Contacts of the strand formed by residues 350 - 362 (chain F) in PDB entry 3VZC
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 VAL 350 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155F LEU* 3.9 29.8 - - + -
156F HIS 3.3 10.8 - - - +
157F THR* 3.8 19.5 - - + -
163F LEU* 6.1 0.2 - - + -
169F LEU* 4.2 16.4 - - + -
241F LEU* 4.7 1.6 - - - -
327F PHE* 4.1 4.0 - - - -
328F ARG* 3.8 0.2 - - - -
329F LEU* 3.1 34.6 + - + +
338F PHE* 3.6 36.8 - - + -
345F MET* 4.2 7.4 - - + -
347F SER* 4.4 3.6 - - - -
349F ALA* 1.3 79.0 - - - +
351F GLN* 1.3 63.3 + - - +
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Residues in contact with GLN 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F LEU* 3.5 6.2 - - - +
156F HIS* 2.8 41.1 + - + +
238F LEU* 3.9 27.5 - - + +
239F VAL 2.8 25.8 + - - +
240F PRO* 4.5 0.3 - - - +
241F LEU* 3.6 22.4 + - + +
245F VAL* 5.2 0.2 - - - +
249F TRP* 4.6 4.8 - - - -
327F PHE* 3.1 17.9 + - - +
328F ARG* 2.8 46.2 + - + +
349F ALA 4.3 0.2 - - - -
350F VAL* 1.3 76.1 - - - +
352F GLY* 1.3 56.9 + - - +
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Residues in contact with GLY 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F LEU* 3.9 13.7 - - - -
154F SER 2.8 14.6 - - - -
155F LEU* 4.2 1.8 - - - -
238F LEU* 3.9 10.1 - - - +
326F ALA* 3.2 4.5 - - - +
327F PHE* 3.0 36.5 + - - +
351F GLN* 1.3 77.1 - - - +
353F GLN* 1.3 61.6 + - - +
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Residues in contact with GLN 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F LEU* 3.7 5.8 - - - +
154F SER* 3.0 28.3 + - - -
234F VAL 4.5 0.4 + - - -
235F ASP* 3.1 38.7 - - + +
236F ALA* 4.4 3.4 - - - +
237F HIS* 2.9 49.2 + - + +
238F LEU* 3.8 4.6 + - + +
285F MET* 5.8 0.2 - - - -
325F VAL 3.2 11.7 - - - +
326F ALA* 4.1 9.2 - - + +
352F GLY* 1.3 76.5 - - - +
354F VAL* 1.3 70.9 + - - +
355F HIS* 3.6 21.9 + - - +
356F PRO* 6.0 0.4 - - - +
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Residues in contact with VAL 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F ASN* 3.6 29.8 - - + -
152F LEU 3.7 6.1 - - - +
153F LEU* 4.5 2.5 - - - +
237F HIS* 5.6 1.0 + - - -
264F LEU* 4.5 11.7 - - + -
283F GLY* 3.7 23.9 - - - +
284F VAL 4.3 4.9 - - - +
285F MET* 3.4 37.0 - - + +
325F VAL* 2.8 26.4 + - - +
353F GLN* 1.3 86.4 + - - +
355F HIS* 1.3 61.4 + - - +
356F PRO* 3.6 7.6 - - - +
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Residues in contact with HIS 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F ASN* 3.4 4.8 - - - +
152F LEU* 2.8 39.8 + - + +
154F SER* 3.8 12.5 - - - -
233F PRO* 4.0 21.8 - - + +
234F VAL 3.3 24.5 - - - -
235F ASP* 2.5 26.6 + - - -
353F GLN* 3.6 26.2 + - + +
354F VAL* 1.3 73.2 - - - +
356F PRO* 1.3 73.5 - - + +
358F TYR* 3.7 32.2 - + + +
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Residues in contact with PRO 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F MET* 5.7 0.2 - - - +
151F ASN* 3.5 7.6 - - - +
282F ALA* 4.2 10.1 - - + -
283F GLY* 3.5 21.3 - - - +
353F GLN* 6.0 0.4 - - - +
354F VAL 3.6 8.3 - - - +
355F HIS* 1.3 89.7 - - + +
