Contacts of the strand formed by residues 319 - 330 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259D LEU* 5.4 0.2 - - + -
288D PHE* 4.2 13.5 - - + -
289D TYR 3.5 7.9 - - - +
290D VAL* 3.7 25.5 - - + +
302D LEU* 4.4 30.5 - - + -
311D HIS* 4.6 10.1 - - + +
312D MET* 3.7 34.0 - - + +
316D CYS* 3.3 24.3 + - + +
317D PRO* 4.4 1.4 - - - +
318D TYR* 1.3 79.2 + - - +
320D VAL* 1.3 65.0 + - - +
321D TYR 4.4 0.3 + - - -
1001D UUL 4.1 22.0 - - + -
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Residues in contact with VAL 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D TYR* 5.5 0.4 - - - +
287D LEU 3.8 0.6 - - - +
288D PHE* 3.3 7.3 - - - +
289D TYR* 2.9 78.0 + - + +
291D ARG* 4.0 24.7 - - - +
317D PRO 4.9 2.5 - - - +
318D TYR 4.8 0.2 - - - -
319D LEU* 1.3 81.0 - - - +
321D TYR* 1.3 65.6 + - - +
322D VAL* 3.9 16.8 - - + -
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Residues in contact with TYR 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D MET* 3.5 33.0 - - + +
286D HIS* 2.8 50.7 - + + -
287D LEU 3.4 7.9 - - - -
288D PHE* 3.5 23.6 - + + -
312D MET* 3.8 23.7 - - + +
319D LEU 4.4 0.4 + - - -
320D VAL* 1.3 77.6 - - - +
322D VAL* 1.3 74.0 + - - +
323D PRO* 3.7 32.9 - - + +
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Residues in contact with VAL 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D TYR* 3.6 45.3 - - + +
214D PRO* 4.4 9.6 - - + -
287D LEU* 2.9 38.7 + - + +
289D TYR* 5.1 3.4 - - + -
320D VAL* 3.9 17.0 - - + -
321D TYR* 1.3 85.2 - - - +
323D PRO* 1.3 81.5 - - + +
324D VAL* 3.5 3.1 - - + +
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Residues in contact with PRO 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D PRO* 3.5 7.1 - - - +
215D VAL* 3.3 35.0 + - + +
284D VAL* 3.9 11.7 - - + -
285D MET 3.5 7.0 - - - +
321D TYR* 3.7 31.4 - - + +
322D VAL* 1.3 90.6 - - + +
324D VAL* 1.3 59.0 + - - +
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Residues in contact with VAL 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D TYR* 3.6 35.4 - - + -
213D LEU 3.5 9.4 - - - +
214D PRO* 4.3 0.4 - - - -
215D VAL* 4.3 1.5 - - - +
284D VAL* 3.6 4.3 - - - -
285D MET* 3.0 55.8 + - + +
287D LEU* 3.8 23.6 - - + -
322D VAL* 3.5 12.6 - - + +
323D PRO* 1.3 80.6 - - - +
325D VAL* 1.3 64.0 + - - +
326D ALA 3.8 17.9 - - - +
327D PHE* 5.0 3.6 - - + -
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Residues in contact with VAL 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D LEU* 2.9 22.2 + - + +
215D VAL* 4.3 18.2 - - + -
218D VAL* 3.7 32.5 - - + -
237D HIS* 3.8 24.5 - - + +
283D GLY 3.3 24.7 - - - +
284D VAL* 4.8 2.0 - - + -
324D VAL* 1.3 77.2 - - - +
326D ALA* 1.3 61.2 + - + +
353D GLN* 3.1 4.2 - - - +
354D VAL* 2.8 36.1 + - + +
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Residues in contact with ALA 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D TYR* 3.3 5.5 - - - +
213D LEU* 2.8 28.3 + - + -
237D HIS* 4.3 6.1 - - + -
238D LEU* 4.0 2.7 - - + -
249D TRP* 3.8 24.0 - - + -
285D MET* 6.0 0.4 - - - -
324D VAL* 3.6 6.5 - - - +
325D VAL* 1.3 91.4 - - + +
327D PHE* 1.3 62.3 + - - +
352D GLY 3.1 15.3 - - - +
353D GLN* 3.9 10.3 - - + +
354D VAL* 5.7 0.2 - - - -
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Residues in contact with PHE 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D LEU* 4.2 9.4 - - + -
155D LEU* 3.8 21.8 - - + -
169D LEU* 3.6 33.2 - - + -
210D LEU* 4.7 8.5 - - + -
211D ALA 3.2 13.5 - - - +
212D TYR* 4.2 6.1 - - + -
249D TRP* 3.5 9.0 - - - -
260D VAL* 5.7 1.8 - - + -
262D ALA* 4.2 21.3 - - + -
285D MET* 4.8 7.2 - - - -
287D LEU* 4.8 13.7 - - + -
324D VAL* 5.0 2.9 - - + -
326D ALA* 1.3 77.4 - - - +
328D ARG* 1.3 70.6 + - - +
329D LEU* 4.4 10.5 - - + -
350D VAL* 4.3 13.5 - - + -
351D GLN* 3.2 6.0 - - - +
352D GLY* 2.9 49.0 + - - +
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Residues in contact with ARG 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D ARG 4.3 1.1 - - - +
210D LEU* 3.4 6.1 - - - +
211D ALA* 2.8 35.0 + - + +
239D VAL* 3.1 28.3 + - - +
240D PRO 3.4 3.4 + - - -
241D LEU* 3.7 27.9 + - + +
243D GLU 2.5 31.5 + - - -
244D PRO* 4.0 1.8 - - - +
245D VAL* 3.6 25.8 - - + +
249D TRP* 3.6 8.5 - - + -
327D PHE* 1.3 76.7 - - - +
329D LEU* 1.3 69.8 + - - +
330D GLU* 4.0 22.5 + - + +
350D VAL 3.5 11.0 - - - +
351D GLN* 2.8 32.6 - - + +
13E ARG 5.4 2.0 + - - -
14E PRO* 5.4 2.2 - - - +
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Residues in contact with LEU 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D LEU* 5.0 5.4 - - + -
171D TRP* 3.6 59.5 - - + -
208D GLY 5.0 0.4 - - - -
209D ARG 3.4 23.3 - - - +
210D LEU* 4.0 18.2 - - + -
257D PHE* 5.3 0.4 - - + -
260D VAL* 3.9 16.4 - - + -
327D PHE* 4.4 11.7 - - + -
328D ARG* 1.3 78.0 - - - +
330D GLU* 1.3 63.4 + - - +
331D PRO* 3.4 8.9 - - + +
338D PHE* 3.9 14.7 - - + -
349D ALA* 3.6 1.6 - - - +
350D VAL* 2.9 36.1 + - + +
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Residues in contact with GLU 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D GLY* 3.2 3.9 - - - -
209D ARG* 2.8 61.8 + - + +
241D LEU* 5.4 3.8 - - - +
328D ARG* 4.0 24.6 + - + -
329D LEU* 1.3 75.0 - - - +
331D PRO* 1.4 63.3 - - - +
332D LYS* 3.3 9.0 - - + +
348D GLU 4.3 2.9 - - - +
349D ALA* 4.2 16.8 - - + -
13E ARG* 5.4 4.3 - - - +
14E PRO* 5.6 4.0 - - - +
46E GLU* 4.5 16.6 - - - +
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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