Contacts of the strand formed by residues 251 - 258 (chain D) in PDB entry 3VI4
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 THR 251 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D TYR* 3.6 31.2 - - + -
122D PRO 3.5 2.5 + - - +
123D ILE* 3.4 22.7 - - + +
124D ASP 3.0 26.5 + - - +
250D VAL* 1.3 75.8 - - - +
252D ARG* 1.3 58.5 + - - +
253D LEU* 4.9 6.2 - - - +
310D ASN* 5.4 0.2 - - - +
312D GLN* 4.4 13.9 - - - +
355D TYR* 5.2 7.2 - - + +
429D GLY 4.5 8.7 - - - +
430D PHE* 4.3 23.3 - - + -
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Residues in contact with ARG 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ASP* 3.3 6.1 - - + -
247D TRP* 3.0 60.5 + - + +
248D ARG 3.2 26.6 + - - +
249D ASN* 4.1 10.8 + - - +
250D VAL 3.3 15.5 - - - +
251D THR* 1.3 74.6 - - - +
253D LEU* 1.3 67.4 + - - +
309D ASN* 4.2 10.1 + - - +
310D ASN* 3.3 44.7 + - + +
311D ILE* 4.0 16.2 - - + -
312D GLN* 3.1 25.1 + - - +
431D THR* 5.6 3.7 - - - +
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Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ILE* 4.2 17.7 - - + -
124D ASP 2.8 15.7 + - - +
125D LEU* 3.3 25.5 - - + +
126D TYR* 2.7 33.1 + - - +
153D MET* 4.5 8.1 - - + -
247D TRP* 3.8 5.6 - - - -
251D THR* 4.9 5.4 - - - +
252D ARG* 1.3 82.6 - - - +
254D LEU* 1.3 55.6 + - - +
255D VAL 4.0 0.4 - - - -
311D ILE* 4.9 0.4 - - - -
312D GLN* 3.4 28.0 - - + +
314D ILE* 4.3 16.2 - - + -
351D ILE* 5.4 0.9 - - + -
355D TYR* 4.1 33.0 - - + -
358D LEU* 4.4 9.4 - - + -
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Residues in contact with LEU 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D TYR* 3.4 17.7 - - + +
128D LEU* 3.7 27.1 - - + -
235D ILE* 4.0 36.6 - - + +
238D VAL* 4.1 26.2 - - + -
239D ALA* 5.9 0.9 - - + +
247D TRP* 5.2 3.4 - - + -
253D LEU* 1.3 73.2 - - - +
255D VAL* 1.3 60.8 + - - +
256D PHE* 3.6 3.3 + - + +
306D LEU* 4.6 2.7 - - + -
311D ILE* 3.6 27.1 - - + +
312D GLN 2.9 10.2 + - - +
313D THR* 3.5 11.4 - - + +
314D ILE* 2.6 34.5 + - - +
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Residues in contact with VAL 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D LEU* 3.7 35.7 - - + -
126D TYR 2.8 11.1 + - - +
127D TYR* 3.7 30.0 - - + -
128D LEU* 2.9 32.2 + - - +
254D LEU* 1.3 73.7 - - - +
256D PHE* 1.3 62.1 + - - +
257D SER 3.7 0.3 + - - -
314D ILE* 3.4 20.9 - - + +
316D ALA* 4.3 17.7 - - + -
351D ILE* 3.9 27.1 - - + -
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Residues in contact with PHE 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D LEU* 3.6 11.2 - - + -
167D PHE* 3.2 36.1 - + - -
231D GLY* 3.7 33.2 - - - -
232D PHE* 4.7 6.3 - + - -
235D ILE* 3.7 24.2 - - + -
254D LEU* 3.6 4.4 + - + -
255D VAL* 1.3 72.5 - - - +
257D SER* 1.3 59.0 + - - +
258D THR* 3.4 22.4 + - + -
262D PHE* 5.7 1.8 - - + -
313D THR* 4.6 7.2 - - + -
314D ILE 2.7 13.4 + - - +
315D PHE* 3.5 29.1 - + + -
316D ALA 2.8 25.6 + - - +
317D VAL* 4.5 0.7 - - + +
325D TYR* 3.8 18.6 - + - -
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Residues in contact with SER 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D TYR* 3.4 25.5 + - - -
128D LEU 3.1 9.3 + - - +
129D MET* 3.7 14.6 - - - +
130D ASP* 3.0 27.4 + - - +
135D MET* 4.0 8.2 - - - +
167D PHE* 4.4 1.9 - - - -
255D VAL* 3.7 1.7 + - - -
256D PHE* 1.3 74.1 - - - +
258D THR* 1.3 61.9 + - - +
316D ALA* 2.9 28.3 - - - -
340D LEU* 3.9 8.8 - - - +
344D SER* 4.7 0.9 + - - -
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Residues in contact with THR 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ASP* 2.9 28.6 + - - -
135D MET* 4.0 8.2 - - - +
167D PHE* 4.1 5.6 - - - -
229D GLU* 4.6 2.8 - - - +
256D PHE* 3.4 35.0 - - + -
257D SER* 1.3 76.6 - - - +
259D ASP* 1.3 68.8 + - - +
260D ALA* 3.1 16.2 + - - +
316D ALA 3.2 2.9 + - - +
317D VAL* 3.3 31.5 - - + +
318D THR* 3.6 2.3 + - - +
325D TYR* 3.6 18.6 - - + +
340D LEU* 4.6 1.6 - - - +
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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