Contacts of the strand formed by residues 319 - 330 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288C PHE* 4.0 19.5 - - + -
289C TYR 3.4 11.0 - - - +
290C VAL* 4.0 18.3 - - + +
302C LEU* 4.2 27.6 - - + -
311C HIS* 4.3 23.1 - - + +
312C MET* 4.4 16.1 - - + +
315C GLU* 6.0 0.2 - - - -
316C CYS* 3.1 31.4 + - + +
317C PRO 4.6 1.1 - - - +
318C TYR* 1.3 75.1 - - - +
320C VAL* 1.3 76.9 + - - +
321C TYR 4.2 0.7 + - - -
1001C UUL 4.4 8.3 - - + -
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Residues in contact with VAL 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C TYR* 5.5 0.2 - - - +
287C LEU 4.5 0.2 - - - -
288C PHE* 3.4 5.0 - - - -
289C TYR* 2.8 82.8 + - + +
291C ARG* 3.6 23.8 - - - +
317C PRO 4.6 1.1 - - - +
318C TYR 4.3 0.9 - - - +
319C LEU* 1.3 83.0 - - - +
321C TYR* 1.3 63.1 + - - +
322C VAL* 3.9 19.5 - - + -
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Residues in contact with TYR 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C MET* 3.7 31.8 - - + +
286C HIS* 2.9 50.1 - + + -
287C LEU 3.4 10.8 - - - -
288C PHE* 3.6 20.4 - + + -
312C MET* 3.7 23.1 - - + -
319C LEU 4.2 1.2 + - - -
320C VAL* 1.3 76.7 - - - +
322C VAL* 1.3 74.9 + - - +
323C PRO* 3.3 35.4 - - + +
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Residues in contact with VAL 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C TYR* 3.5 43.5 - - + +
214C PRO* 3.8 11.4 - - + -
287C LEU* 3.0 38.7 + - + +
289C TYR* 5.3 1.8 - - + -
320C VAL* 3.9 17.3 - - + -
321C TYR* 1.3 84.1 - - - +
323C PRO* 1.4 82.0 - - + +
324C VAL* 3.4 3.3 - - + +
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Residues in contact with PRO 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C PRO* 3.4 6.1 - - - +
215C VAL* 3.1 38.1 + - + +
284C VAL* 3.9 11.7 - - + -
285C MET 3.6 7.0 - - - +
321C TYR* 3.3 33.4 - - + +
322C VAL* 1.4 87.5 - - + +
324C VAL* 1.3 60.0 + - - +
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Residues in contact with VAL 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C TYR* 3.6 29.6 - - + -
213C LEU 3.5 10.3 - - - +
214C PRO* 4.1 0.7 - - - -
215C VAL* 3.8 2.0 - - - +
284C VAL* 3.6 6.1 - - - -
285C MET* 2.8 58.6 + - + +
287C LEU* 3.7 22.7 - - + -
322C VAL* 3.4 15.0 - - + +
323C PRO* 1.3 79.0 - - - +
325C VAL* 1.3 65.8 + - - +
326C ALA 3.8 18.8 - - - +
327C PHE* 5.0 1.1 - - + -
354C VAL* 4.0 0.3 - - - +
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Residues in contact with VAL 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C LEU* 3.0 41.4 + - + +
214C PRO 4.8 1.1 - - - +
215C VAL* 4.5 23.1 - - + +
237C HIS* 4.2 19.3 - - + +
283C GLY 3.6 18.4 - - - +
284C VAL* 5.4 1.3 - - + -
324C VAL* 1.3 75.7 - - - +
326C ALA* 1.3 65.1 + - + +
353C GLN* 3.4 5.9 - - + +
354C VAL* 3.0 38.0 + - + +
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Residues in contact with ALA 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C TYR* 3.4 3.5 - - - +
213C LEU* 3.0 24.9 + - + -
237C HIS* 4.3 8.7 - - + -
238C LEU* 4.0 6.7 - - + -
249C TRP* 3.7 26.0 - - + -
285C MET* 5.6 0.4 - - - -
324C VAL* 3.6 8.2 - - - +
325C VAL* 1.3 91.5 - - + +
327C PHE* 1.3 67.2 + - - +
352C GLY 3.1 14.8 - - - +
353C GLN* 4.4 1.1 - - - -
354C VAL* 5.4 0.4 - - - -
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Residues in contact with PHE 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C LEU* 4.1 6.1 - - + -
155C LEU* 3.9 17.5 - - + -
169C LEU* 3.8 32.8 - - + -
210C LEU* 4.7 5.2 - - + -
211C ALA 3.3 13.0 - - - +
212C TYR* 3.9 9.0 - - + +
249C TRP* 3.7 7.6 - - - -
260C VAL* 5.8 2.0 - - + -
262C ALA* 3.9 8.3 - - + -
285C MET* 3.3 35.2 - - + -
287C LEU* 4.6 15.7 - - + -
324C VAL* 5.0 0.7 - - + -
326C ALA* 1.3 75.6 - - - +
328C ARG* 1.3 71.0 + - - +
329C LEU* 4.2 9.9 - - + -
350C VAL* 4.1 14.4 - - + -
351C GLN* 3.1 7.9 - - - +
352C GLY* 3.0 45.3 + - - +
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Residues in contact with ARG 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C ARG 3.5 3.3 - - - +
210C LEU* 3.5 2.3 - - - +
211C ALA* 2.7 42.0 + - + +
239C VAL* 2.8 37.0 + - - +
240C PRO 3.0 12.5 + - - -
241C LEU* 3.7 27.6 + - + +
243C GLU 2.9 21.4 + - - -
244C PRO* 3.9 10.5 - - - +
245C VAL* 3.7 21.6 - - + +
249C TRP* 4.1 9.0 - - + -
327C PHE* 1.3 78.2 - - - +
329C LEU* 1.3 63.7 + - - +
330C GLU* 3.6 27.6 + - + +
350C VAL 3.5 5.4 - - - +
351C GLN* 2.9 28.7 - - + +
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Residues in contact with LEU 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C LEU* 4.8 6.7 - - + -
171C TRP* 3.8 45.8 - - + -
208C GLY 4.9 1.1 - - - -
209C ARG 3.7 14.4 - - - +
210C LEU* 4.2 13.2 - - + -
257C PHE* 5.3 0.7 - - + -
260C VAL* 3.6 38.6 - - + -
327C PHE* 4.2 10.7 - - + -
328C ARG* 1.3 74.5 - - - +
330C GLU* 1.3 68.1 + - - +
331C PRO* 4.1 3.5 - - + +
338C PHE* 4.1 16.5 - - + -
349C ALA* 3.7 1.7 - - - -
350C VAL 2.7 37.9 + - - +
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Residues in contact with GLU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C GLY* 3.2 2.8 - - - -
209C ARG* 2.8 74.7 + - - +
241C LEU* 5.2 4.5 - - - +
328C ARG* 3.6 33.9 + - + -
329C LEU* 1.3 78.0 - - - +
331C PRO* 1.3 64.7 - - - +
348C GLU 3.8 9.4 - - - +
349C ALA* 4.3 12.0 - - + +
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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