Contacts of the helix formed by residues 304 - 319 (chain B) in PDB entry 1VDV
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 ALA 304 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302B ALA 3.3 4.4 + - - +
303B CYS* 1.3 76.0 - - - +
305B LEU* 1.3 67.1 + - - +
306B SER* 3.8 13.0 - - - +
307B SER* 2.9 23.9 + - - +
308B VAL* 3.0 10.6 + - - +
343B LYS 3.8 2.5 - - - +
344B SER 3.6 24.9 - - - +
345B VAL* 4.5 3.4 - - - +
346B ALA 3.1 10.8 - - - +
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ALA* 1.3 72.1 - - - +
306B SER* 1.3 56.5 + - - +
308B VAL* 3.2 7.2 + - + +
309B GLU* 2.8 30.4 + - - +
334B LEU* 3.9 15.7 - - + +
337B PHE* 3.4 47.8 - - + -
343B LYS* 3.3 16.9 + - + +
346B ALA* 2.8 35.2 + - + +
347B SER 4.3 2.7 - - - +
348B LEU* 4.0 28.9 - - + +
361B LEU* 3.8 21.8 - - + -
4005B FAD 4.3 3.1 - - - +
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Residues in contact with SER 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 6.1 0.2 - - - +
304B ALA* 3.8 6.6 - - - +
305B LEU* 1.3 77.8 - - - +
307B SER* 1.3 60.7 + - - +
309B GLU* 3.3 14.8 + - - +
310B LYS* 3.0 27.9 + - - +
343B LYS* 2.9 27.3 + - - -
344B SER* 3.4 20.8 + - - -
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Residues in contact with SER 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLN* 5.6 4.7 + - - -
299B PHE* 4.9 1.8 - - - -
303B CYS* 4.8 9.2 - - - -
304B ALA* 2.9 24.9 + - - +
306B SER* 1.3 78.0 + - - +
308B VAL* 1.3 65.8 + - - +
310B LYS* 3.8 6.0 - - - +
311B THR* 3.0 29.7 + - - -
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Residues in contact with VAL 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PHE* 3.8 29.8 - - + -
303B CYS* 4.3 4.9 - - + -
304B ALA 3.0 14.2 + - - +
305B LEU* 3.4 11.2 - - + +
307B SER* 1.3 76.0 - - - +
309B GLU* 1.3 63.6 + - - +
311B THR* 3.8 1.0 - - - -
312B LEU* 3.0 42.9 + - + +
330B VAL* 4.7 2.9 - - + -
334B LEU* 4.5 9.6 - - + -
348B LEU* 3.6 38.8 - - + -
409B ILE* 4.4 8.3 - - + -
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Residues in contact with GLU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU 2.8 17.1 + - - +
306B SER* 3.5 13.8 - - - +
308B VAL* 1.3 78.3 - - - +
310B LYS* 1.3 56.6 + - - +
313B LEU* 3.0 47.4 + - + +
331B LEU* 3.7 18.9 - - + +
334B LEU* 3.8 30.1 - - + +
335B ARG* 4.4 3.8 + - - -
340B LYS* 4.2 17.1 + - - +
343B LYS* 3.8 24.4 + - - +
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Residues in contact with LYS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLN* 5.1 9.1 + - - -
306B SER 3.0 16.5 + - - +
307B SER* 3.3 6.9 + - - +
309B GLU* 1.3 75.4 - - - +
311B THR* 1.3 64.5 + - - +
313B LEU* 3.3 9.9 + - - +
314B GLU* 3.0 51.5 + - + +
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Residues in contact with THR 311 (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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290B VAL* 4.1 21.6 - - + +
292B HIS* 4.1 20.5 - - + +
297B ILE* 4.3 3.8 - - + -
299B PHE* 3.6 31.6 - - + -
307B SER* 3.0 18.0 + - - -
310B LYS* 1.3 76.3 - - - +
312B LEU* 1.3 59.8 + - - +
314B GLU* 3.3 15.6 + - - +
315B ALA* 3.0 24.4 + - - +
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Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ILE* 4.3 8.3 - - + -
299B PHE* 4.0 19.3 - - + -
308B VAL* 3.0 31.7 + - + +
311B THR* 1.3 73.5 - - - +
313B LEU* 1.3 61.3 + - - +
315B ALA* 3.1 3.2 + - - +
316B VAL* 2.9 34.1 + - - +
327B PHE* 3.8 42.2 - - + +
330B VAL* 3.6 37.7 - - + -
331B LEU* 3.9 18.6 - - + -
334B LEU* 5.2 0.2 - - + -
409B ILE* 4.1 7.9 - - + -
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B GLU* 3.0 39.6 + - + +
310B LYS* 3.7 8.7 - - - +
312B LEU* 1.3 76.0 - - - +
314B GLU* 1.3 63.6 + - + +
316B VAL* 3.3 6.3 + - + +
317B ALA* 3.1 22.7 + - - +
331B LEU* 3.6 27.1 - - + -
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LYS* 3.0 43.5 + - + +
311B THR* 3.6 14.5 + - - +
313B LEU* 1.3 77.2 - - + +
315B ALA* 1.3 61.8 + - - +
317B ALA* 3.4 6.1 + - - +
318B LYS* 3.1 54.9 + - - +
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B HIS* 5.6 2.2 - - + -
297B ILE* 3.9 25.8 - - + -
311B THR 3.0 13.8 + - - +
312B LEU* 3.1 9.8 + - - +
314B GLU* 1.3 77.7 - - - +
316B VAL* 1.3 58.7 + - - +
318B LYS* 4.9 2.5 - - - -
319B LEU* 2.9 45.5 + - + +
324B THR* 4.3 2.0 - - - -
327B PHE* 4.0 15.0 - - + -
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Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU 2.9 20.3 + - - +
313B LEU* 3.3 7.4 + - + +
315B ALA* 1.3 75.1 - - - +
317B ALA* 1.3 60.0 + - - +
319B LEU 3.7 12.5 - - - +
321B THR* 6.0 0.5 - - - -
324B THR* 3.9 18.5 + - - +
327B PHE* 4.0 9.6 - - + -
328B ARG* 3.4 37.2 - - + +
331B LEU* 3.7 18.6 - - + -
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU 3.1 16.2 + - - +
314B GLU* 3.8 7.6 - - - +
315B ALA 3.2 0.2 - - - -
316B VAL* 1.3 79.7 - - - +
318B LYS* 1.3 62.2 + - + +
319B LEU 4.8 1.1 - - - +
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Residues in contact with LYS 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU* 3.1 42.0 + - - +
315B ALA* 4.2 2.5 - - - +
317B ALA* 1.3 83.1 - - + +
319B LEU* 1.3 68.5 + - + +
320B PRO* 4.3 1.9 - - - +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ILE* 5.4 0.9 - - + -
315B ALA* 2.9 34.8 + - + +
316B VAL 3.7 14.2 - - - +
317B ALA 4.8 1.0 - - - +
318B LYS* 1.3 86.9 - - + +
320B PRO* 1.3 79.6 - - + +
321B THR* 3.5 1.9 + - - -
323B LYS* 4.8 10.1 - - + -
324B THR* 4.0 10.7 - - + +
327B PHE* 4.4 3.8 - - + -
411B TYR* 3.5 38.8 - - + +
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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
------------------------------------------------------------
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