Contacts of the strand formed by residues 319 - 330 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288E PHE* 4.4 18.4 - - + -
289E TYR 3.7 10.5 - - - +
290E VAL* 3.9 17.2 - - + +
302E LEU* 4.2 29.8 - - + -
311E HIS* 4.4 25.4 - - + +
312E MET* 4.7 11.7 - - - -
316E CYS* 3.0 27.5 + - + +
317E PRO* 4.3 1.8 - - - +
318E TYR* 1.3 76.3 - - - +
320E VAL* 1.3 73.5 - - - +
321E TYR* 4.4 0.8 + - + -
1001E UUL 4.6 10.5 - - + -
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Residues in contact with VAL 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E TYR* 5.8 0.2 - - - +
287E LEU 3.9 0.5 - - - +
288E PHE* 3.4 5.2 - - - -
289E TYR* 2.9 78.9 + - + +
291E ARG* 3.9 15.7 - - - -
317E PRO 4.2 8.5 - - - +
319E LEU* 1.3 83.7 - - - +
321E TYR* 1.3 69.6 + - - +
322E VAL* 4.2 8.1 - - + -
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Residues in contact with TYR 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PRO* 6.1 1.3 - - + -
357A ASN* 5.2 3.8 + - - +
360A TRP* 4.2 24.5 - + + -
277E MET* 3.4 30.4 - - + +
286E HIS* 2.8 49.8 + + + -
287E LEU 3.5 4.7 - - - -
288E PHE* 3.3 34.1 - + + -
312E MET* 4.0 13.7 - - + -
319E LEU* 4.4 1.1 + - + -
320E VAL* 1.3 78.0 - - - +
322E VAL* 1.3 72.9 + - - +
323E PRO* 3.5 33.9 - - + +
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Residues in contact with VAL 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLN* 6.2 2.7 - - - +
212E TYR* 3.6 45.3 - - + +
214E PRO* 4.4 7.6 - - + -
287E LEU* 2.9 41.4 + - + +
289E TYR* 4.7 4.0 - - + -
320E VAL* 4.2 15.7 - - + -
321E TYR* 1.3 82.4 - - - +
323E PRO* 1.4 79.6 - - + +
324E VAL* 4.1 8.3 - - + -
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Residues in contact with PRO 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A ASN* 5.3 12.6 - - + +
360A TRP* 6.0 0.9 - - + -
214E PRO* 3.6 5.4 - - - +
215E VAL* 3.2 37.2 + - + -
284E VAL* 4.0 12.6 - - + -
285E MET 3.5 7.4 - - - +
321E TYR* 3.5 31.0 - - + +
322E VAL* 1.4 87.5 - - + +
324E VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E TYR* 3.5 36.1 - - + -
213E LEU 3.3 9.9 - - - +
214E PRO* 4.2 0.7 - - + -
215E VAL* 4.2 3.1 - - - +
262E ALA* 6.3 0.2 - - + -
284E VAL 3.7 0.7 - - - -
285E MET* 2.9 54.8 + - + +
287E LEU* 3.8 27.8 - - + -
322E VAL* 3.8 9.2 - - + +
323E PRO* 1.3 79.5 - - - +
325E VAL* 1.3 62.7 + - - +
326E ALA 3.6 17.3 - - - +
327E PHE* 4.9 4.0 - - + -
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Residues in contact with VAL 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E LEU* 3.0 28.9 + - + -
215E VAL* 4.4 14.6 - - + -
218E VAL* 3.7 24.7 - - + -
237E HIS* 3.7 30.5 - - + +
283E GLY 3.5 19.7 - - - +
284E VAL* 4.9 1.3 - - + -
324E VAL* 1.3 75.7 - - - +
326E ALA* 1.3 61.1 + - + +
353E GLN* 3.4 2.9 - - - +
354E VAL* 2.8 40.7 + - + +
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Residues in contact with ALA 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E TYR* 3.4 4.9 - - - +
213E LEU* 2.9 30.2 + - + -
237E HIS* 4.3 13.2 - - + -
238E LEU* 4.3 2.9 - - + -
249E TRP* 3.8 21.8 - - + -
324E VAL* 3.5 7.3 - - - +
325E VAL* 1.3 88.5 - - + +
327E PHE* 1.3 67.9 + - - +
352E GLY 3.1 14.6 - - - +
353E GLN* 4.4 1.6 - - - -
354E VAL* 5.3 0.2 - - - -
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Residues in contact with PHE 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E LEU* 4.0 28.0 - - + -
155E LEU* 3.8 16.6 - - + -
169E LEU* 3.3 35.4 - - + -
210E LEU* 4.7 7.2 - - + -
211E ALA 3.3 13.7 - - - +
212E TYR* 4.2 5.6 - - + -
249E TRP* 3.4 9.1 - - - -
260E VAL* 6.2 2.2 - - + -
262E ALA* 4.1 14.1 - - + -
285E MET* 4.3 11.9 - - - -
287E LEU* 4.9 10.3 - - + -
324E VAL* 4.9 3.6 - - + -
326E ALA* 1.3 80.1 - - - +
328E ARG* 1.3 69.4 + - - +
329E LEU* 4.3 7.9 - - + -
350E VAL 4.1 13.2 - - - -
351E GLN* 3.3 4.4 - - - +
352E GLY* 3.0 38.4 + - - +
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Residues in contact with ARG 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E ARG 3.8 0.7 - - - +
210E LEU* 3.4 5.4 - - - +
211E ALA* 2.8 35.7 + - + +
239E VAL* 3.3 21.0 + - - +
240E PRO 3.0 17.4 + - - -
241E LEU* 3.6 26.0 + - + +
243E GLU 2.7 31.7 + - - -
244E PRO* 3.9 2.4 - - - +
245E VAL* 3.6 32.4 - - + +
249E TRP* 3.3 13.8 - - + -
327E PHE* 1.3 76.8 - - - +
329E LEU* 1.3 66.9 + - - +
330E GLU* 3.5 27.3 + - + +
350E VAL 3.5 4.9 - - - +
351E GLN* 3.4 23.2 - - + +
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Residues in contact with LEU 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E LEU* 5.1 6.3 - - + -
171E TRP* 3.6 61.5 - - + -
209E ARG 3.4 18.4 - - - +
210E LEU* 4.1 21.5 - - + -
257E PHE* 5.4 0.2 - - + -
260E VAL* 4.2 13.0 - - + -
327E PHE* 4.3 10.3 - - + -
328E ARG* 1.3 77.0 - - - +
330E GLU* 1.3 57.4 + - - +
331E PRO* 3.7 6.7 - - + +
338E PHE* 3.7 18.5 - - + -
349E ALA* 3.5 1.4 - - - -
350E VAL* 2.7 43.0 + - + +
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Residues in contact with GLU 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E GLY* 4.2 0.7 - - - -
209E ARG* 2.8 75.3 + - + +
241E LEU* 5.1 2.4 - - - +
328E ARG* 3.5 32.7 + - + -
329E LEU* 1.3 72.3 - - - +
331E PRO* 1.3 61.8 - - - +
332E LYS* 3.2 8.9 - - + +
348E GLU 3.7 4.5 - - - +
349E ALA* 3.8 19.1 - - + +
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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