Contacts of the strand formed by residues 319 - 330 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A PHE* 4.3 12.1 - - + -
289A TYR 3.5 9.6 - - - +
290A VAL* 3.6 24.0 - - + -
302A LEU* 4.4 30.1 - - + -
311A HIS* 4.3 16.4 - - + +
312A MET* 3.7 38.1 - - + +
316A CYS* 3.3 23.6 + - + +
317A PRO* 3.4 2.1 - - - +
318A TYR* 1.3 78.2 - - - +
320A VAL* 1.3 64.8 + - - +
1001A UUL 4.2 20.4 - - + -
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Residues in contact with VAL 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TYR* 5.5 0.7 - - - +
287A LEU 3.6 0.7 - - - +
288A PHE* 3.2 8.1 - - - +
289A TYR* 2.8 83.8 + - + +
291A ARG* 4.5 15.7 - - + -
317A PRO 4.7 5.6 - - - +
319A LEU* 1.3 80.5 - - - +
321A TYR* 1.3 63.9 + - - +
322A VAL* 4.0 17.5 - - + -
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Residues in contact with TYR 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A MET* 3.6 31.5 - - + +
286A HIS* 2.7 51.6 + + + -
287A LEU 3.3 6.3 - - - -
288A PHE* 3.6 21.8 - + + -
312A MET* 3.9 23.6 - - + +
319A LEU 4.3 1.0 + - - -
320A VAL* 1.3 75.2 - - - +
322A VAL* 1.3 75.0 + - - +
323A PRO* 3.8 35.8 - - + +
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TYR* 3.6 44.0 - - + +
214A PRO* 4.5 8.3 - - + -
287A LEU* 2.9 39.3 + - + +
289A TYR* 5.3 2.0 - - + -
320A VAL* 4.0 15.5 - - + -
321A TYR* 1.3 85.4 - - - +
323A PRO* 1.3 83.9 - - + +
324A VAL* 4.0 3.6 - - + -
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Residues in contact with PRO 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A PRO* 4.2 0.3 - - - +
215A VAL* 3.4 34.8 + - + +
284A VAL* 3.9 10.5 - - + -
285A MET 3.5 7.6 - - - +
321A TYR* 3.8 30.7 - - + +
322A VAL* 1.3 94.2 - - + +
324A VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TYR* 3.4 37.0 - - + -
213A LEU 3.3 11.0 - - - +
214A PRO* 4.2 0.7 - - - -
215A VAL* 4.2 0.9 - - - +
284A VAL* 3.6 4.2 - - - -
285A MET* 2.9 57.1 + - + +
287A LEU* 3.9 23.1 - - + -
322A VAL* 3.7 11.2 - - + +
323A PRO* 1.3 80.6 - - - +
325A VAL* 1.3 65.3 + - - +
326A ALA 3.8 16.4 - - - +
327A PHE* 5.0 2.2 - - + -
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Residues in contact with VAL 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU* 2.9 40.0 + - + +
215A VAL* 4.5 7.4 - - - -
217A ARG* 3.4 35.9 - - - +
237A HIS* 4.0 20.8 + - + +
283A GLY 3.4 23.1 - - - +
284A VAL* 4.7 4.5 - - + -
285A MET* 5.4 0.2 - - - -
324A VAL* 1.3 77.9 - - - +
326A ALA* 1.3 61.9 + - + +
353A GLN* 3.2 5.0 - - - +
354A VAL* 2.9 35.3 + - - +
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A TYR* 3.4 4.0 - - - +
213A LEU* 2.8 33.9 + - + -
237A HIS* 4.3 5.6 - - + -
238A LEU* 4.1 2.7 - - + -
249A TRP* 3.9 23.6 - - + -
285A MET* 5.8 0.4 - - - -
324A VAL* 3.6 6.4 - - - +
325A VAL* 1.3 88.3 - - + +
327A PHE* 1.3 62.4 + - - +
352A GLY 3.1 15.5 - - - +
353A GLN* 3.8 9.9 - - + +
354A VAL* 5.6 0.2 - - - -
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Residues in contact with PHE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 4.4 8.3 - - + -
155A LEU* 3.8 27.1 - - + -
169A LEU* 3.9 28.3 - - + -
210A LEU* 4.6 8.3 - - + -
211A ALA 3.2 13.0 - - - +
212A TYR* 4.1 7.6 - - + -
249A TRP* 3.6 10.1 - - - -
260A VAL* 6.0 1.6 - - + -
262A ALA* 4.2 20.2 - - + -
285A MET* 4.6 9.2 - - - -
287A LEU* 4.8 12.6 - - + -
324A VAL* 5.0 2.0 - - + -
326A ALA* 1.3 76.6 - - - +
328A ARG* 1.3 70.1 + - - +
329A LEU* 4.2 10.5 - - + -
350A VAL* 4.2 17.3 - - + -
351A GLN* 3.2 6.3 - - - +
352A GLY* 3.0 46.2 + - - +
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Residues in contact with ARG 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ARG 4.2 1.3 - - - +
210A LEU* 3.4 6.9 - - - +
211A ALA* 2.7 37.9 + - + +
239A VAL* 3.2 27.5 + - - +
240A PRO 3.2 11.3 + - - -
241A LEU* 3.5 26.0 + - + +
243A GLU 2.6 24.4 + - - -
244A PRO* 3.8 2.0 - - - +
245A VAL* 3.5 35.9 - - + +
249A TRP* 4.2 0.4 - - + -
327A PHE* 1.3 77.4 - - - +
329A LEU* 1.3 68.6 + - - +
330A GLU* 4.9 14.3 + - + +
350A VAL 3.5 10.8 - - - +
351A GLN* 2.9 34.7 - - + +
13B ARG 5.2 2.0 + - - -
14B PRO* 5.3 2.4 - - - +
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Residues in contact with LEU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 4.7 7.2 - - + -
171A TRP* 3.7 59.7 - - + -
208A GLY 4.9 0.4 - - - -
209A ARG 3.2 16.8 - - - +
210A LEU* 4.4 12.8 - - + -
257A PHE* 5.4 0.4 - - + -
260A VAL* 4.0 18.8 - - + -
327A PHE* 4.4 11.2 - - + -
328A ARG* 1.3 77.9 - - - +
330A GLU* 1.3 67.8 + - - +
331A PRO* 3.9 2.9 - - + +
338A PHE* 3.8 17.4 - - + -
349A ALA* 3.6 2.4 - - - +
350A VAL* 2.8 36.0 + - + +
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Residues in contact with GLU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A GLY* 3.3 2.6 - - - -
209A ARG* 2.7 59.0 + - + +
241A LEU* 5.2 5.2 - - - +
328A ARG* 5.0 14.3 + - + -
329A LEU* 1.3 77.9 - - - +
331A PRO* 1.3 65.9 - - - +
332A LYS* 3.6 6.5 + - - +
348A GLU 3.6 15.7 - - - +
349A ALA* 3.9 12.5 - - + +
46B GLU* 4.4 14.1 - - - +
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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