357F ASN* 1.3 74.1 + - + +
358F TYR* 2.9 9.1 + - + +
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Residues in contact with ASN 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F MET* 3.3 22.7 - - - +
149F PRO* 3.4 41.1 - - + +
150F MET* 3.4 9.8 - - - -
151F ASN* 3.0 14.7 + - - +
282F ALA* 3.3 27.8 + - - +
355F HIS 3.6 0.4 + - - -
356F PRO* 1.3 72.7 - - + +
358F TYR* 1.3 58.9 + - - +
359F PHE 3.7 1.1 - - - -
1002F EDO 5.2 1.2 + - - -
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Residues in contact with TYR 358 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F MET* 3.6 23.9 - - + +
92F MET* 3.9 25.4 - - + -
97F TRP* 3.2 19.6 - + - -
101F ILE* 4.2 31.1 - - + +
102F GLN* 5.4 0.9 - - - +
150F MET 2.7 8.9 + - - -
152F LEU* 3.7 33.9 - - + -
233F PRO* 3.2 26.9 - - + +
355F HIS* 3.7 34.8 - - + +
356F PRO* 2.9 7.1 + - + -
357F ASN* 1.3 74.2 - - - +
359F PHE* 1.3 58.2 + - - +
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Residues in contact with PHE 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F MET* 5.7 0.9 - - - -
84F MET* 5.8 0.4 - - + -
88F VAL* 4.8 0.9 - - + -
101F ILE* 3.4 34.5 - - + +
103F LYS 5.6 0.2 - - - +
105F LEU* 4.0 24.5 - - + -
149F PRO* 3.3 4.8 - - - +
150F MET* 2.8 37.9 + - + -
151F ASN 3.3 26.0 - - - -
152F LEU* 3.6 32.1 - - + -
166F VAL* 3.9 23.6 - - + -
265F HIS* 5.9 0.2 - - - -
357F ASN 3.7 0.4 - - - -
358F TYR* 1.3 77.5 - - + +
360F TRP* 1.3 72.0 + - - +
361F MET* 3.1 34.8 - - + -
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Residues in contact with TRP 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F MET* 3.7 50.7 - - + +
7F GLY 3.9 2.7 - - - +
8F SER* 3.8 26.0 - - - -
9F GLY* 3.9 15.0 - - - -
101F ILE 4.6 2.0 + - - -
102F GLN* 3.5 31.4 - - + +
103F LYS 4.3 1.5 + - - +
104F PRO* 3.5 21.8 - - + +
105F LEU* 2.8 34.9 + - - +
147F LEU* 3.8 21.5 - - + -
148F SER 3.7 6.5 - - - -
149F PRO* 3.6 45.5 - - + -
359F PHE* 1.3 80.4 - - - +
361F MET* 1.3 54.9 + - - +
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Residues in contact with MET 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F MET* 4.3 12.3 - - + -
105F LEU* 3.3 25.6 - - + +
106F CYS* 4.1 3.1 - - - +
107F SER* 4.6 1.6 - - - -
116F LEU* 3.6 37.7 - - + -
120F LEU* 3.9 20.4 - - + -
147F LEU* 3.2 5.0 - - - -
148F SER* 2.8 33.0 + - - +
150F MET* 3.8 24.5 - - + -
265F HIS* 5.4 0.7 - - + -
359F PHE* 3.1 36.5 + - + -
360F TRP* 1.3 72.5 - - - +
362F VAL* 1.3 67.9 + - - +
363F SER* 3.4 1.9 + - - -
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Residues in contact with VAL 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F LEU* 4.2 15.9 - - + -
74F ALA* 5.4 2.7 - - + -
104F PRO* 5.6 0.4 - - + -
105F LEU 3.0 17.3 + - - +
106F CYS* 3.4 33.8 - - + -
107F SER 5.2 0.2 - - - +
120F LEU* 3.5 21.1 - - - +
138F CYS 4.6 0.7 - - - +
141F LEU* 4.1 9.2 - - + +
142F LEU* 3.7 29.2 - - + +
146F LEU 3.3 12.1 - - - +
147F LEU* 3.8 17.2 - - + +
361F MET* 1.3 73.5 - - - +
363F SER* 1.3 63.0 + - - +
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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