Contacts of the strand formed by residues 319 - 330 (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 LEU 319 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288F PHE* 4.3 8.5 - - + -
289F TYR 3.5 7.9 - - - +
290F VAL* 3.7 26.5 - - + -
302F LEU* 4.2 20.2 - - + -
311F HIS* 4.0 20.9 - - + +
312F MET* 4.0 32.6 - - + +
315F GLU* 5.2 4.9 - - - +
316F CYS* 3.1 25.4 + - + +
317F PRO 4.9 0.9 - - - -
318F TYR* 1.3 75.7 - - - +
320F VAL* 1.3 68.3 + - - +
321F TYR 4.1 0.9 + - - -
1001F UUL 4.1 21.8 - - + -
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Residues in contact with VAL 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212F TYR* 5.4 1.1 - - - +
287F LEU 4.5 0.2 - - - -
288F PHE* 3.2 6.9 - - - +
289F TYR* 2.7 82.7 + - + +
291F ARG* 3.5 28.7 - - - +
317F PRO 4.9 0.7 - - - +
318F TYR 4.1 0.9 - - - +
319F LEU* 1.3 76.3 - - - +
321F TYR* 1.3 64.4 + - - +
322F VAL* 4.2 15.7 - - + -
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Residues in contact with TYR 321 (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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277F MET* 3.4 36.8 - - + +
286F HIS* 2.9 46.9 - + + -
287F LEU 3.4 9.0 - - - -
288F PHE* 3.7 27.1 - + + -
312F MET* 4.0 21.1 - - + -
319F LEU 4.1 1.2 + - - -
320F VAL* 1.3 77.3 - - - +
322F VAL* 1.3 78.8 + - - +
323F PRO* 3.9 28.2 - - + +
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Residues in contact with VAL 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212F TYR* 3.3 47.3 - - + +
214F PRO* 4.3 7.0 - - + -
286F HIS 3.8 0.2 - - - -
287F LEU* 2.8 39.4 + - + +
289F TYR* 5.2 2.2 - - + -
320F VAL* 4.2 13.9 - - + -
321F TYR* 1.3 86.5 - - - +
323F PRO* 1.3 85.1 - - + +
324F VAL* 3.8 7.9 - - + -
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Residues in contact with PRO 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214F PRO* 4.1 0.2 - - - +
215F VAL* 3.2 39.3 + - + +
284F VAL* 4.2 11.0 - - + -
285F MET 3.8 6.3 - - - +
286F HIS* 6.0 0.4 - - + -
321F TYR* 3.9 27.8 - - + +
322F VAL* 1.3 95.4 - - + +
324F VAL* 1.3 62.6 + - - +
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Residues in contact with VAL 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212F TYR* 3.7 26.2 - - + -
213F LEU 3.6 11.7 - - - +
215F VAL* 3.6 3.9 - - - +
262F ALA* 6.3 0.4 - - + -
284F VAL* 3.7 4.2 - - - -
285F MET* 2.9 58.0 + - + +
287F LEU* 3.8 25.8 - - + -
322F VAL* 3.7 13.2 - - + +
323F PRO* 1.3 80.8 - - - +
325F VAL* 1.3 66.6 + - - +
326F ALA 3.8 16.2 - - - +
327F PHE* 5.1 2.7 - - + -
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Residues in contact with VAL 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213F LEU* 3.1 26.1 + - + -
214F PRO 5.1 0.9 - - - +
215F VAL* 3.9 25.8 - - + +
237F HIS* 3.6 32.3 + - + +
283F GLY 3.4 20.6 - - - +
284F VAL* 5.0 0.7 - - + -
285F MET* 5.1 0.4 - - - -
324F VAL* 1.3 79.0 - - - +
326F ALA* 1.3 61.1 + - + +
353F GLN* 3.2 6.8 - - - +
354F VAL* 2.8 40.0 + - + +
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Residues in contact with ALA 326 (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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212F TYR* 3.5 5.0 - - - +
213F LEU* 3.2 27.3 + - + -
237F HIS* 4.3 6.3 - - + -
238F LEU* 4.3 2.5 - - + -
249F TRP* 3.5 26.2 - - + -
285F MET* 5.8 0.2 - - - -
324F VAL* 3.7 8.2 - - - +
325F VAL* 1.3 87.4 - - + +
327F PHE* 1.3 69.5 + - - +
352F GLY 3.2 12.6 - - - +
353F GLN* 4.1 8.7 - - + -
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Residues in contact with PHE 327 (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* 4.0 28.0 - - + -
155F LEU* 3.7 13.9 - - + -
169F LEU* 3.3 37.7 - - + -
210F LEU* 4.8 7.6 - - + -
211F ALA 3.2 12.6 - - - +
212F TYR* 4.2 6.5 - - + -
249F TRP* 3.5 9.6 - - - -
260F VAL* 6.3 2.2 - - + -
262F ALA* 4.1 15.3 - - + -
285F MET* 4.4 12.3 - - - -
287F LEU* 4.8 10.5 - - + -
324F VAL* 5.1 2.5 - - + -
326F ALA* 1.3 78.8 - - - +
328F ARG* 1.3 72.2 + - - +
329F LEU* 4.1 9.6 - - + -
350F VAL 4.1 13.2 - - - -
351F GLN* 3.1 20.4 - - - +
352F GLY 3.0 23.4 + - - +
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Residues in contact with ARG 328 (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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209F ARG* 3.6 4.9 - - + +
210F LEU* 3.4 5.3 - - - +
211F ALA* 2.6 48.6 + - + +
239F VAL* 3.7 11.9 + - - +
240F PRO 3.1 25.7 + - - -
241F LEU* 3.6 22.1 + - + +
243F GLU 2.9 21.8 + - - -
244F PRO* 4.2 1.2 - - - +
245F VAL* 3.9 24.1 - - - +
249F TRP* 4.3 6.3 - - + -
327F PHE* 1.3 77.1 - - - +
329F LEU* 1.3 66.3 + - - +
330F GLU* 3.7 25.1 + - + +
350F VAL 3.8 7.0 - - - +
351F GLN* 2.8 41.0 + - + +
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Residues in contact with LEU 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F LEU* 5.3 9.0 - - + -
171F TRP* 3.6 62.1 - - + -
208F GLY* 5.0 0.4 - - - -
209F ARG 3.3 10.5 - - - +
210F LEU* 4.2 14.1 - - + -
257F PHE* 5.5 0.2 - - + -
260F VAL* 3.9 24.0 - - + +
327F PHE* 4.1 9.6 - - + -
328F ARG* 1.3 75.4 - - - +
330F GLU* 1.3 72.4 + - - +
331F PRO* 4.2 4.2 - - + +
338F PHE* 4.0 15.8 - - + -
349F ALA* 4.0 0.3 - - - -
350F VAL* 3.1 35.7 + - + +
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Residues in contact with GLU 330 (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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208F GLY* 3.1 7.6 - - - -
209F ARG* 2.7 55.8 + - + +
241F LEU* 5.4 3.2 - - - +
328F ARG* 3.7 29.4 + - + -
329F LEU* 1.3 83.4 - - - +
331F PRO* 1.3 62.6 - - - +
332F LYS* 3.7 30.4 - - + +
348F GLU 4.1 1.3 - - - +
349F ALA* 4.0 21.4 - - + +
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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