0 16.8 - - + -
247A VAL 3.2 11.7 - - - +
248A ALA* 4.3 2.0 - - + -
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Residues in contact with LYS 234 (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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70A SER 3.6 23.1 - - - +
71A THR* 3.6 9.2 - - - +
73A LYS* 4.1 4.5 - - + -
74A VAL* 3.5 26.7 - - + +
126A ALA 3.8 15.5 - - - -
127A ILE* 3.4 31.0 + - + +
130A GLY* 4.6 1.8 - - - +
211A MET* 4.1 0.2 - - - +
214A ASP* 5.0 5.7 + - - +
216A VAL* 5.1 2.8 - - - +
233A ASP* 1.3 75.0 - - - +
235A THR* 1.3 85.8 + - - +
246A ILE* 3.5 0.9 - - - -
247A VAL* 2.9 39.2 + - + +
301A SA2 2.7 41.5 + - - -
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Residues in contact with THR 235 (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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70A SER* 3.5 6.1 - - - -
71A THR* 3.9 3.6 - - - -
214A ASP* 4.9 1.3 + - - -
216A VAL* 4.0 22.7 - - - +
217A ALA* 3.6 26.2 - - + +
233A ASP* 3.8 4.2 + - - +
234A LYS* 1.3 106.0 + - - +
236A GLY* 1.3 60.3 + - - +
244A ARG* 4.1 14.4 + - - -
245A GLY 3.3 9.2 - - - +
246A ILE* 3.8 21.3 - - + -
301A SA2 3.5 3.8 + - - +
303A MA4 3.8 15.9 - - + +
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Residues in contact with GLY 236 (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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69A MET* 3.7 13.0 - - - -
70A SER 4.0 8.1 - - - -
71A THR* 3.9 2.6 - - - +
235A THR* 1.3 75.2 - - - +
237A ALA* 1.3 57.8 + - - -
244A ARG* 2.8 19.1 + - - -
245A GLY 2.9 27.1 + - - -
301A SA2 3.0 14.6 - - - -
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Residues in contact with ALA 237 (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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69A MET* 3.4 11.2 - - - +
170A ASN* 2.9 19.4 + - - -
236A GLY* 1.3 75.9 - - - +
238A GLY* 1.3 59.5 + - - +
243A ALA 3.5 7.4 - - - +
244A ARG* 3.8 20.4 - - - +
272A MET* 5.1 7.2 - - + -
275A ARG* 4.9 4.5 - - - +
301A SA2 2.8 35.4 + - - +
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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