Contacts of the helix formed by residues 295 - 307 (chain B) 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 SER 295 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203B LEU* 4.5 0.4 - - - -
293B GLY 3.5 1.7 + - - -
294B VAL* 1.3 81.0 - - - +
296B ARG* 1.3 64.6 + - - +
297B ALA* 3.4 9.1 + - - +
298B MET* 3.1 24.5 + - - +
299B LEU* 3.3 18.2 + - - +
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Residues in contact with ARG 296 (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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200B LEU* 3.3 34.3 + - + +
201B ALA* 3.5 21.7 + - - +
202B ALA* 4.0 3.4 - - - +
203B LEU* 3.4 51.6 + - + +
294B VAL 3.8 1.0 + - - -
295B SER* 1.3 73.8 - - - +
297B ALA* 1.3 62.9 + - - +
298B MET 3.4 0.2 + - - -
299B LEU* 3.4 2.1 + - - -
300B LEU* 3.2 20.4 + - - +
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Residues in contact with ALA 297 (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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295B SER* 3.2 8.7 + - - +
296B ARG* 1.3 79.1 - - - +
298B MET* 1.3 61.1 + - - +
300B LEU* 3.6 11.3 + - - +
301B ARG* 3.2 31.9 + - - +
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Residues in contact with MET 298 (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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294B VAL* 3.5 22.4 - - + -
295B SER* 3.1 17.4 + - - +
297B ALA* 1.3 75.1 - - - +
299B LEU* 1.3 54.6 + - - +
301B ARG* 2.9 26.8 + - - +
302B LEU* 2.8 44.1 + - + +
314B TYR* 4.4 14.4 - - + +
315B GLU 3.6 24.9 - - - +
316B CYS* 3.6 24.7 - - + -
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Residues in contact with LEU 299 (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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173B PHE* 4.6 8.5 - - + -
200B LEU* 3.7 17.9 - - + -
203B LEU* 4.2 25.4 - - + -
258B VAL* 3.9 31.6 - - + -
259B LEU* 5.1 2.0 - - + -
290B VAL* 5.1 4.3 - - + -
294B VAL* 4.1 13.9 - - + +
295B SER 3.3 9.3 + - - +
296B ARG 3.7 4.5 - - - +
298B MET* 1.3 77.8 - - - +
300B LEU* 1.3 57.1 + - - +
302B LEU* 3.2 21.0 + - + +
303B PHE* 2.8 26.7 + - - +
1001B UUL 3.5 36.1 - - + -
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Residues in contact with LEU 300 (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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196B THR* 6.3 0.2 - - + -
197B PHE* 3.5 32.5 - - + -
200B LEU* 3.4 32.4 - - + +
296B ARG 3.2 7.4 + - - +
297B ALA* 3.6 13.9 - - - +
299B LEU* 1.3 76.3 - - - +
301B ARG* 1.3 55.5 + - - +
303B PHE* 3.1 6.1 + - + +
304B LEU* 2.8 58.8 + - + +
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Residues in contact with ARG 301 (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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297B ALA* 3.2 27.4 + - - +
298B MET* 2.9 22.1 + - - +
300B LEU* 1.3 79.9 - - - +
302B LEU* 1.3 56.9 + - - +
304B LEU* 3.9 8.2 + - - +
305B ALA* 3.1 28.6 + - - +
314B TYR* 3.3 43.6 + - + +
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Residues in contact with LEU 302 (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* 5.3 5.4 - - + -
294B VAL* 5.1 1.8 - - + -
298B MET* 2.8 25.6 + - + +
299B LEU* 3.3 25.8 - - + +
300B LEU 3.2 0.2 - - - -
301B ARG* 1.3 75.2 - - - +
303B PHE* 1.3 59.6 + - - +
305B ALA* 3.1 1.4 + - - -
306B MET* 2.9 28.5 + - - +
311B HIS* 3.4 43.9 - - + +
314B TYR* 4.3 17.3 - - + -
316B CYS* 4.2 25.4 - - + -
319B LEU* 4.2 22.0 - - + -
1001B UUL 5.1 10.9 - - + -
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Residues in contact with PHE 303 (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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192B PHE 4.2 4.0 - - - -
193B THR* 3.6 25.4 - - - -
196B THR* 3.7 26.0 - - + -
197B PHE* 4.0 26.7 - + - -
200B LEU* 5.7 0.7 - - + -
272B MET* 4.0 11.9 - - + -
299B LEU 2.8 17.2 + - - +
300B LEU* 3.5 10.5 - - + +
302B LEU* 1.3 71.8 - - - +
304B LEU* 1.3 70.8 + - + +
306B MET* 3.1 37.7 + - + +
307B GLU* 3.8 2.9 + - - +
1001B UUL 3.4 56.5 - + - -
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Residues in contact with LEU 304 (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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197B PHE* 4.2 29.2 - - + -
300B LEU* 2.8 41.3 + - + +
301B ARG* 4.0 7.2 - - - +
303B PHE* 1.3 78.0 - - + +
305B ALA* 1.3 59.9 + - - +
307B GLU* 3.6 19.9 + - - +
308B LYS* 4.8 1.2 + - - +
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Residues in contact with ALA 305 (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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301B ARG 3.1 20.9 + - - +
302B LEU 3.1 5.5 + - - +
304B LEU* 1.3 71.9 - - - +
306B MET* 1.3 64.3 + - - +
307B GLU 3.1 2.5 - - - -
308B LYS* 3.1 8.1 + - - +
309B GLY 3.0 3.8 + - - -
310B ARG* 2.9 31.6 + - + +
311B HIS* 3.7 20.4 - - - +
314B TYR* 3.9 17.3 - - + +
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Residues in contact with MET 306 (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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268B LEU* 4.1 1.3 - - + -
272B MET* 3.9 29.4 - - + -
273B PHE 3.1 26.6 + - - +
274B ALA* 3.7 24.5 - - - -
302B LEU 2.9 10.3 + - - +
303B PHE* 3.1 36.7 + - + +
305B ALA* 1.3 74.0 - - - +
307B GLU* 1.3 65.7 + - - +
309B GLY 2.9 9.3 + - - +
311B HIS* 3.3 19.9 + - + +
1001B UUL 3.7 41.5 - - + +
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Residues in contact with GLU 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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128B GLN* 2.8 38.4 + - - +
271B GLU* 3.4 42.0 + - + +
273B PHE* 3.9 0.9 + - - +
303B PHE 3.8 3.6 + - - +
304B LEU 3.6 16.2 + - - +
305B ALA 3.1 0.8 - - - -
306B MET* 1.3 78.9 - - - +
308B LYS* 1.3 74.4 + - + +
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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