Contacts of the helix formed by residues 313 - 326 (chain B) in PDB entry 5VBL
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 ASP 313 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B ARG* 2.9 32.0 + - - -
68B ILE* 5.1 2.9 - - - +
249B ILE* 3.4 21.8 - - + +
309B TYR* 2.9 44.5 + - + +
312B PHE* 1.3 74.8 - - - +
314B PRO* 1.4 63.4 - - - +
315B ARG* 3.0 19.4 + - - +
316B PHE* 2.8 33.7 + - + -
317B ARG* 3.4 17.4 + - - -
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Residues in contact with PRO 314 (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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62B ARG* 5.8 0.2 - - - +
245B ARG* 3.7 33.2 - - + +
249B ILE* 4.4 7.6 - - + -
312B PHE 3.4 9.2 - - - +
313B ASP* 1.4 85.1 - - - +
315B ARG* 1.4 60.0 + - + +
316B PHE 3.4 0.2 - - - -
317B ARG* 3.4 21.9 - - + +
318B GLN* 3.0 43.4 + - + +
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Residues in contact with ARG 315 (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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52B THR 5.7 1.4 + - - -
53B VAL* 6.2 2.2 - - - +
56B SER* 3.2 28.2 + - - -
60B LYS* 2.8 32.7 + - - +
61B ARG* 4.7 0.8 - - - +
62B ARG* 3.5 33.8 - - - +
65B ASP* 3.4 24.0 + - - -
313B ASP* 3.0 9.3 + - - +
314B PRO* 1.4 77.7 - - + +
316B PHE* 1.4 59.7 + - - +
318B GLN* 4.0 7.9 + - + +
319B ALA* 3.1 30.0 + - + +
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Residues in contact with PHE 316 (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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48B LEU* 4.0 14.6 - - + -
49B VAL* 3.7 43.1 - - + -
52B THR* 3.6 17.7 - - + -
53B VAL* 6.4 0.2 - - + -
62B ARG* 4.9 1.3 - - - +
306B PRO* 3.7 23.8 - - + -
309B TYR* 3.6 26.9 - + + -
310B ALA* 3.9 9.9 - - + -
313B ASP* 2.8 30.9 + - + +
315B ARG* 1.4 68.7 - - - +
317B ARG* 1.4 61.1 + - - +
319B ALA* 3.4 5.3 + - - +
320B CYS* 3.1 57.6 + - - -
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Residues in contact with ARG 317 (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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310B ALA* 3.3 29.8 + - + +
311B PHE* 3.6 18.0 + - - -
312B PHE* 3.5 25.1 + - - +
313B ASP 3.4 9.8 + - - +
314B PRO* 3.4 26.4 - - + +
316B PHE* 1.4 81.1 - - - +
318B GLN* 1.4 59.7 + - + +
320B CYS* 3.9 4.4 - - - +
321B THR* 3.0 34.1 + - + +
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Residues in contact with GLN 318 (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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314B PRO* 3.0 29.5 + - + +
315B ARG* 4.1 8.1 + - + +
317B ARG* 1.4 74.9 - - + +
319B ALA* 1.4 57.8 + - - +
321B THR* 3.0 17.7 + - - +
322B SER* 3.2 18.0 + - - -
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Residues in contact with ALA 319 (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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51B TRP* 5.9 1.2 - - - -
52B THR* 3.8 33.6 - - + +
55B ARG* 4.3 17.2 + - - +
56B SER* 6.4 0.7 - - - -
315B ARG* 3.1 20.7 + - + +
316B PHE* 3.8 1.6 - - - +
317B ARG 3.4 0.2 - - - -
318B GLN* 1.4 74.6 - - - +
320B CYS* 1.4 62.7 + - - +
322B SER* 3.5 18.4 + - - -
323B MET* 3.5 10.6 + - - +
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Residues in contact with CYS 320 (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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48B LEU* 3.8 24.2 - - + -
52B THR* 3.8 14.8 - - - -
316B PHE* 3.1 53.9 + - - +
317B ARG* 3.9 6.1 - - - +
318B GLN 3.4 0.2 - - - -
319B ALA* 1.4 74.2 - - - +
321B THR* 1.3 64.3 + - + +
323B MET* 3.6 6.7 + - - +
324B LEU* 3.4 19.6 + - - +
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Residues in contact with THR 321 (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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317B ARG* 3.0 20.0 + - + +
318B GLN* 3.0 17.7 + - - +
320B CYS* 1.3 75.2 - - + +
322B SER* 1.4 62.4 + - - +
323B MET 3.4 0.2 - - - -
324B LEU* 3.4 31.6 + - + +
325B LEU* 3.4 21.0 - - - +
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Residues in contact with SER 322 (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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55B ARG* 3.7 24.7 + - - -
318B GLN 3.2 17.2 + - - -
319B ALA* 3.5 10.1 - - - -
320B CYS 3.3 0.4 - - - -
321B THR* 1.4 78.6 - - - +
323B MET* 1.4 57.8 + - - +
324B LEU 3.3 1.0 + - - -
325B LEU* 3.9 10.2 - - - +
326B MET* 3.6 25.6 + - - +
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Residues in contact with MET 323 (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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51B TRP* 3.5 45.3 - - + +
55B ARG* 3.5 22.4 - - - +
319B ALA 3.5 8.7 + - - +
320B CYS* 3.6 6.4 + - - +
322B SER* 1.4 75.9 - - - +
324B LEU* 1.4 57.1 - - - +
325B LEU 3.7 0.2 - - - -
326B MET* 5.2 1.1 - - + -
327B GLY* 3.3 43.6 + - - +
328B GLN* 4.0 10.0 + - - +
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Residues in contact with LEU 324 (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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320B CYS 3.4 13.2 + - - +
321B THR* 3.4 26.7 - - + +
322B SER 3.3 0.2 - - - -
323B MET* 1.4 78.7 - - - +
325B LEU* 1.3 63.4 + - + +
328B GLN* 3.1 42.8 - - - +
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Residues in contact with LEU 325 (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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321B THR* 3.4 20.9 - - - +
322B SER* 3.9 10.5 - - - +
324B LEU* 1.3 84.0 - - + +
326B MET* 1.3 73.5 + - + +
329B SER* 3.4 22.5 + - - -
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Residues in contact with MET 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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322B SER 3.6 14.4 + - - +
323B MET* 5.2 1.3 - - + -
325B LEU* 1.3 93.0 - - + +
327B GLY* 1.3 64.0 + - - +
328B GLN 3.6 0.2 - - - -
329B SER* 4.1 2.7 - - - -
330B ARG* 3.5 31.3 + - - +
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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