Contacts of the helix formed by residues 300 - 312 (chain B) in PDB entry 5VZ4
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 GLU 300 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B LEU* 3.6 28.9 - - + +
225B ARG* 3.8 15.7 + - - -
296B ILE* 4.3 12.6 - - + +
297B THR* 3.2 26.9 + - - +
299B SER* 1.3 76.2 - - - +
301B GLU* 1.3 57.1 + - - +
302B SER 3.6 1.1 - - - -
303B LEU* 3.5 17.0 + - + +
304B CYS* 3.0 28.9 + - - +
403B EDO 5.3 3.8 + - - -
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Residues in contact with GLU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B CYS* 5.0 3.4 - - + +
296B ILE* 3.7 20.3 - - + +
297B THR 3.5 4.9 + - - +
298B GLN* 3.3 36.9 + - - +
299B SER 3.2 2.4 + - - -
300B GLU* 1.3 73.9 - - - +
302B SER* 1.3 62.0 + - - +
304B CYS* 3.2 4.9 + - - +
305B LYS* 3.0 57.1 + - - +
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Residues in contact with SER 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B SER* 3.7 18.4 + - - -
299B SER 4.5 6.0 + - - -
300B GLU 3.6 0.2 - - - -
301B GLU* 1.3 78.6 - - - +
303B LEU* 1.3 58.8 + - - +
305B LYS* 3.3 9.4 + - - +
306B ILE* 2.8 41.0 + - - +
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 3.8 12.3 - - + -
225B ARG* 4.3 4.0 - - - +
256B GLU* 3.2 56.5 - - + +
259B ILE* 3.9 15.3 - - + -
260B SER* 4.1 19.0 - - - +
299B SER 5.3 0.6 + - - +
300B GLU* 3.5 19.4 + - + +
301B GLU 3.3 0.4 - - - -
302B SER* 1.3 78.9 + - - +
304B CYS* 1.3 56.2 - - - +
306B ILE* 3.3 3.2 + - - +
307B PHE* 3.1 53.9 + - + -
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Residues in contact with CYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B CYS* 3.6 16.4 - - - +
221B LEU* 3.4 22.1 - - + +
292B THR 3.5 8.3 - - - -
293B CYS* 2.1 58.1 - - + -
296B ILE* 4.5 10.1 - - + -
300B GLU 3.0 14.7 + - - +
301B GLU* 3.2 11.2 + - - +
303B LEU* 1.3 74.4 - - - +
305B LYS* 1.3 56.9 + - - +
307B PHE* 3.2 4.4 + - - +
308B GLN* 2.8 24.8 + - - +
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Residues in contact with LYS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B CYS* 3.8 23.0 - - + +
301B GLU* 3.0 47.2 + - - +
302B SER* 3.8 8.5 - - - +
304B CYS* 1.3 75.2 - - - +
306B ILE* 1.3 59.3 + - + +
308B GLN* 3.7 13.1 + - - +
309B HIS* 3.0 28.4 + - - +
401B SO4 5.8 2.0 + - - -
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ILE* 3.4 45.5 - - + +
260B SER* 4.1 15.3 - - - +
262B LEU* 4.7 11.9 - - + +
267B LEU* 3.7 37.7 - - + -
302B SER* 2.8 27.3 + - - +
303B LEU 3.7 4.5 - - - +
304B CYS 3.1 0.2 - - - -
305B LYS* 1.3 76.7 - - + +
307B PHE* 1.3 65.1 + - - +
309B HIS* 3.2 7.2 + - - +
310B MET* 3.0 29.5 + - + +
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Residues in contact with PHE 307 (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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220B CYS* 4.3 7.6 - - + -
221B LEU* 3.7 16.6 - - + -
224B ILE* 3.5 49.6 - - + -
225B ARG* 6.1 0.7 - - - -
228B GLN* 5.9 0.4 - - - -
237B TYR* 3.8 12.3 - + - -
256B GLU* 4.6 13.2 - - + -
259B ILE* 4.1 23.8 - - + -
303B LEU* 3.1 48.1 + - + -
304B CYS 3.6 5.2 - - - +
306B ILE* 1.3 73.3 - - - +
308B GLN* 1.3 65.7 + - - +
310B MET* 3.1 28.8 + - + +
311B LEU* 3.0 30.1 + - + +
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Residues in contact with GLN 308 (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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220B CYS* 3.5 24.1 - - - +
291B CYS* 3.2 23.7 - - - +
292B THR* 4.0 1.9 - - - -
293B CYS* 4.1 8.8 - - - +
304B CYS 2.8 17.1 + - - +
305B LYS* 3.7 14.7 + - - +
306B ILE 3.3 0.2 - - - -
307B PHE* 1.3 73.3 - - - +
309B HIS* 1.3 61.8 + - - +
311B LEU* 3.5 3.5 + - - +
312B HIS* 3.3 25.2 + - + +
401B SO4 3.0 34.1 + - - -
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Residues in contact with HIS 309 (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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245B TRP* 3.7 23.7 - + - -
264B LYS* 5.4 12.4 + - - -
267B LEU* 4.1 30.3 + - + +
305B LYS 3.0 18.6 + - - +
306B ILE* 3.5 6.7 - - - +
307B PHE 3.1 0.2 - - - -
308B GLN* 1.3 77.0 - - - +
310B MET* 1.3 62.5 + - + +
312B HIS* 3.4 6.1 + - - -
315B SER* 2.8 53.3 + - - -
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Residues in contact with MET 310 (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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237B TYR* 3.5 14.1 - - - +
240B PHE* 3.2 26.4 - - + -
241B GLN* 3.3 18.8 - - - +
245B TRP* 3.2 46.5 + - + +
248B VAL* 4.1 22.0 - - + -
259B ILE* 4.6 4.5 - - + -
267B LEU* 4.8 4.0 - - + -
306B ILE* 3.0 30.3 + - + +
307B PHE* 3.1 38.8 + - + +
309B HIS* 1.3 78.2 - - + +
311B LEU* 1.3 60.8 + - + +
312B HIS 3.5 3.3 + - - +
316B CYS* 5.2 0.7 - - - -
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B CYS 5.1 0.4 - - - +
223B VAL* 3.7 29.8 - - + -
224B ILE* 3.8 16.8 - - + -
237B TYR* 4.4 9.4 - - + -
240B PHE* 4.2 21.8 - - + -
279B TYR* 4.5 12.1 - - - -
282B ILE* 4.5 5.9 - - + +
287B LEU* 4.1 41.0 - - + +
289B VAL 6.2 0.2 - - - +
291B CYS* 4.6 14.1 - - - -
307B PHE* 3.0 21.4 + - + +
308B GLN* 3.9 5.4 - - - +
310B MET* 1.3 76.3 - - + +
312B HIS* 1.3 61.3 + - - +
313B ARG 3.6 1.9 + - - -
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Residues in contact with HIS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLN* 5.2 11.9 + - - -
308B GLN* 3.3 18.4 + - + +
309B HIS* 3.4 2.7 + - - +
310B MET 3.3 5.0 - - - +
311B LEU* 1.3 77.9 - - - +
313B ARG* 1.3 66.1 + - + +
314B LYS* 3.2 37.2 + - + +
315B SER* 3.2 30.4 + - - +
316B CYS* 3.9 4.2 + - - +
402B SO4 4.1 28.5 + - - -
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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