Contacts of the strand formed by residues 319 - 330 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B PHE* 4.2 11.4 - - + -
289B TYR 3.6 5.2 - - - +
290B VAL* 3.9 22.6 - - + +
302B LEU* 4.2 19.5 - - + -
311B HIS* 3.9 37.0 - - + +
312B MET* 4.4 13.2 - - - -
315B GLU* 5.0 9.7 - - - +
316B CYS* 3.0 29.4 + - + +
317B PRO 4.4 0.2 - - - +
318B TYR* 1.3 77.3 - - - +
320B VAL* 1.3 65.3 + - - +
321B TYR* 4.4 0.4 + - + -
1001B UUL 4.0 24.7 - - + -
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Residues in contact with VAL 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B TYR* 5.8 0.4 - - - +
287B LEU 3.9 0.2 - - - +
288B PHE* 3.3 9.9 - - - +
289B TYR* 2.8 80.2 + - + +
291B ARG* 4.5 5.8 - - - +
317B PRO 4.0 15.5 - - - +
318B TYR 4.1 3.4 - - - +
319B LEU* 1.3 80.5 - - - +
321B TYR* 1.3 67.4 + - - +
322B VAL* 4.2 12.6 - - + -
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Residues in contact with TYR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B MET* 3.4 34.7 - - + +
286B HIS* 2.9 45.7 + + + -
287B LEU 3.4 9.9 - - - -
288B PHE* 3.6 21.8 - + + -
312B MET* 4.0 15.7 - - + -
319B LEU* 4.4 0.6 + - + -
320B VAL* 1.3 77.9 - - - +
322B VAL* 1.3 76.9 + - - +
323B PRO* 3.7 35.3 - - + +
149D PRO* 5.6 2.5 - - + -
357D ASN* 5.2 4.5 + - - -
360D TRP* 4.1 24.3 - + + -
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B TYR* 3.8 44.4 - - + +
214B PRO* 4.2 8.5 - - + -
287B LEU* 2.8 41.9 + - + +
289B TYR* 4.9 3.4 - - + -
320B VAL* 4.2 15.0 - - + -
321B TYR* 1.3 85.1 - - - +
323B PRO* 1.3 83.7 - - + +
324B VAL* 4.0 8.5 - - + -
102D GLN* 6.2 2.2 - - - +
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Residues in contact with PRO 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B PRO* 3.5 4.2 - - - +
215B VAL* 3.1 38.6 + - + -
284B VAL* 4.1 10.3 - - + -
285B MET 3.6 6.7 - - - +
321B TYR* 3.7 28.5 - - + +
322B VAL* 1.3 90.8 - - + +
324B VAL* 1.3 62.4 + - - +
102D GLN* 6.1 2.2 - - - +
357D ASN* 5.2 15.3 - - + +
360D TRP* 6.3 0.9 - - + -
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Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B TYR* 3.8 35.9 - - + -
213B LEU 3.4 10.1 - - - +
214B PRO* 4.1 1.6 - - + -
215B VAL* 4.1 2.2 - - - +
284B VAL* 3.7 4.2 - - - -
285B MET* 2.9 62.2 + - + +
287B LEU* 3.9 22.0 - - + -
322B VAL* 4.0 12.1 - - + +
323B PRO* 1.3 79.7 - - - +
325B VAL* 1.3 64.1 + - - +
326B ALA 3.8 13.5 - - - +
327B PHE* 5.1 3.1 - - + -
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Residues in contact with VAL 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LEU* 2.9 41.5 + - + +
214B PRO 4.6 2.5 - - - +
215B VAL* 4.5 21.1 - - + +
218B VAL 5.4 4.7 - - - +
237B HIS* 4.3 19.5 - - + +
283B GLY 3.3 20.2 - - - +
284B VAL* 4.9 2.0 - - + -
285B MET* 5.3 0.2 - - - -
324B VAL* 1.3 76.3 - - - +
326B ALA* 1.3 60.1 + - + +
353B GLN* 3.3 5.9 - - - +
354B VAL* 2.8 41.0 + - + +
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B TYR* 3.5 3.6 - - - +
213B LEU* 2.9 29.6 + - + +
237B HIS* 4.2 14.6 - - + -
238B LEU* 4.0 6.7 - - + -
249B TRP* 3.9 22.9 - - + -
285B MET* 5.8 0.9 - - - -
324B VAL* 3.7 6.5 - - - +
325B VAL* 1.3 80.5 - - + +
327B PHE* 1.3 67.6 + - - +
352B GLY 3.1 15.0 - - - +
353B GLN* 4.2 1.8 - - - -
354B VAL* 5.5 0.2 - - - -
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Residues in contact with PHE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LEU* 4.1 11.7 - - + -
155B LEU* 4.0 12.8 - - + -
169B LEU* 3.4 35.0 - - + -
210B LEU* 4.9 9.0 - - + -
211B ALA 3.3 12.3 - - - +
212B TYR* 4.2 6.7 - - + -
249B TRP* 3.8 10.1 - - - -
260B VAL* 5.7 2.7 - - + -
262B ALA* 4.3 7.2 - - + -
285B MET* 3.8 30.3 - - + -
287B LEU* 5.0 10.5 - - + -
324B VAL* 5.1 3.1 - - + -
326B ALA* 1.3 78.3 - - - +
328B ARG* 1.3 69.6 + - - +
329B LEU* 4.6 15.0 - - + -
350B VAL* 4.7 6.5 - - + -
351B GLN* 3.2 6.4 - - - +
352B GLY* 2.9 47.1 + - - +
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Residues in contact with ARG 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ARG 3.5 1.4 - - - +
210B LEU* 3.5 3.8 - - - +
211B ALA* 2.7 44.1 + - + +
239B VAL* 3.5 13.3 + - - +
240B PRO 3.4 14.8 + - - -
241B LEU* 3.4 25.0 + - + +
243B GLU 3.1 27.5 + - - -
244B PRO* 4.4 1.8 - - - +
245B VAL* 3.7 28.1 - - + +
249B TRP* 4.2 9.0 - - + -
327B PHE* 1.3 79.1 - - - +
329B LEU* 1.3 63.9 - - - +
330B GLU* 3.6 36.7 + - + -
350B VAL 3.5 13.2 - - - +
351B GLN* 3.1 30.1 - - + +
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Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LEU* 4.8 8.1 - - + -
171B TRP* 3.5 61.2 - - + -
208B GLY 5.1 0.2 - - - -
209B ARG 3.4 18.6 - - - +
210B LEU* 4.2 9.6 - - + -
260B VAL* 4.0 25.8 - - + -
327B PHE* 4.4 10.3 - - + -
328B ARG* 1.3 75.1 - - - +
330B GLU* 1.3 64.5 + - - +
331B PRO* 4.2 4.2 - - + +
338B PHE* 3.8 16.1 - - + -
349B ALA* 3.5 1.6 - - - -
350B VAL* 2.9 36.6 + - + +
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Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLY* 4.2 0.2 - - - -
209B ARG* 2.8 59.5 + - + +
241B LEU* 5.6 2.2 - - - -
328B ARG* 3.6 37.8 + - + -
329B LEU* 1.3 76.3 - - - +
331B PRO* 1.3 64.3 - - - +
332B LYS* 3.2 8.4 + - - +
348B GLU 3.8 4.3 - - - +
349B ALA* 3.8 17.3 - - + +
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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